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License: GNU General Public License v3.0
An efficient index for the colored, compacted, de Bruijn graph
License: GNU General Public License v3.0
Hi I followed your installation instructions
> git clone [email protected]:COMBINE-lab/pufferfish.git
> cd pufferfish
> mkdir build
> cd build
> cmake ../
> make
but I didn't get pufferfish
executable. It's not in pufferfish/
or pufferfish/bin
. Is there any thing else I should do?
Hello, your project seems very interesting.
Is it already possible to use it for assembly? If yes could you give me a hint where to start?
The initial fixFasta step of Pufferfish indexing is single-threaded, and when there are a lot of sequences in the reference it takes a lot of time. From the outside it seems like this step could be parallelized, with the input reference FASTA split into parts, e.g. using the fast SeqKit toolkit and split2 command, which can output gzipped or regular split FASTA files from a gzipped or regular input reference FASTA (to save disk space for example), and then processing each split using fixFasta and concatenating the fixed splits into one.
I cannot seem to get Cedar to properly work without segfaulting. My input SAM is produced by PuffAligner against a CAMI example paired-end FASTQ and a Pufferfish index of 100 genomes. I'm using the Cedar --flat
option. No matter what I try it always segfaults. @fataltes do you have any idea?
$ /home/hermidalc/projects/github/hermidalc/pufferfish/bin/pufferfish/c4db524/linux-x64/cedar --flat --sam results/pufferfish/cami/cami1/CAMI_low/CAMI_low_RL_S001__insert_270_pufferfish.sam.gz --output quant.sf
[2022-10-24 05:17:37.424] [console] [info] Cedar: Construct ..
[2022-10-24 05:17:37.425] [console] [info] Cedar: Load Mapping File ..
[2022-10-24 05:17:37.425] [console] [info] Mapping Output File: results/pufferfish/cami/cami1/CAMI_low/CAMI_low_RL_S001__insert_270_pufferfish.sam.gz
[2022-10-24 05:17:37.433] [console] [info] # of targets: 6260
0 0 | RL|S1|R0 | 150 | 1 | -1 | -1 | 0
1 0 | RL|S1|R0 | 150 | 1 | -1 | -1 | 0
2 0 | RL|S1|R1 | 150 | 1 | -1 | -1 | 0
3 0 | RL|S1|R1 | 150 | 1 | -1 | -1 | 0
4 0 | RL|S1|R2 | 150 | 1 | -1 | -1 | 0
5 0 | RL|S1|R2 | 150 | 1 | -1 | -1 | 0
6 0 | RL|S1|R3 | 150 | 1 | -1 | -1 | 0
7 0 | RL|S1|R3 | 150 | 1 | -1 | -1 | 0
8 0 | RL|S1|R4 | 150 | 1 | -1 | -1 | 0
9 0 | RL|S1|R4 | 150 | 1 | -1 | -1 | 0
...
6390 0 | RL|S1|R3195 | 150 | 1 | -1 | -1 | 0
6391 0 | RL|S1|R3195 | 150 | 1 | -1 | -1 | 0
6392 0 | RL|S1|R3196 | 150 | 1 | -1 | -1 | 0
6393 0 | RL|S1|R3196 | 150 | 1 | -1 | -1 | 0
6394 0 | RL|S1|R3197 | 150 | 1 | -1 | -1 | 0
6395 0 | RL|S1|R3197 | 150 | 1 | -1 | -1 | 0
6396 0 | RL|S1|R3198 | 150 | 1 | -1 | -1 | 0
6397 0 | RL|S1|R3198 | 150 | 1 | -1 | -1 | 0
6398 0 | RL|S1|R3199 | 150 | 1 | -1 | -1 | 0
6399 0 | RL|S1|R3199 | 150 | 1 | -1 | -1 | 0
6400 1 | RL|S1|R3200 | 150 | 1 | 4479 | 4938059 | 0
[2022-10-24 05:17:37.577] [console] [info] is dataset paired end? true
Segmentation fault (core dumped)
It appears that the Pufferfish indexer supports using a gzipped FASTA reference file as input. Add description to help that it can do this.
Hey,
the readMe file links to a blogpost and a paper. Both explain partial what each output file contains but it is not consistent anymore with the output files Pufferfish generates. I run Pufferfish last week and got more files than mentioned in the paper/post and also the names are different. Is there a new paper or post where the output is explained?
Also is there any way to check that the Pufferfish calculations went well?
It seems the pufferfish is dependant on json, SeqLib, htslib etc.
I installed json and SeqLib, and also downloaded htslib,
Now while building it, I am stuck with the following error:
gcc -shared -Wl,-soname,libhts.so.2 -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico -llzma -lbz2 -lz -lm -lpthread
/usr/bin/ld: /gpfs/software/bzip2-1.0.6/lib/libbz2.a(bzlib.o): relocation R_X86_64_32S against `BZ2_crc32Table' can not be used when making a shared object; recompile with -fPIC
/gpfs/software/bzip2-1.0.6/lib/libbz2.a: could not read symbols: Bad value
Is there a stable release of cedar that I can obtain?
I'm opening this issue here because I believe it's more of a pufferfish-related matter, but will use the issue template from your salmon repository.
Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?
salmon/pufferfish
Describe the bug
When running salmon v1.0 using a rather large index, I receive an error raised from the cereal library "Index requested greater than vector's size". The log reads:
-----------------------------------------
| Loading contig table | Time = 12.954 s
-----------------------------------------
size = 35010142
-----------------------------------------
| Loading contig offsets | Time = 269.18 ms
-----------------------------------------
-----------------------------------------
| Loading reference lengths | Time = 7.8427 ms
-----------------------------------------
-----------------------------------------
| Loading eq table | Time = 3.3896 s
-----------------------------------------
-----------------------------------------
| Loading mphf table | Time = 3.8301 s
-----------------------------------------
size = 3567796961
Number of ones: 35010141
Number of ones per inventory item: 512
Inventory entries filled: 68380
-----------------------------------------
| Loading contig boundaries | Time = 11.288 s
-----------------------------------------
size = 3567796961
-----------------------------------------
| Loading sequence | Time = 7.763 s
-----------------------------------------
size = 2517492731
-----------------------------------------
| Loading positions | Time = 171.81 s
-----------------------------------------
size = 3221360466
-----------------------------------------
| Loading reference sequence | Time = 7.9564 s
-----------------------------------------
-----------------------------------------
| Loading reference accumulative lengths | Time = 35.741 ms
-----------------------------------------
Index requested greater than vector's size: 6442720932>6442720932
Index requested greater than vector's size: 6442720996>6442720932
Index requested greater than vector's size: 6442721060>6442720932
Index requested greater than vector's size: 6442721124>6442720932
Index requested greater than vector's size: 6442721188>6442720932
Index requested greater than vector's size: 6442721252>6442720932
Index requested greater than vector's size: 6442721316>6442720932
Index requested greater than vector's size: 6442721380>6442720932
Index requested greater than vector's size: 6442721444>6442720932
...
The index does not finish loading, and so salmon does not enter read quantification routines.
To Reproduce
Expected behavior
I expected index loading to complete successfully.
Desktop (please complete the following information):
Additional context
I've uploaded the index file archive here and the transcripts fasta file here.
Four suggestions based off of 8c24fb1:
The index directory -h does not seem to exist
-i, --index <index>
directory where the pufferfish index is stored
-t, --threads <num threads>
Specify the number of threads (default=8)
...
-t, --type <statType>
statType (options:ctab)
allowSoftclip
is off by default (end-to-end alignment), but if the option could output: --allowSoftclip
Allow soft-clipping at start and end of alignments (default=off)
Full output of the help message:
pufferfish/build/src/pufferfish align -h
Parsing command line failed with exception: The index directory -h does not seem to exist.
SYNOPSIS
pufferfish index -r <ref_file>... -o <output_dir> [--headerSep <sep_strs>] [--keepFixedFasta] [--keepDuplicates] [-d <decoy_list>] [-f <filt_size>] [--tmpdir <twopaco_tmp_dir>] [-k <kmer_length>] [-p <threads>] [-l] [-q] [-s] [-e <extension_size>] [-v]
pufferfish index -r <ref_file>... -o <output_dir> [--headerSep <sep_strs>] [--keepFixedFasta] [--keepDuplicates] [-d <decoy_list>] [-f <filt_size>] [--tmpdir <twopaco_tmp_dir>] [-k <kmer_length>] [-p <threads>] [-l] [-q] [-x <lossy_rate>] [-v]
pufferfish validate -i <index> [-v]
pufferfish lookup -i <index> -r <ref> [-v]
pufferfish align -i <index> --mate1 <mate 1> --mate2 <mate 2> [-b] [--coverageScoreRatio <score ratio>] [-t <num threads>] [-m] (--noOutput | (-o <output file>)) [--allowSoftclip] [--allowOverhangSoftclip] [--maxSpliceGap <max splice gap>] [--maxFragmentLength <max frag length>] [--noOrphans] [--orphanRecovery] [--noDiscordant] [--noDovetail] [-z] [-k|-p] [--verbose] [--fullAlignment] [--heuristicChaining] [--bestStrata] [--genomicReads] [--primaryAlignment] [--filterGenomics <genes names file>] [--filterBestScoreMicrobiome <genes ID file>] [--filterMicrobiome <genes ID file>] [--bt2DefaultThreshold] [--minScoreFraction <minScoreFraction>] [--consensusFraction <consensus fraction>] [--noAlignmentCache] [-v]
pufferfish align -i <index> --read <reads> [-b] [--coverageScoreRatio <score ratio>] [-t <num threads>] [-m] (--noOutput | (-o <output file>)) [--allowSoftclip] [--allowOverhangSoftclip] [--maxSpliceGap <max splice gap>] [--maxFragmentLength <max frag length>] [--noOrphans] [--orphanRecovery] [--noDiscordant] [--noDovetail] [-z] [-k|-p] [--verbose] [--fullAlignment] [--heuristicChaining] [--bestStrata] [--genomicReads] [--primaryAlignment] [--filterGenomics <genes names file>] [--filterBestScoreMicrobiome <genes ID file>] [--filterMicrobiome <genes ID file>] [--bt2DefaultThreshold] [--minScoreFraction <minScoreFraction>] [--consensusFraction <consensus fraction>] [--noAlignmentCache] [-v]
pufferfish examine -i <index> [--dump-fasta <fasta_out>] [--dump-kmer-freq <kmer_freq_out>] [-v]
pufferfish stat [-t <statType>] -i <index> [-v]
pufferfish help [-v]
OPTIONS
-r, --ref <ref_file>
path to the reference fasta file
-o, --output <output_dir>
directory where index is written
--headerSep <sep_strs>
Instead of a space or tab, break the header at the first occurrence of this string, and name the transcript as the token before the first separator (default = space & tab)
--keepFixedFasta
Retain the fixed fasta file (without short transcripts and duplicates, clipped, etc.) generated during indexing
--keepDuplicates
Retain duplicate references in the input
-d, --decoys <decoy_list>
Treat these sequences as decoys that may be sequence-similar to some known indexed reference
-f, --filt-size <filt_size>
filter size to pass to TwoPaCo when building the reference dBG
--tmpdir <twopaco_tmp_dir>
temporary work directory to pass to TwoPaCo when building the reference dBG
-k, --klen <kmer_length>
length of the k-mer with which the dBG was built (default = 31)
-p, --threads <threads>
total number of threads to use for building MPHF (default = 16)
-l, --build-edges
build and record explicit edge table for the contaigs of the ccdBG (default = false)
-q, --build-eqclses
build and record equivalence classes (default = false)
-s, --sparse
use the sparse pufferfish index (less space, but slower lookup)
-e, --extension <extension_size>
length of the extension to store in the sparse index (default = 4)
<lossy_rate>
use the lossy sampling index with a sampling rate of x (less space and fast, but lower sensitivity)
-i, --index <index>
directory where the pufferfish index is stored
-i, --index <index>
directory where the pufferfish index is stored
-r, --ref <ref>
fasta file with reference sequences
-i, --index <index>
Directory where the Pufferfish index is stored
--mate1, -1 <mate 1>
Path to the left end of the read files
--mate2, -2 <mate 2>
Path to the right end of the read files
--read <reads>
Path to single-end read files
-b, --batchOfReads
Is each input a file containing the list of reads? (default=false)
--coverageScoreRatio <score ratio>
Discard mappings with a coverage score < scoreRatio * OPT (default=0.6)
-t, --threads <num threads>
Specify the number of threads (default=8)
-m, --just-mapping
don't attempt alignment validation; just do mapping
--noOutput Run without writing SAM file
-o, --outdir <output file>
Output file where the alignment results will be stored
--allowSoftclip
Allow soft-clipping at start and end of alignments
--allowOverhangSoftclip
Allow soft-clipping part of a read that overhangs the reference (the regular --allowSoftclip flag overrides this one)
--maxSpliceGap <max splice gap>
Specify maximum splice gap that two uni-MEMs should have
--maxFragmentLength <max frag length>
Specify the maximum distance between the last uni-MEM of the left and first uni-MEM of the right end of the read pairs (default:1000)
--noOrphans Write Orphans flag
--orphanRecovery
Recover mappings for the other end of orphans using alignment
--noDiscordant
Write Orphans flag
--noDovetail
Disallow dovetail alignment for paired end reads
-z, --compressedOutput
Compress (gzip) the output file
-k, --krakOut
Write output in the format required for krakMap
-p, --pam Write output in the format required for salmon
--verbose Print out auxilary information to trace program's flow
--fullAlignment
Perform full alignment instead of gapped alignment
--heuristicChaining
Whether or not perform only 2 rounds of chaining
--bestStrata
Keep only the alignments with the best score for each read
--genomicReads
Align genomic dna-seq reads instead of RNA-seq reads
--primaryAlignment
Report at most one alignment per read
--filterGenomics <genes names file>
Path to the file containing gene IDs. Filters alignments to the IDs listed in the file. Used to filter genomic reads while aligning to both genome and transcriptome.A read will be reported with only the valid gene ID alignments and will be discarded if the best alignment is to an invalid IDThe IDs are the same as the IDs in the fasta file provided for the index construction phase
--filterBestScoreMicrobiome <genes ID file>
Path to the file containing gene IDs. Same as option "filterGenomics" except that a read will be discarded if aligned equally best to a valid and invalid gene ID.
--filterMicrobiome <genes ID file>
Path to the file containing gene IDs. Same as option "filterGenomics" except that a read will be discarded if an invalid gene ID is in the list of alignments.
--bt2DefaultThreshold
mimic the default threshold function of Bowtie2 which is t = -0.6 -0.6 * read_len
--minScoreFraction <minScoreFraction>
Discard alignments with alignment score < minScoreFraction * max_alignment_score for that read (default=0.65)
--consensusFraction <consensus fraction>
The fraction of mems, relative to the reference with the maximum number of mems, that a reference must contain in order to move forward with computing an optimal chain score (default=0.65)
--noAlignmentCache
Do not use the alignment cache during the alignment.
-i, --index <index>
pufferfish index directory
--dump-fasta <fasta_out>
dump the reference sequences in the index in the provided fasta file
--dump-kmer-freq <kmer_freq_out>
dump the frequency histogram of k-mers
-t, --type <statType>
statType (options:ctab)
-i, --index <index>
directory where the pufferfish index is stored
-v, --version
I tried to load the latest GENCODE human genome FASTA as a decoy into pufferfish index and the fixFasta
component immediately give the following error:
[2022-08-19 14:27:01.875] [puff::index::jointLog] [info] Running fixFasta
[2022-08-19 14:27:01.875] [puff::index::jointLog] [critical] The decoy name NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN was encountered more than once --- please ensure all decoy names and sequences are unique.
[2022-08-19 14:27:01.875] [puff::index::jointLog] [error] The fixFasta phase failed with exit code 1
Even though the genome file head looks like this:
$ head -10 GRCh38.primary_assembly.genome.fa
>chr1 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
I first thought it was the leading N
s but even after clipping all leading and trailing N
s in all sequence entries it still gives the same error with the first sequence. It appears that when processing the decoy FASTA file fixFasta has a bug, because it doesn't notice the >
header(s).
Hey Team Pufferfish-
I'm just wondering your opinions on best practices if I were to want to index many (hundreds? thousands?) of whole human genomes and then query them. Let's say I have a handful of k=25
mers and I want to find out whether, which, where, and how many matches there are in my index. Although the index is huge, the query will always be small, no more than a few hundred at a time, unlike alignment of RNA-seq reads or similar.
In a somewhat-miniaturized (albeit still relatively giant) test, I grabbed sequences from the Human Pangenome Reference (n=94 genomes + CHM13) and am attempting to index them with pufferfish. This alone used >600GB of RAM just in the counting step, and is seemingly nowhere near complete after 24hrs of runtime with 12 threads.
Is this at all feasible? Is Pufferfish an appropriate tool for this? Or are related tools like fulgor or cuttlefish or others better suited for this scale?
I figured other standard k-mer counting tools may be more efficient but from my non-expert perspective it seemed I'd likely sacrifice knowing the genomic locations of the match, and perhaps also sacrifice knowing if a given k-mer matched multiple times in the same genomes and/or within the whole index. Unless it is truly necessary to do otherwise, this is information I'd like to retain in my output. Also note I'm currently approaching this without any downsampling or sparsity (in other words, it is a fully dense all-k-mers-represented index), but if needed I may be able to employ some k-mer selection tricks.
Curious to hear your thoughts on this, and thanks as always!
At NCBI each genome FASTA can have multiple entries, generally the assembly plus unplaced additional contigs. Would is be more efficient to merge these into one FASTA entry per genome before index
and align
?
Hi!
During compilation I got the following error:
/usr/bin/ld: cannot open output file cedar: Is a directory
OS: Ubuntu 20.04.1
I solved simply by renaming the folder cedar
to cedar.dir
and replacing it in line 181 in the CMakeList.txt
Pufferfish does not "make install" fully. This is on CentOS 8.
package=pufferfish #from current_version.txt in download
pversion=1.0.0
TOPDIR=/usr/common/modules/el8/x86_64/software/${package}/${pversion}-CentOS-vanilla
THELUA=/usr/common/modules/el8/x86_64/modules/all/${package}/${pversion}-CentOS-vanilla.lua
#as modules on 2020/06/09 for CentOS 8
cd /usr/common/src
git clone https://github.com/COMBINE-lab/pufferfish.git
mv ${package} ${package}-${pversion}
cd ${package}-${pversion}
#Findjemalloc.cmake is broken, use the one from Salmon
cd cmake/Modules
mv FindJemalloc.cmake Hide_FindJemalloc.cmake
cp ../../../salmon-1.2.1/cmake/Modules/FindJemalloc.cmake .
cd ../..
mkdir build
cd build
module load htslib #apparently ignored, it built its own anyway
cmake -DCMAKE_INSTALL_PREFIX=$TOPDIR .. | tee cmake_2020_06_09.log
make 2>&1 | tee build_2020_06_09.log
make install 2>&1 | tee install_2020_06_09.log
#does not install everything
mkdir -p $TOPDIR/bin
cd src
mv bcalm_pufferize cedar edgedensity edgedensity2 \
filtersam krakmap pufferfish $TOPDIR/bin
mv lib*.a $TOPDIR/lib64
After that these are the contents of $TOPDIR:
$TOPDIR/lib
$TOPDIR/lib/libntcard.a
$TOPDIR/lib/ntcard
$TOPDIR/lib/ntcard/ntcard-targets.cmake
$TOPDIR/lib/ntcard/ntcard-targets-release.cmake
$TOPDIR/lib/libgraphdump.a
$TOPDIR/lib/graphdump
$TOPDIR/lib/graphdump/graphdump-targets.cmake
$TOPDIR/lib/graphdump/graphdump-targets-release.cmake
$TOPDIR/lib/libtwopaco.a
$TOPDIR/lib/twopaco
$TOPDIR/lib/twopaco/twopaco-targets.cmake
$TOPDIR/lib/twopaco/twopaco-targets-release.cmake
$TOPDIR/cmake
$TOPDIR/cmake/Async++Config.cmake
$TOPDIR/cmake/Async++.cmake
$TOPDIR/cmake/Async++-release.cmake
$TOPDIR/lib64
$TOPDIR/lib64/libasync++.a
$TOPDIR/lib64/libksw2pp.a
$TOPDIR/lib64/libpuffer.a
$TOPDIR/include
$TOPDIR/include/async++.h
$TOPDIR/include/async++
$TOPDIR/include/async++/aligned_alloc.h
$TOPDIR/include/async++/cancel.h
$TOPDIR/include/async++/continuation_vector.h
$TOPDIR/include/async++/parallel_for.h
$TOPDIR/include/async++/parallel_invoke.h
$TOPDIR/include/async++/parallel_reduce.h
$TOPDIR/include/async++/partitioner.h
$TOPDIR/include/async++/range.h
$TOPDIR/include/async++/ref_count.h
$TOPDIR/include/async++/scheduler.h
$TOPDIR/include/async++/scheduler_fwd.h
$TOPDIR/include/async++/task.h
$TOPDIR/include/async++/task_base.h
$TOPDIR/include/async++/traits.h
$TOPDIR/include/async++/when_all_any.h
$TOPDIR/bin
$TOPDIR/bin/bcalm_pufferize
$TOPDIR/bin/cedar
$TOPDIR/bin/edgedensity
$TOPDIR/bin/edgedensity2
$TOPDIR/bin/filtersam
$TOPDIR/bin/krakmap
$TOPDIR/bin/pufferfish
Unclear to me which if any of the files that install initially placed under $TOPDIR really should be there. The documentation for building pufferfish only describes up to "make".
The other issue - pufferfish built this way does not run.
cd src
./pufferfish
Segmentation fault (core dumped)
./pufferfish -h # or -help or --help
Segmentation fault(core dumped)
cat >/tmp/some.fasta <<'EOD'
>one
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>two
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
>three
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
>four
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
EOD
./pufferfish index -r /tmp/some.fasta -o /tmp
Segmentation fault (core dumped)
ldd ./pufferfish
linux-vdso.so.1 (0x00007ffeee9c1000)
libz.so.1 => /lib64/libz.so.1 (0x00007f99a3236000)
libtbbmalloc_proxy.so.2 => /lib64/libtbbmalloc_proxy.so.2 (0x00007f99a3032000)
libtbbmalloc.so.2 => /lib64/libtbbmalloc.so.2 (0x00007f99a2e01000)
libtbb.so.2 => /lib64/libtbb.so.2 (0x00007f99a2bc3000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f99a29bf000)
libjemalloc.so.2 => /lib64/libjemalloc.so.2 (0x00007f99a2520000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f99a218b000)
libm.so.6 => /lib64/libm.so.6 (0x00007f99a1e09000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f99a1bf1000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f99a19d1000)
libc.so.6 => /lib64/libc.so.6 (0x00007f99a160e000)
/lib64/ld-linux-x86-64.so.2 (0x00007f99a344d000)
librt.so.1 => /lib64/librt.so.1 (0x00007f99a1405000)
It finds TBB_VERSION as "."
Version: 1.5.2
OS: FreeBSD 13
In align
if index, mate1, mate2, output aren't in a specific order then the command shows the help and exits or fails with strange messages about the index missing. The is counterintuitive since all options are options with flags not positional parameters.
Hi,
I've indexed a fasta file with pufferfish and it worked. Then I wanted to find the locations of a set of kmers and tried pufferfish kquery, I got :
There is no command "kquery"
The valid commands to pufferfish are : {align, examine, index, kquery, lookup, stat, validate}
Any idea what went wrong?
Hi,
Could I align FASTA file reads to reference index, using pufferfish align?
Or, do I get to use only fastq files as input files?
Thank you
In many cases, I get a single FASTQ with pared end reads "interleaved", namely reads for a pair are consecutive, have the same name except for a trailing /1
or /2
to identify the end of the pair. I see --mate1
and --mate2
for paired-end reads, and --read
for single end reads.
During make
of pufferfish I'm getting the following error. You can see just above the error it does the presence and sanity checks for zlib.h
and all good, so something wrong with an include path or something else that I canโt see during the build?
It looks like some of the pufferfish dependencies cannot build within a conda environment that has the requisite dependencies such as cmake, cxx-compiler, zlib, bzip2. Trying to figure out why because being able to build within a conda environment is important for developers using pufferfish as a submodule in project that they want to make redistributable, where mamba/conda is a very popular framework for software dependency management.
make
...
[ 10%] Creating directories for 'libseqlib'
[ 11%] Performing download step (git clone) for 'libseqlib'
Cloning into 'seqlib'...
Already on 'master'
Your branch is up to date with 'origin/master'.
Submodule 'htslib' (https://github.com/samtools/htslib.git) registered for path 'htslib'
Cloning into '/home/hermidalc/projects/github/hermidalc/functional-profiler/pufferfish/external/seqlib/htslib'...
Submodule path 'htslib': checked out 'be22a2a1082f6e570718439b9ace2db17a609eae'
[ 12%] No patch step for 'libseqlib'
[ 13%] Performing configure step for 'libseqlib'
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
/home/hermidalc/projects/github/hermidalc/functional-profiler/pufferfish/external/seqlib/missing: Unknown `--is-lightweight' option
Try `/home/hermidalc/projects/github/hermidalc/functional-profiler/pufferfish/external/seqlib/missing --help' for more information
configure: WARNING: 'missing' script is too old or missing
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether /home/hermidalc/soft/mambaforge/envs/functional-profiler/bin/x86_64-conda-linux-gnu-c++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of /home/hermidalc/soft/mambaforge/envs/functional-profiler/bin/x86_64-conda-linux-gnu-c++... gcc3
checking for x86_64-conda-linux-gnu-gcc... /home/hermidalc/soft/mambaforge/envs/functional-profiler/bin/x86_64-conda-linux-gnu-cc
checking whether we are using the GNU C compiler... yes
checking whether /home/hermidalc/soft/mambaforge/envs/functional-profiler/bin/x86_64-conda-linux-gnu-cc accepts -g... yes
checking for /home/hermidalc/soft/mambaforge/envs/functional-profiler/bin/x86_64-conda-linux-gnu-cc option to accept ISO C89... none needed
checking whether /home/hermidalc/soft/mambaforge/envs/functional-profiler/bin/x86_64-conda-linux-gnu-cc understands -c and -o together... yes
checking dependency style of /home/hermidalc/soft/mambaforge/envs/functional-profiler/bin/x86_64-conda-linux-gnu-cc... gcc3
checking for x86_64-conda-linux-gnu-ranlib... /home/hermidalc/soft/mambaforge/envs/functional-profiler/bin/x86_64-conda-linux-gnu-ranlib
checking how to run the C++ preprocessor... /home/hermidalc/soft/mambaforge/envs/functional-profiler/bin/x86_64-conda-linux-gnu-c++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for library containing gzopen... -lz
checking for library containing lzma_code... -llzma
checking for library containing BZ2_bzBuffToBuffDecompress... -lbz2
checking for library containing clock_gettime... -lrt
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/seqtools/Makefile
config.status: creating config.h
config.status: executing depfiles commands
[ 14%] Performing build step for 'libseqlib'
Making all in htslib
In file included from bgzf.c:43:
htslib/bgzf.h:35:10: fatal error: zlib.h: No such file or directory
35 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.
make[5]: *** [Makefile:121: bgzf.o] Error 1
make[4]: *** [Makefile:358: all-recursive] Error 1
make[3]: *** [Makefile:299: all] Error 2
make[2]: *** [CMakeFiles/libseqlib.dir/build.make:85: libseqlib-prefix/src/libseqlib-stamp/libseqlib-build] Error 2
make[1]: *** [CMakeFiles/Makefile2:235: CMakeFiles/libseqlib.dir/all] Error 2
make: *** [Makefile:156: all] Error 2
While trying to compile https://github.com/COMBINE-lab/salmon on an IBM Power system, compilation fails during the pufferfish build phase because of SSE flags passed to the compiler for constituent ksw2pp:
236.4 Scanning dependencies of target ksw2pp_sse4
236.4 [ 40%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o
236.4 cc: error: unrecognized command line option '-msse'
236.4 cc: error: unrecognized command line option '-msse2'
236.4 cc: error: unrecognized command line option '-msse3'
236.4 cc: error: unrecognized command line option '-mssse3'
236.4 cc: error: unrecognized command line option '-msse4'
236.4 cc: error: unrecognized command line option '-msse4.1'
236.4 make[2]: *** [external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build.make:63: external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o] Error 1
236.4 make[1]: *** [CMakeFiles/Makefile2:484: external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/all] Error 2
236.4 make: *** [Makefile:163: all] Error 2
Obviously, -msse
flags are not meaningful on non-AMD architectures (I don't have an ARM platform handy to test whether gcc pukes on this arch as well but presumably it does). I'm not sure whether -march=native is important here or not.
I see that Pufferish can be built for both amd64 and arm64 architectures, so presumably there should be a way around this, but I am not seeing it. Please let me know if you have ideas and if successful, I"ll try to submit a PR to broaden support if I can get it working. Normally I would troubleshoot this myself, but the use heavy use of intrinsics in this library has me stumped.
Kind regards
I've test both with --compressedOutput
and without, and surprised how much slower align
is when it is activated, writing of the compressed SAM file becomes a bottleneck to the entire command, and thread usage is much lower than what is specified. This is surprising as I haven't see writing to a compressed stream to cause such a bottleneck and change in performance with other tools.
Hey!
I got one question: the pufferfish align
command has a --genomicReads
parameter, which I assume activates a non-splice alignment mode. However the README says that spliced-alignment is not currently supported.
Should we expect --genomicReads
to give the same results as the default parameters for now? Also, does this mean that you plan puffalign to be splice-aware by default in the future?
Thanks!
Hello COMBINE-lab, I am trying to use salmon to quantify genes from a gene catalogue (Integrative Gene Catalogue for human gut microbe genes) using shotgun reads from HMP2, but my pipeline seems to be stuck at the index building phase, specifically, the twopaco step of the index. The only line of code I have run so far is:
salmon index -t data/IGC/IGC.fa -i processed/IGC_index --threads 16 -f 37
where IGC.fa
is a fasta file with ~9,870,000 genes, and takes up 7.7gb (ntHll estimated 6,091,444,578 distinct k-mers). the recommended filter size was 2^37, so on a subsequent run, I just included the -f 37
flag to save time calculating that.
The only issue now is that it seems to be stuck at this building step for a while (program has been running for 24 hrs) so I wanted to check if that was normal, or if I should modify my parameters to somehow get past this point. I am running this on a HPC and I requested 500gb of RAM, so I don't think memory is the problem.
Here is the current state of the error log:
Version Info: This is the most recent version of salmon.
index ["processed/IGC_index"] did not previously exist . . . creating it
[2020-05-29 11:14:16.148] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.
[2020-05-29 11:14:16.148] [jLog] [info] building index
out : processed/IGC_index
[2020-05-29 11:14:16.149] [puff::index::jointLog] [info] Running fixFasta[Step 1 of 4] : counting k-mers
counted k-mers for 9870000 transcripts
[2020-05-29 11:19:53.983] [puff::index::jointLog] [info] Replaced 85,915 non-ATCG nucleotides
[2020-05-29 11:19:53.983] [puff::index::jointLog] [info] Clipped poly-A tails from 13 transcripts
wrote 9879896 cleaned references
And here is the current state of the output log:
Threads = 16
Vertex length = 31
Hash functions = 5
Filter size = 137438953472
Capacity = 2
Files:
processed/IGC_index/ref_k31_fixed.faRound 0, 0:137438953472
Pass Filling Filtering
1 6242 7686
2 2040 30
True junctions count = 51430096
False junctions count = 26751117
Hash table size = 78181213
Candidate marks count = 222470897Reallocating bifurcations time: 80
Let me know if there is anything else I should provide you with
The --decoys <decoy_list>
option doesn't tell you how to provide a list of FASTA files. If I do --decoys decoys1.fa decoys2.fa
that doesn't work, if I do --decoys decoys1.fa,decoys2.fa
that also doesn't work. How do you provide a list of decoy FASTA files using this option?
Hello,
I tried to install pufferfish on Ubuntu 22.04.3 LTS following the guide
git clone [email protected]:COMBINE-lab/pufferfish.git
cd pufferfish
mkdir build
cd build
cmake ../
make
but it showed me the error
/bin/sh: 1: curl: not found
make[2]: *** [CMakeFiles/libtbb.dir/build.make:99: libtbb-prefix/src/libtbb-stamp/libtbb-download] Error 127
make[1]: *** [CMakeFiles/Makefile2:209: CMakeFiles/libtbb.dir/all] Error 2
make: *** [Makefile:156: all] Error 2
could you help me figure out how to solve this problem.
Thank you
The supplied cmake/Modules/FindJemalloc.cmake does not work on CentOS 8 even though jemalloc and jemalloc-devel are both installed from RPMs. It was replaced with the FindJeMalloc.cmake from inkscape and that did find the jemalloc files. Salmon 1.2.1 also found jemalloc and its cmake file is nearly identical to the one in Pufferfish, so perhaps you may want to use the one from Salmon in Pufferfish too.
diff FindJemalloc.cmake ../../../pufferfish-1.0.0/cmake/Modules/Hide_FindJemalloc.cmake
22c22
< find_library(JEMALLOC_LIBRARY NAMES jemalloc libjemalloc
---
> #[[find_library(JEMALLOC_LIBRARY NAMES jemalloc libjemalloc
38c38
< endif()
---
> endif()]]
Hi,
There are some applications where it's important to identify reads pairs where the reads map to different references. Even though Puffaligner map reads independently ("(โฆ) we consider the chaining and chain filtering for each end of the read separately."), I couldn't find any pair consisting of mates that map to different references.
In comparison, Bowtie2 maps โ 1.6% of the read pairs to different references with the same inputs.
Output unmapped reads to FASTQ names file (like Salmon --writeUnmappedNames
feature), alignments SAM file, or FASTQ files
Installation failed with make: *** [all] Error 2
Do you have any suggestions how to solve this?
Thanks
...
oneTBB-2021.5.0/test/tbbmalloc/test_malloc_regression.cpp
oneTBB-2021.5.0/test/tbbmalloc/test_malloc_shutdown_hang.cpp
oneTBB-2021.5.0/test/tbbmalloc/test_malloc_used_by_lib.cpp
oneTBB-2021.5.0/test/tbbmalloc/test_malloc_whitebox.cpp
oneTBB-2021.5.0/test/tbbmalloc/test_scalable_allocator.cpp
oneTBB-2021.5.0/third-party-programs.txt
[ 3%] No update step for 'libtbb'
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-- Check for working CXX compiler: /usr/bin/c++ - skipped
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-- Found Threads: TRUE
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-- The C compiler identification is GNU 7.5.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- HWLOC target HWLOC::hwloc_1_11 doesn't exist. The tbbbind target cannot be created
-- HWLOC target HWLOC::hwloc_2 doesn't exist. The tbbbind_2_0 target cannot be created
-- HWLOC target HWLOC::hwloc_2_5 doesn't exist. The tbbbind_2_5 target cannot be created
-- Configuring done
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-- Build files have been written to: /home/pufferfish/external/oneTBB-2021.5.0
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Install the project...
-- Install configuration: "Release"
-- Installing: /home/pufferfish/external/install/include
-- Installing: /home/pufferfish/external/install/include/tbb
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-- Installing: /home/pufferfish/external/install/include/tbb/global_control.h
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-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_exception.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_pipeline_filters.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_template_helpers.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_flow_graph_node_set_impl.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_flow_graph_nodes_deduction.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_flow_graph_item_buffer_impl.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_flow_graph_cache_impl.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_config.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_segment_table.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_task_handle.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_concurrent_unordered_base.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_mutex_common.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_allocator_traits.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_export.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_flow_graph_node_impl.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_hash_compare.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_rtm_rw_mutex.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_pipeline_filters_deduction.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_intrusive_list_node.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_flow_graph_join_impl.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_waitable_atomic.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_range_common.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_aggregator.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_assert.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_flow_graph_tagged_buffer_impl.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_namespace_injection.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_containers_helpers.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_concurrent_skip_list.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_concurrent_queue_base.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_string_resource.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_node_handle.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_flow_graph_trace_impl.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_flow_graph_body_impl.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/detail/_scoped_lock.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/task_group.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/cache_aligned_allocator.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/concurrent_set.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/mutex.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/spin_rw_mutex.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/parallel_reduce.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/rw_mutex.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/flow_graph.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/concurrent_lru_cache.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/queuing_rw_mutex.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/task_arena.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/concurrent_vector.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/tbbmalloc_proxy.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/blocked_range3d.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/profiling.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/parallel_invoke.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/parallel_pipeline.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/task.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/concurrent_unordered_map.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/info.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/tick_count.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/parallel_for_each.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/spin_mutex.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/partitioner.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/version.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/queuing_mutex.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/tbb_allocator.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/memory_pool.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/enumerable_thread_specific.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb/concurrent_priority_queue.h
-- Installing: /home/pufferfish/external/install/include/oneapi/tbb.h
-- Installing: /home/pufferfish/external/install/lib/cmake/TBB/TBBTargets.cmake
-- Installing: /home/pufferfish/external/install/lib/cmake/TBB/TBBTargets-release.cmake
-- Installing: /home/pufferfish/external/install/lib/cmake/TBB/TBBConfig.cmake
-- Installing: /home/pufferfish/external/install/lib/cmake/TBB/TBBConfigVersion.cmake
-- Installing: /home/pufferfish/external/install/share/doc/TBB/README.md
-- Installing: /home/pufferfish/external/install/lib/libtbb.so.12.5
-- Installing: /home/pufferfish/external/install/lib/libtbb.so.12
-- Installing: /home/pufferfish/external/install/lib/libtbb.so
-- Installing: /home/pufferfish/external/install/lib/pkgconfig/tbb.pc
-- Installing: /home/pufferfish/external/install/lib/libtbbmalloc.so.2.5
-- Installing: /home/pufferfish/external/install/lib/libtbbmalloc.so.2
-- Installing: /home/pufferfish/external/install/lib/libtbbmalloc.so
-- Installing: /home/pufferfish/external/install/lib/libtbbmalloc_proxy.so.2.5
-- Installing: /home/pufferfish/external/install/lib/libtbbmalloc_proxy.so.2
-- Set runtime path of "/home/pufferfish/external/install/lib/libtbbmalloc_proxy.so.2.5" to ""
-- Installing: /home/pufferfish/external/install/lib/libtbbmalloc_proxy.so
[ 7%] Performing reconfigure step for 'libtbb'
CC: gcc
CC version:
Detected non-ARM host. Setting USE_ARM to false.
version: 1.0.0
Top-level source directory variable not set externally; setting it to /home/pufferfish
setting -DHAVE_NUMERIC_LIMITS128
-- Could NOT find Jemalloc (missing: JEMALLOC_LIBRARY JEMALLOC_INCLUDE_DIR)
-- Could NOT find TBB (missing: TBB_DIR)
Build system will fetch and build Intel Threading Building Blocks
==================================================================
fetching oneAPI::TBB : TBB_SOURCE_DIR = /home/pufferfish/external/oneTBB-2021.5.0, TBB_INSTALL_DIR = /home/pufferfish/external/install
-- Could NOT find LibLZMA (missing: LIBLZMA_LIBRARY LIBLZMA_INCLUDE_DIR LIBLZMA_HAS_AUTO_DECODER LIBLZMA_HAS_EASY_ENCODER LIBLZMA_HAS_LZMA_PRESET)
Will attempt to fetch and build liblzma
=======================================
-- Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR)
Will attempt to fetch and build libbz2
=======================================
TBB_INCLUDE_DIRS = /home/pufferfish/external/install/include
TBB_LIBRARY_DIRS = /home/pufferfish/external/install/lib
TBB_INSTALL_DIR = /home/pufferfish/external/install
TBB_LIBRARIES = /home/pufferfish/external/install/lib/libtbbmalloc.so;/home/pufferfish/external/install/lib/libtbbmalloc_proxy.so;/home/pufferfish/external/install/lib/libtbb.so
-- setting COMPACT_VECTOR_DIR for graphdump to be /home/pufferfish/external/twopaco/graphdump
adding externally-fetched tbb as dependency of twopaco
add library puffer : PufferfishIndexer.cpp;PufferfishBaseIndex.cpp;PufferfishIndex.cpp;PufferfishSparseIndex.cpp;PufferfishLossyIndex.cpp;edlib.cpp;Util.cpp;rank9sel.cpp;rank9b.cpp;PufferfishValidate.cpp;PufferfishStats.cpp;PufferfishTestLookup.cpp;PufferfishExamine.cpp;PufferfishKmerQuery.cpp;FastxParser.cpp;PufferfishBinaryGFAReader.cpp;PufferFS.cpp;xxhash.c;FixFasta.cpp;MemCollector.cpp;MemChainer.cpp;PuffAligner.cpp;PufferfishAligner.cpp;RefSeqConstructor.cpp;metro/metrohash64.cpp
adding /home/pufferfish/external/twopaco/graphdump to include path for libpuffer
Building extra components
-- Configuring done
-- Generating done
-- Build files have been written to: /home/pufferfish/build
[ 8%] Completed 'libtbb'
[ 8%] Built target libtbb
[ 9%] Creating directories for 'liblzma'
[ 9%] Performing download step for 'liblzma'
xz-5.2.2.tar.gz: FAILED
sha256sum: WARNING: 1 computed checksum did NOT match
xz-5.2.2.tar.gz did not match expected SHA256! Exiting.
CMakeFiles/liblzma.dir/build.make:97: recipe for target 'liblzma-prefix/src/liblzma-stamp/liblzma-download' failed
make[2]: *** [liblzma-prefix/src/liblzma-stamp/liblzma-download] Error 1
CMakeFiles/Makefile2:238: recipe for target 'CMakeFiles/liblzma.dir/all' failed
make[1]: *** [CMakeFiles/liblzma.dir/all] Error 2
Makefile:155: recipe for target 'all' failed
make: *** [all] Error 2
Hi,
Thanks for publishing pufferfish! I was interested in trying it for genome alignment, but when I tried to index GRCh38 it printed out a lot of warnings as if it was interpreting it as a transcriptome:
pufferfish index -r Homo_sapiens_assembly38.fasta -o pufferfish
[2020-08-25 22:30:24.855] [puff::index::jointLog] [info] Running fixFasta
[Step 1 of 4] : counting k-mers
[2020-08-25 22:30:34.352] [puff::index::jointLog] [warning] Entry with header [chr1] was longer than 200000 nucleotides. This is probably a chromosome instead of a transcript.
[2020-08-25 22:30:38.014] [puff::index::jointLog] [warning] Entry with header [chr2] was longer than 200000 nucleotides. This is probably a chromosome instead of a transcript.
[2020-08-25 22:30:41.037] [puff::index::jointLog] [warning] Entry with header [chr3] was longer than 200000 nucleotides. This is probably a chromosome instead of a transcript.
[2020-08-25 22:30:44.030] [puff::index::jointLog] [warning] Entry with header [chr4] was longer than 200000 nucleotides. This is probably a chromosome instead of a transcript.
[2020-08-25 22:30:46.990] [puff::index::jointLog] [warning] Entry with header [chr5] was longer than 200000 nucleotides. This is probably a chromosome instead of a transcript.
Is there a different procedure for indexing a genome? Or are these warnings misleading?
NB: it would be also good to know if there is any handling for alt contigs or if these should be removed from a reference to avoid multimapped alignments from them?
Thanks!
Hello,
I would like to test puffAligner but the installation fails with the wrong C++ compiler detected when following the installation instructions. It seems that cmake it is skipping my local g++
, and the error occurs at the make
stage.
I am on a server without root access and use cmake
and g++
in a conda environment. The system-installed cmake
and g++
are too old for building puffalign (I tried with them before updating cmake and g++).
Any suggestions for fixing this, or is it possible to supply a static build of puffaligner?
Here are the versions:
$ g++ --version
g++ (conda-forge 11.2.0-15) 11.2.0
(cmake) [kris@rackham3 build]$ cmake --version
cmake version 3.18.2
Log when running cmake:
$ cmake ../
CC: gcc
CC version:
Detected non-ARM host. Setting USE_ARM to false.
-- The CXX compiler identification is GNU 11.2.0
-- The C compiler identification is GNU 11.2.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /proj/snic2020-15-201/anaconda3/envs/cmake/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /proj/snic2020-15-201/anaconda3/envs/cmake/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
version: 1.0.0
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Found Threads: TRUE
Top-level source directory variable not set externally; setting it to /home/kris/source/pufferfish
setting -DHAVE_NUMERIC_LIMITS128
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1")
-- Could NOT find Jemalloc (missing: JEMALLOC_LIBRARY JEMALLOC_INCLUDE_DIR)
-- Could NOT find TBB (missing: TBB_DIR)
Build system will fetch and build Intel Threading Building Blocks
==================================================================
fetching oneAPI::TBB : TBB_SOURCE_DIR = /home/kris/source/pufferfish/external/oneTBB-2021.5.0, TBB_INSTALL_DIR = /home/kris/source/pufferfish/external/install
-- Looking for lzma_auto_decoder in /usr/lib64/liblzma.so
-- Looking for lzma_auto_decoder in /usr/lib64/liblzma.so - not found
-- Looking for lzma_easy_encoder in /usr/lib64/liblzma.so
-- Looking for lzma_easy_encoder in /usr/lib64/liblzma.so - not found
-- Looking for lzma_lzma_preset in /usr/lib64/liblzma.so
-- Looking for lzma_lzma_preset in /usr/lib64/liblzma.so - not found
-- Could NOT find LibLZMA (missing: LIBLZMA_HAS_AUTO_DECODER LIBLZMA_HAS_EASY_ENCODER LIBLZMA_HAS_LZMA_PRESET) (found version "5.2.2")
Will attempt to fetch and build liblzma
=======================================
-- Found BZip2: /usr/lib64/libbz2.so (found version "1.0.6")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - not found
Found libbz2 library: /usr/lib64/libbz2.so
===========================================
TBB_INCLUDE_DIRS = /home/kris/source/pufferfish/external/install/include
TBB_LIBRARY_DIRS = /home/kris/source/pufferfish/external/install/lib
TBB_LIBRARIES = /home/kris/source/pufferfish/external/install/lib/libtbb.so;/home/kris/source/pufferfish/external/install/lib/libtbbmalloc.so;/home/kris/source/pufferfish/external/install/lib/libtbbmalloc_proxy.so
adding externally-fetched tbb as dependency of twopaco
add library puffer : PufferfishIndexer.cpp;PufferfishBaseIndex.cpp;PufferfishIndex.cpp;PufferfishSparseIndex.cpp;PufferfishLossyIndex.cpp;edlib.cpp;Util.cpp;rank9sel.cpp;rank9b.cpp;PufferfishValidate.cpp;PufferfishStats.cpp;PufferfishTestLookup.cpp;PufferfishExamine.cpp;PufferfishKmerQuery.cpp;FastxParser.cpp;PufferfishBinaryGFAReader.cpp;PufferFS.cpp;xxhash.c;FixFasta.cpp;MemCollector.cpp;MemChainer.cpp;PuffAligner.cpp;PufferfishAligner.cpp;RefSeqConstructor.cpp;metro/metrohash64.cpp
Building extra components
-- Configuring done
-- Generating done
-- Build files have been written to: /home/kris/source/pufferfish/build
Log when running make:
$ make
Scanning dependencies of target libtbb
[ 1%] Creating directories for 'libtbb'
[ 2%] Performing download step for 'libtbb'
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 138 100 138 0 0 364 0 --:--:-- --:--:-- --:--:-- 365
0 0 0 2405k 0 0 2481k 0 --:--:-- --:--:-- --:--:-- 8315k
v2021.5.tar.gz: OK
oneTBB-2021.5.0/
oneTBB-2021.5.0/.bazelrc
oneTBB-2021.5.0/.bazelversion
oneTBB-2021.5.0/.gitattributes
oneTBB-2021.5.0/.github/
oneTBB-2021.5.0/.github/pull_request_template.md
oneTBB-2021.5.0/.github/scripts/
oneTBB-2021.5.0/.github/scripts/codespell.sh
oneTBB-2021.5.0/.github/workflows/
oneTBB-2021.5.0/.github/workflows/ci.yml
oneTBB-2021.5.0/.gitignore
oneTBB-2021.5.0/BUILD.bazel
oneTBB-2021.5.0/Bazel.md
oneTBB-2021.5.0/CMakeLists.txt
oneTBB-2021.5.0/CONTRIBUTING.md
oneTBB-2021.5.0/LICENSE.txt
oneTBB-2021.5.0/README.md
oneTBB-2021.5.0/WORKSPACE.bazel
oneTBB-2021.5.0/cmake/
oneTBB-2021.5.0/cmake/README.md
oneTBB-2021.5.0/cmake/android/
oneTBB-2021.5.0/cmake/android/device_environment_cleanup.cmake
oneTBB-2021.5.0/cmake/android/environment.cmake
oneTBB-2021.5.0/cmake/android/test_launcher.cmake
oneTBB-2021.5.0/cmake/compilers/
oneTBB-2021.5.0/cmake/compilers/AppleClang.cmake
oneTBB-2021.5.0/cmake/compilers/Clang.cmake
oneTBB-2021.5.0/cmake/compilers/GNU.cmake
oneTBB-2021.5.0/cmake/compilers/Intel.cmake
oneTBB-2021.5.0/cmake/compilers/IntelLLVM.cmake
oneTBB-2021.5.0/cmake/compilers/MSVC.cmake
oneTBB-2021.5.0/cmake/compilers/QCC.cmake
oneTBB-2021.5.0/cmake/config_generation.cmake
oneTBB-2021.5.0/cmake/hwloc_detection.cmake
oneTBB-2021.5.0/cmake/memcheck.cmake
oneTBB-2021.5.0/cmake/packaging.cmake
oneTBB-2021.5.0/cmake/post_install/
oneTBB-2021.5.0/cmake/post_install/CMakeLists.txt
oneTBB-2021.5.0/cmake/python/
oneTBB-2021.5.0/cmake/python/test_launcher.cmake
oneTBB-2021.5.0/cmake/sanitize.cmake
oneTBB-2021.5.0/cmake/scripts/
oneTBB-2021.5.0/cmake/scripts/cmake_gen_github_configs.cmake
oneTBB-2021.5.0/cmake/suppressions/
oneTBB-2021.5.0/cmake/suppressions/lsan.suppressions
oneTBB-2021.5.0/cmake/templates/
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oneTBB-2021.5.0/cmake/templates/TBBConfigVersion.cmake.in
oneTBB-2021.5.0/cmake/test_spec.cmake
oneTBB-2021.5.0/cmake/toolchains/
oneTBB-2021.5.0/cmake/toolchains/mips.cmake
oneTBB-2021.5.0/cmake/utils.cmake
oneTBB-2021.5.0/cmake/vars_utils.cmake
oneTBB-2021.5.0/doc/
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oneTBB-2021.5.0/doc/DoxygenLayout.xml
oneTBB-2021.5.0/doc/GSG/
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oneTBB-2021.5.0/doc/main/intro/Benefits.rst
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oneTBB-2021.5.0/doc/main/intro/help_support.rst
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oneTBB-2021.5.0/doc/main/intro/notices_and_disclaimers.rst
oneTBB-2021.5.0/doc/main/reference/
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oneTBB-2021.5.0/doc/main/reference/scalable_memory_pools/
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oneTBB-2021.5.0/doc/main/reference/task_group_extensions/
oneTBB-2021.5.0/doc/main/reference/task_group_extensions/task_handle.rst
oneTBB-2021.5.0/doc/main/reference/this_task_arena_extensions.rst
oneTBB-2021.5.0/doc/main/reference/type_specified_message_keys.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/
oneTBB-2021.5.0/doc/main/tbb_userguide/Advanced_Example.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Advanced_Topic_Other_Kinds_of_Iteration_Spaces.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Allocator_Configuration.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Automatic_Chunking.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Automically_Replacing_malloc.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Bandwidth_and_Cache_Affinity.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Basic_Flow_Graph_concepts.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Cancellation_Without_An_Exception.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Cancellation_and_Nested_Parallelism.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Concurrent_Queue_Classes.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Constraints.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Containers.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Controlling_Chunking.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Cook_Until_Done_parallel_do.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Data_Flow_Graph.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Debug_Versus_Release_Libraries.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Dependence_Graph.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Edges.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Exceptions_and_Cancellation.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Flow_Graph.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Flow_Graph_Buffering_in_Nodes.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Flow_Graph_Message_Passing_Protocol.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Flow_Graph_Reservation.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Flow_Graph_Single_Vs_Broadcast.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Flow_Graph_Tips.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Flow_Graph_exception_tips.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Flow_Graph_making_edges_tips.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Flow_Graph_nested_parallelism_tips.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Flow_Graph_resource_tips.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Flow_Graph_waiting_tips.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Graph_Main_Categories.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Graph_Object.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Guiding_Task_Scheduler_Execution.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Images/
oneTBB-2021.5.0/doc/main/tbb_userguide/Images/dependence_graph.jpg
oneTBB-2021.5.0/doc/main/tbb_userguide/Images/execution_timeline2node.jpg
oneTBB-2021.5.0/doc/main/tbb_userguide/Images/execution_timeline_dependence.jpg
oneTBB-2021.5.0/doc/main/tbb_userguide/Images/flow_graph.jpg
oneTBB-2021.5.0/doc/main/tbb_userguide/Images/flow_graph_complex.jpg
oneTBB-2021.5.0/doc/main/tbb_userguide/Images/flow_graph_message_passing_protocol.jpg
oneTBB-2021.5.0/doc/main/tbb_userguide/Images/flow_graph_reserve_buffers_1.png
oneTBB-2021.5.0/doc/main/tbb_userguide/Images/flow_graph_reserve_buffers_2.png
oneTBB-2021.5.0/doc/main/tbb_userguide/Images/flow_graph_reserve_buffers_3.png
oneTBB-2021.5.0/doc/main/tbb_userguide/Images/flow_graph_reserve_buffers_4.png
oneTBB-2021.5.0/doc/main/tbb_userguide/Images/flow_graph_reserve_buffers_5.png
oneTBB-2021.5.0/doc/main/tbb_userguide/Images/flow_graph_reserve_buffers_6.png
oneTBB-2021.5.0/doc/main/tbb_userguide/Images/flow_graph_reserve_buffers_7.png
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oneTBB-2021.5.0/doc/main/tbb_userguide/Initializing_and_Terminating_the_Library.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Iterating_Over_a_Concurrent_Queue_for_Debugging.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Lambda_Expressions.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Linux_C_Dynamic_Memory_Interface_Replacement.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Linux_OS.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Lock_Pathologies.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Mac_OS.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Mapping_Nodes2Tasks.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Memory_Allocation.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Migration_Guide.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Migration_Guide/
oneTBB-2021.5.0/doc/main/tbb_userguide/Migration_Guide/Mixing_Two_Runtimes.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Migration_Guide/Task_API.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Migration_Guide/Task_Scheduler_Init.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/More_on_HashCompare.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Mutex_Flavors.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Mutual_Exclusion.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Nodes.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Non-Linear_Pipelines.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Package_Contents.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Parallelizing_Complex_Loops.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Parallelizing_Flow_Graph.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Parallelizing_Simple_Loops.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Partitioner_Summary.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Predefined_Node_Types.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Reader_Writer_Mutexes.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/References.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Scalable_Memory_Allocator.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Summary_of_Containers.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Summary_of_Loops_and_Pipelines.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Task-Based_Programming.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Task_Scheduler_Summary.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/The_Task_Scheduler.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Throughput_of_pipeline.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Timing.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/UpgradeDowngrade.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Using_Circular_Buffers.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/When_Not_to_Use_Queues.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/When_Task-Based_Programming_Is_Inappropriate.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Which_Dynamic_Libraries_to_Use.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Windows_C_Dynamic_Memory_Interface_Replacement.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Windows_OS_ug.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/Working_on_the_Assembly_Line_pipeline.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/always_use_wait_for_all.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/appendix_A.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/appendix_B.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/avoid_dynamic_node_removal.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/avoiding_data_races.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/broadcast_or_send.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/cancel_a_graph.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/cancelling_nested_parallelism.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/catching_exceptions.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/communicate_with_nodes.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/concurrent_hash_map.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/concurrent_vector_ug.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/create_token_based_system.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/design_patterns/
oneTBB-2021.5.0/doc/main/tbb_userguide/design_patterns/Agglomeration.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/design_patterns/Design_Patterns.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/design_patterns/Divide_and_Conquer.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/design_patterns/Elementwise.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/design_patterns/Fenced_Data_Transfer.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/design_patterns/GUI_Thread.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/design_patterns/General_References.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/design_patterns/Images/
oneTBB-2021.5.0/doc/main/tbb_userguide/design_patterns/Images/image002a.jpg
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oneTBB-2021.5.0/doc/main/tbb_userguide/design_patterns/Local_Serializer.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/design_patterns/Non-Preemptive_Priorities.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/design_patterns/Odd-Even_Communication.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/design_patterns/Reduction.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/design_patterns/Reference_Counting.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/design_patterns/Wavefront.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/destroy_graphs_outside_main_thread.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/estimate_flow_graph_performance.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/parallel_for.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/parallel_reduce.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/title.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/use_concurrency_limits.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/use_graph_reset.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/use_input_node.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/use_limiter_node.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/use_make_edge.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/use_nested_algorithms.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/use_nested_flow_graphs.rst
oneTBB-2021.5.0/doc/main/tbb_userguide/work_isolation.rst
oneTBB-2021.5.0/doc/test_classification.dox
oneTBB-2021.5.0/examples/
oneTBB-2021.5.0/examples/.clang-format
oneTBB-2021.5.0/examples/CMakeLists.txt
oneTBB-2021.5.0/examples/README.md
oneTBB-2021.5.0/examples/common/
oneTBB-2021.5.0/examples/common/cmake/
oneTBB-2021.5.0/examples/common/cmake/common.cmake
oneTBB-2021.5.0/examples/common/cmake/modules/
oneTBB-2021.5.0/examples/common/cmake/modules/FindTBB.cmake
oneTBB-2021.5.0/examples/common/gui/
oneTBB-2021.5.0/examples/common/gui/CMakeLists.txt
oneTBB-2021.5.0/examples/common/gui/convideo.cpp
oneTBB-2021.5.0/examples/common/gui/d2dvideo.cpp
oneTBB-2021.5.0/examples/common/gui/gdivideo.cpp
oneTBB-2021.5.0/examples/common/gui/macvideo.cpp
oneTBB-2021.5.0/examples/common/gui/video.hpp
oneTBB-2021.5.0/examples/common/gui/winvideo.hpp
oneTBB-2021.5.0/examples/common/gui/xcode/
oneTBB-2021.5.0/examples/common/gui/xcode/tbbExample/
oneTBB-2021.5.0/examples/common/gui/xcode/tbbExample/OpenGLView.h
oneTBB-2021.5.0/examples/common/gui/xcode/tbbExample/OpenGLView.m
oneTBB-2021.5.0/examples/common/gui/xcode/tbbExample/PkgInfo
oneTBB-2021.5.0/examples/common/gui/xcode/tbbExample/en.lproj/
oneTBB-2021.5.0/examples/common/gui/xcode/tbbExample/en.lproj/InfoPlist.strings
oneTBB-2021.5.0/examples/common/gui/xcode/tbbExample/en.lproj/MainMenu.nib
oneTBB-2021.5.0/examples/common/gui/xcode/tbbExample/en.lproj/MainMenu.xib
oneTBB-2021.5.0/examples/common/gui/xcode/tbbExample/iOS.storyboard
oneTBB-2021.5.0/examples/common/gui/xcode/tbbExample/main.m
oneTBB-2021.5.0/examples/common/gui/xcode/tbbExample/tbbAppDelegate.h
oneTBB-2021.5.0/examples/common/gui/xcode/tbbExample/tbbAppDelegate.m
oneTBB-2021.5.0/examples/common/gui/xcode/tbbExample/tbbExample-Info.ios.plist
oneTBB-2021.5.0/examples/common/gui/xcode/tbbExample/tbbExample-Info.plist
oneTBB-2021.5.0/examples/common/gui/xvideo.cpp
oneTBB-2021.5.0/examples/common/utility/
oneTBB-2021.5.0/examples/common/utility/fast_random.hpp
oneTBB-2021.5.0/examples/common/utility/get_default_num_threads.hpp
oneTBB-2021.5.0/examples/common/utility/utility.hpp
oneTBB-2021.5.0/examples/concurrent_hash_map/
oneTBB-2021.5.0/examples/concurrent_hash_map/README.md
oneTBB-2021.5.0/examples/concurrent_hash_map/count_strings/
oneTBB-2021.5.0/examples/concurrent_hash_map/count_strings/CMakeLists.txt
oneTBB-2021.5.0/examples/concurrent_hash_map/count_strings/README.md
oneTBB-2021.5.0/examples/concurrent_hash_map/count_strings/count_strings.cpp
oneTBB-2021.5.0/examples/concurrent_priority_queue/
oneTBB-2021.5.0/examples/concurrent_priority_queue/README.md
oneTBB-2021.5.0/examples/concurrent_priority_queue/shortpath/
oneTBB-2021.5.0/examples/concurrent_priority_queue/shortpath/CMakeLists.txt
oneTBB-2021.5.0/examples/concurrent_priority_queue/shortpath/README.md
oneTBB-2021.5.0/examples/concurrent_priority_queue/shortpath/shortpath.cpp
oneTBB-2021.5.0/examples/getting_started/
oneTBB-2021.5.0/examples/getting_started/README.md
oneTBB-2021.5.0/examples/getting_started/sub_string_finder/
oneTBB-2021.5.0/examples/getting_started/sub_string_finder/CMakeLists.txt
oneTBB-2021.5.0/examples/getting_started/sub_string_finder/README.md
oneTBB-2021.5.0/examples/getting_started/sub_string_finder/sub_string_finder.cpp
oneTBB-2021.5.0/examples/getting_started/sub_string_finder/sub_string_finder_extended.cpp
oneTBB-2021.5.0/examples/getting_started/sub_string_finder/sub_string_finder_pretty.cpp
oneTBB-2021.5.0/examples/graph/
oneTBB-2021.5.0/examples/graph/README.md
oneTBB-2021.5.0/examples/graph/binpack/
oneTBB-2021.5.0/examples/graph/binpack/CMakeLists.txt
oneTBB-2021.5.0/examples/graph/binpack/README.md
oneTBB-2021.5.0/examples/graph/binpack/binpack.cpp
oneTBB-2021.5.0/examples/graph/cholesky/
oneTBB-2021.5.0/examples/graph/cholesky/CMakeLists.txt
oneTBB-2021.5.0/examples/graph/cholesky/README.md
oneTBB-2021.5.0/examples/graph/cholesky/cholesky.cpp
oneTBB-2021.5.0/examples/graph/cholesky/init.cpp
oneTBB-2021.5.0/examples/graph/dining_philosophers/
oneTBB-2021.5.0/examples/graph/dining_philosophers/CMakeLists.txt
oneTBB-2021.5.0/examples/graph/dining_philosophers/README.md
oneTBB-2021.5.0/examples/graph/dining_philosophers/dining_philosophers.cpp
oneTBB-2021.5.0/examples/graph/fgbzip2/
oneTBB-2021.5.0/examples/graph/fgbzip2/CMakeLists.txt
oneTBB-2021.5.0/examples/graph/fgbzip2/README.md
oneTBB-2021.5.0/examples/graph/fgbzip2/blocksort.cpp
oneTBB-2021.5.0/examples/graph/fgbzip2/bzlib.cpp
oneTBB-2021.5.0/examples/graph/fgbzip2/bzlib.hpp
oneTBB-2021.5.0/examples/graph/fgbzip2/bzlib_private.hpp
oneTBB-2021.5.0/examples/graph/fgbzip2/compress.cpp
oneTBB-2021.5.0/examples/graph/fgbzip2/crctable.cpp
oneTBB-2021.5.0/examples/graph/fgbzip2/decompress.cpp
oneTBB-2021.5.0/examples/graph/fgbzip2/fgbzip2.cpp
oneTBB-2021.5.0/examples/graph/fgbzip2/huffman.cpp
oneTBB-2021.5.0/examples/graph/fgbzip2/randtable.cpp
oneTBB-2021.5.0/examples/graph/logic_sim/
oneTBB-2021.5.0/examples/graph/logic_sim/CMakeLists.txt
oneTBB-2021.5.0/examples/graph/logic_sim/D_latch.hpp
oneTBB-2021.5.0/examples/graph/logic_sim/README.md
oneTBB-2021.5.0/examples/graph/logic_sim/basics.hpp
oneTBB-2021.5.0/examples/graph/logic_sim/four_bit_adder.hpp
oneTBB-2021.5.0/examples/graph/logic_sim/one_bit_adder.hpp
oneTBB-2021.5.0/examples/graph/logic_sim/test_all.cpp
oneTBB-2021.5.0/examples/graph/logic_sim/two_bit_adder.hpp
oneTBB-2021.5.0/examples/graph/som/
oneTBB-2021.5.0/examples/graph/som/CMakeLists.txt
oneTBB-2021.5.0/examples/graph/som/README.md
oneTBB-2021.5.0/examples/graph/som/som.cpp
oneTBB-2021.5.0/examples/graph/som/som.hpp
oneTBB-2021.5.0/examples/graph/som/som_graph.cpp
oneTBB-2021.5.0/examples/parallel_for/
oneTBB-2021.5.0/examples/parallel_for/README.md
oneTBB-2021.5.0/examples/parallel_for/game_of_life/
oneTBB-2021.5.0/examples/parallel_for/game_of_life/Board.hpp
oneTBB-2021.5.0/examples/parallel_for/game_of_life/CMakeLists.txt
oneTBB-2021.5.0/examples/parallel_for/game_of_life/Evolution.cpp
oneTBB-2021.5.0/examples/parallel_for/game_of_life/Evolution.hpp
oneTBB-2021.5.0/examples/parallel_for/game_of_life/Game_of_life.cpp
oneTBB-2021.5.0/examples/parallel_for/game_of_life/README.md
oneTBB-2021.5.0/examples/parallel_for/game_of_life/Update_state.cpp
oneTBB-2021.5.0/examples/parallel_for/polygon_overlay/
oneTBB-2021.5.0/examples/parallel_for/polygon_overlay/CMakeLists.txt
oneTBB-2021.5.0/examples/parallel_for/polygon_overlay/README.md
oneTBB-2021.5.0/examples/parallel_for/polygon_overlay/gui/
oneTBB-2021.5.0/examples/parallel_for/polygon_overlay/gui/polygon_overlay.rc
oneTBB-2021.5.0/examples/parallel_for/polygon_overlay/gui/resource.h
oneTBB-2021.5.0/examples/parallel_for/polygon_overlay/polymain.cpp
oneTBB-2021.5.0/examples/parallel_for/polygon_overlay/polymain.hpp
oneTBB-2021.5.0/examples/parallel_for/polygon_overlay/polyover.cpp
oneTBB-2021.5.0/examples/parallel_for/polygon_overlay/polyover.hpp
oneTBB-2021.5.0/examples/parallel_for/polygon_overlay/pover_global.hpp
oneTBB-2021.5.0/examples/parallel_for/polygon_overlay/pover_video.cpp
oneTBB-2021.5.0/examples/parallel_for/polygon_overlay/pover_video.hpp
oneTBB-2021.5.0/examples/parallel_for/polygon_overlay/rpolygon.hpp
oneTBB-2021.5.0/examples/parallel_for/polygon_overlay/speedup.gif
oneTBB-2021.5.0/examples/parallel_for/seismic/
oneTBB-2021.5.0/examples/parallel_for/seismic/CMakeLists.txt
oneTBB-2021.5.0/examples/parallel_for/seismic/README.md
oneTBB-2021.5.0/examples/parallel_for/seismic/gui/
oneTBB-2021.5.0/examples/parallel_for/seismic/gui/SeismicSimulation.ico
oneTBB-2021.5.0/examples/parallel_for/seismic/gui/resource.h
oneTBB-2021.5.0/examples/parallel_for/seismic/gui/seismic.rc
oneTBB-2021.5.0/examples/parallel_for/seismic/gui/small.ico
oneTBB-2021.5.0/examples/parallel_for/seismic/main.cpp
oneTBB-2021.5.0/examples/parallel_for/seismic/resource.hpp
oneTBB-2021.5.0/examples/parallel_for/seismic/seismic_video.cpp
oneTBB-2021.5.0/examples/parallel_for/seismic/seismic_video.hpp
oneTBB-2021.5.0/examples/parallel_for/seismic/universe.cpp
oneTBB-2021.5.0/examples/parallel_for/seismic/universe.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/
oneTBB-2021.5.0/examples/parallel_for/tachyon/CMakeLists.txt
oneTBB-2021.5.0/examples/parallel_for/tachyon/README.md
oneTBB-2021.5.0/examples/parallel_for/tachyon/dat/
oneTBB-2021.5.0/examples/parallel_for/tachyon/dat/820spheres.dat
oneTBB-2021.5.0/examples/parallel_for/tachyon/dat/balls.dat
oneTBB-2021.5.0/examples/parallel_for/tachyon/dat/balls3.dat
oneTBB-2021.5.0/examples/parallel_for/tachyon/dat/lattice.dat
oneTBB-2021.5.0/examples/parallel_for/tachyon/dat/model2.dat
oneTBB-2021.5.0/examples/parallel_for/tachyon/dat/teapot.dat
oneTBB-2021.5.0/examples/parallel_for/tachyon/dat/trypsin4pti.dat
oneTBB-2021.5.0/examples/parallel_for/tachyon/gui/
oneTBB-2021.5.0/examples/parallel_for/tachyon/gui/gui.ico
oneTBB-2021.5.0/examples/parallel_for/tachyon/gui/resource.h
oneTBB-2021.5.0/examples/parallel_for/tachyon/gui/small.ico
oneTBB-2021.5.0/examples/parallel_for/tachyon/gui/tachyon.rc
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/api.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/api.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/apigeom.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/apitrigeom.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/apitrigeom.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/bndbox.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/bndbox.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/box.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/box.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/camera.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/camera.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/coordsys.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/coordsys.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/cylinder.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/cylinder.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/extvol.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/extvol.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/global.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/global.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/grid.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/grid.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/imageio.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/imageio.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/imap.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/imap.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/intersect.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/intersect.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/jpeg.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/jpeg.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/light.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/light.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/machine.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/macros.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/main.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/objbound.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/objbound.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/parse.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/parse.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/plane.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/plane.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/ppm.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/ppm.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/pthread.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/pthread_w.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/quadric.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/quadric.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/render.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/render.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/ring.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/ring.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/shade.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/shade.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/sphere.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/sphere.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/tachyon_video.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/tachyon_video.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/texture.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/texture.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/tgafile.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/tgafile.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/trace.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/trace.omp.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/trace.serial.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/trace.simple.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/trace.taskq.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/trace.tbb.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/trace.tbb1d.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/trace.threads.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/trace.threads2d.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/trace_rest.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/triangle.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/triangle.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/types.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/ui.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/ui.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/util.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/util.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/vector.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/vector.hpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/vol.cpp
oneTBB-2021.5.0/examples/parallel_for/tachyon/src/vol.hpp
oneTBB-2021.5.0/examples/parallel_for_each/
oneTBB-2021.5.0/examples/parallel_for_each/README.md
oneTBB-2021.5.0/examples/parallel_for_each/parallel_preorder/
oneTBB-2021.5.0/examples/parallel_for_each/parallel_preorder/CMakeLists.txt
oneTBB-2021.5.0/examples/parallel_for_each/parallel_preorder/Graph.cpp
oneTBB-2021.5.0/examples/parallel_for_each/parallel_preorder/Graph.hpp
oneTBB-2021.5.0/examples/parallel_for_each/parallel_preorder/Matrix.hpp
oneTBB-2021.5.0/examples/parallel_for_each/parallel_preorder/README.md
oneTBB-2021.5.0/examples/parallel_for_each/parallel_preorder/main.cpp
oneTBB-2021.5.0/examples/parallel_for_each/parallel_preorder/parallel_preorder.cpp
oneTBB-2021.5.0/examples/parallel_pipeline/
oneTBB-2021.5.0/examples/parallel_pipeline/README.md
oneTBB-2021.5.0/examples/parallel_pipeline/square/
oneTBB-2021.5.0/examples/parallel_pipeline/square/CMakeLists.txt
oneTBB-2021.5.0/examples/parallel_pipeline/square/README.md
oneTBB-2021.5.0/examples/parallel_pipeline/square/gen_input.cpp
oneTBB-2021.5.0/examples/parallel_pipeline/square/square.cpp
oneTBB-2021.5.0/examples/parallel_reduce/
oneTBB-2021.5.0/examples/parallel_reduce/README.md
oneTBB-2021.5.0/examples/parallel_reduce/convex_hull/
oneTBB-2021.5.0/examples/parallel_reduce/convex_hull/CMakeLists.txt
oneTBB-2021.5.0/examples/parallel_reduce/convex_hull/README.md
oneTBB-2021.5.0/examples/parallel_reduce/convex_hull/convex_hull.hpp
oneTBB-2021.5.0/examples/parallel_reduce/convex_hull/convex_hull_bench.cpp
oneTBB-2021.5.0/examples/parallel_reduce/convex_hull/convex_hull_sample.cpp
oneTBB-2021.5.0/examples/parallel_reduce/primes/
oneTBB-2021.5.0/examples/parallel_reduce/primes/CMakeLists.txt
oneTBB-2021.5.0/examples/parallel_reduce/primes/README.md
oneTBB-2021.5.0/examples/parallel_reduce/primes/main.cpp
oneTBB-2021.5.0/examples/parallel_reduce/primes/primes.cpp
oneTBB-2021.5.0/examples/parallel_reduce/primes/primes.hpp
oneTBB-2021.5.0/examples/task_arena/
oneTBB-2021.5.0/examples/task_arena/README.md
oneTBB-2021.5.0/examples/task_arena/fractal/
oneTBB-2021.5.0/examples/task_arena/fractal/CMakeLists.txt
oneTBB-2021.5.0/examples/task_arena/fractal/README.md
oneTBB-2021.5.0/examples/task_arena/fractal/fractal.cpp
oneTBB-2021.5.0/examples/task_arena/fractal/fractal.hpp
oneTBB-2021.5.0/examples/task_arena/fractal/fractal_video.hpp
oneTBB-2021.5.0/examples/task_arena/fractal/gui/
oneTBB-2021.5.0/examples/task_arena/fractal/gui/fractal.rc
oneTBB-2021.5.0/examples/task_arena/fractal/gui/gui.ico
oneTBB-2021.5.0/examples/task_arena/fractal/gui/resource.h
oneTBB-2021.5.0/examples/task_arena/fractal/gui/small.ico
oneTBB-2021.5.0/examples/task_arena/fractal/main.cpp
oneTBB-2021.5.0/examples/task_group/
oneTBB-2021.5.0/examples/task_group/README.md
oneTBB-2021.5.0/examples/task_group/sudoku/
oneTBB-2021.5.0/examples/task_group/sudoku/CMakeLists.txt
oneTBB-2021.5.0/examples/task_group/sudoku/README.md
oneTBB-2021.5.0/examples/task_group/sudoku/input1
oneTBB-2021.5.0/examples/task_group/sudoku/input2
oneTBB-2021.5.0/examples/task_group/sudoku/input3
oneTBB-2021.5.0/examples/task_group/sudoku/input4
oneTBB-2021.5.0/examples/task_group/sudoku/sudoku.cpp
oneTBB-2021.5.0/examples/test_all/
oneTBB-2021.5.0/examples/test_all/README.md
oneTBB-2021.5.0/examples/test_all/fibonacci/
oneTBB-2021.5.0/examples/test_all/fibonacci/CMakeLists.txt
oneTBB-2021.5.0/examples/test_all/fibonacci/README.md
oneTBB-2021.5.0/examples/test_all/fibonacci/fibonacci.cpp
oneTBB-2021.5.0/include/
oneTBB-2021.5.0/include/oneapi/
oneTBB-2021.5.0/include/oneapi/tbb.h
oneTBB-2021.5.0/include/oneapi/tbb/
oneTBB-2021.5.0/include/oneapi/tbb/blocked_range.h
oneTBB-2021.5.0/include/oneapi/tbb/blocked_range2d.h
oneTBB-2021.5.0/include/oneapi/tbb/blocked_range3d.h
oneTBB-2021.5.0/include/oneapi/tbb/blocked_rangeNd.h
oneTBB-2021.5.0/include/oneapi/tbb/cache_aligned_allocator.h
oneTBB-2021.5.0/include/oneapi/tbb/collaborative_call_once.h
oneTBB-2021.5.0/include/oneapi/tbb/combinable.h
oneTBB-2021.5.0/include/oneapi/tbb/concurrent_hash_map.h
oneTBB-2021.5.0/include/oneapi/tbb/concurrent_lru_cache.h
oneTBB-2021.5.0/include/oneapi/tbb/concurrent_map.h
oneTBB-2021.5.0/include/oneapi/tbb/concurrent_priority_queue.h
oneTBB-2021.5.0/include/oneapi/tbb/concurrent_queue.h
oneTBB-2021.5.0/include/oneapi/tbb/concurrent_set.h
oneTBB-2021.5.0/include/oneapi/tbb/concurrent_unordered_map.h
oneTBB-2021.5.0/include/oneapi/tbb/concurrent_unordered_set.h
oneTBB-2021.5.0/include/oneapi/tbb/concurrent_vector.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/
oneTBB-2021.5.0/include/oneapi/tbb/detail/_aggregator.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_aligned_space.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_allocator_traits.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_assert.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_concurrent_queue_base.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_concurrent_skip_list.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_concurrent_unordered_base.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_config.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_containers_helpers.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_exception.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_export.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_flow_graph_body_impl.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_flow_graph_cache_impl.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_flow_graph_impl.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_flow_graph_indexer_impl.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_flow_graph_item_buffer_impl.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_flow_graph_join_impl.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_flow_graph_node_impl.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_flow_graph_node_set_impl.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_flow_graph_nodes_deduction.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_flow_graph_tagged_buffer_impl.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_flow_graph_trace_impl.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_flow_graph_types_impl.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_hash_compare.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_intrusive_list_node.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_machine.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_mutex_common.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_namespace_injection.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_node_handle.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_pipeline_filters.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_pipeline_filters_deduction.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_range_common.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_rtm_mutex.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_rtm_rw_mutex.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_scoped_lock.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_segment_table.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_small_object_pool.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_string_resource.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_task.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_task_handle.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_template_helpers.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_utils.h
oneTBB-2021.5.0/include/oneapi/tbb/detail/_waitable_atomic.h
oneTBB-2021.5.0/include/oneapi/tbb/enumerable_thread_specific.h
oneTBB-2021.5.0/include/oneapi/tbb/flow_graph.h
oneTBB-2021.5.0/include/oneapi/tbb/flow_graph_abstractions.h
oneTBB-2021.5.0/include/oneapi/tbb/global_control.h
oneTBB-2021.5.0/include/oneapi/tbb/info.h
oneTBB-2021.5.0/include/oneapi/tbb/memory_pool.h
oneTBB-2021.5.0/include/oneapi/tbb/mutex.h
oneTBB-2021.5.0/include/oneapi/tbb/null_mutex.h
oneTBB-2021.5.0/include/oneapi/tbb/null_rw_mutex.h
oneTBB-2021.5.0/include/oneapi/tbb/parallel_for.h
oneTBB-2021.5.0/include/oneapi/tbb/parallel_for_each.h
oneTBB-2021.5.0/include/oneapi/tbb/parallel_invoke.h
oneTBB-2021.5.0/include/oneapi/tbb/parallel_pipeline.h
oneTBB-2021.5.0/include/oneapi/tbb/parallel_reduce.h
oneTBB-2021.5.0/include/oneapi/tbb/parallel_scan.h
oneTBB-2021.5.0/include/oneapi/tbb/parallel_sort.h
oneTBB-2021.5.0/include/oneapi/tbb/partitioner.h
oneTBB-2021.5.0/include/oneapi/tbb/profiling.h
oneTBB-2021.5.0/include/oneapi/tbb/queuing_mutex.h
oneTBB-2021.5.0/include/oneapi/tbb/queuing_rw_mutex.h
oneTBB-2021.5.0/include/oneapi/tbb/rw_mutex.h
oneTBB-2021.5.0/include/oneapi/tbb/scalable_allocator.h
oneTBB-2021.5.0/include/oneapi/tbb/spin_mutex.h
oneTBB-2021.5.0/include/oneapi/tbb/spin_rw_mutex.h
oneTBB-2021.5.0/include/oneapi/tbb/task.h
oneTBB-2021.5.0/include/oneapi/tbb/task_arena.h
oneTBB-2021.5.0/include/oneapi/tbb/task_group.h
oneTBB-2021.5.0/include/oneapi/tbb/task_scheduler_observer.h
oneTBB-2021.5.0/include/oneapi/tbb/tbb_allocator.h
oneTBB-2021.5.0/include/oneapi/tbb/tbbmalloc_proxy.h
oneTBB-2021.5.0/include/oneapi/tbb/tick_count.h
oneTBB-2021.5.0/include/oneapi/tbb/version.h
oneTBB-2021.5.0/include/tbb/
oneTBB-2021.5.0/include/tbb/blocked_range.h
oneTBB-2021.5.0/include/tbb/blocked_range2d.h
oneTBB-2021.5.0/include/tbb/blocked_range3d.h
oneTBB-2021.5.0/include/tbb/blocked_rangeNd.h
oneTBB-2021.5.0/include/tbb/cache_aligned_allocator.h
oneTBB-2021.5.0/include/tbb/collaborative_call_once.h
oneTBB-2021.5.0/include/tbb/combinable.h
oneTBB-2021.5.0/include/tbb/concurrent_hash_map.h
oneTBB-2021.5.0/include/tbb/concurrent_lru_cache.h
oneTBB-2021.5.0/include/tbb/concurrent_map.h
oneTBB-2021.5.0/include/tbb/concurrent_priority_queue.h
oneTBB-2021.5.0/include/tbb/concurrent_queue.h
oneTBB-2021.5.0/include/tbb/concurrent_set.h
oneTBB-2021.5.0/include/tbb/concurrent_unordered_map.h
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oneTBB-2021.5.0/test/tbb/test_multifunction_node.cpp
oneTBB-2021.5.0/test/tbb/test_mutex.cpp
oneTBB-2021.5.0/test/tbb/test_mutex.h
oneTBB-2021.5.0/test/tbb/test_openmp.cpp
oneTBB-2021.5.0/test/tbb/test_overwrite_node.cpp
oneTBB-2021.5.0/test/tbb/test_parallel_for.cpp
oneTBB-2021.5.0/test/tbb/test_parallel_for_each.cpp
oneTBB-2021.5.0/test/tbb/test_parallel_invoke.cpp
oneTBB-2021.5.0/test/tbb/test_parallel_pipeline.cpp
oneTBB-2021.5.0/test/tbb/test_parallel_reduce.cpp
oneTBB-2021.5.0/test/tbb/test_parallel_scan.cpp
oneTBB-2021.5.0/test/tbb/test_parallel_sort.cpp
oneTBB-2021.5.0/test/tbb/test_partitioner.cpp
oneTBB-2021.5.0/test/tbb/test_partitioner.h
oneTBB-2021.5.0/test/tbb/test_priority_queue_node.cpp
oneTBB-2021.5.0/test/tbb/test_profiling.cpp
oneTBB-2021.5.0/test/tbb/test_queue_node.cpp
oneTBB-2021.5.0/test/tbb/test_resumable_tasks.cpp
oneTBB-2021.5.0/test/tbb/test_scheduler_mix.cpp
oneTBB-2021.5.0/test/tbb/test_semaphore.cpp
oneTBB-2021.5.0/test/tbb/test_sequencer_node.cpp
oneTBB-2021.5.0/test/tbb/test_split_node.cpp
oneTBB-2021.5.0/test/tbb/test_tagged_msg.cpp
oneTBB-2021.5.0/test/tbb/test_task.cpp
oneTBB-2021.5.0/test/tbb/test_task_arena.cpp
oneTBB-2021.5.0/test/tbb/test_task_group.cpp
oneTBB-2021.5.0/test/tbb/test_tbb_fork.cpp
oneTBB-2021.5.0/test/tbb/test_tbb_header.cpp
oneTBB-2021.5.0/test/tbb/test_tbb_header_secondary.cpp
oneTBB-2021.5.0/test/tbb/test_tick_count.cpp
oneTBB-2021.5.0/test/tbb/test_write_once_node.cpp
oneTBB-2021.5.0/test/tbbmalloc/
oneTBB-2021.5.0/test/tbbmalloc/test_malloc_atexit.cpp
oneTBB-2021.5.0/test/tbbmalloc/test_malloc_compliance.cpp
oneTBB-2021.5.0/test/tbbmalloc/test_malloc_init_shutdown.cpp
oneTBB-2021.5.0/test/tbbmalloc/test_malloc_lib_unload.cpp
oneTBB-2021.5.0/test/tbbmalloc/test_malloc_new_handler.cpp
oneTBB-2021.5.0/test/tbbmalloc/test_malloc_overload.cpp
oneTBB-2021.5.0/test/tbbmalloc/test_malloc_overload_disable.cpp
oneTBB-2021.5.0/test/tbbmalloc/test_malloc_pools.cpp
oneTBB-2021.5.0/test/tbbmalloc/test_malloc_pure_c.c
oneTBB-2021.5.0/test/tbbmalloc/test_malloc_regression.cpp
oneTBB-2021.5.0/test/tbbmalloc/test_malloc_shutdown_hang.cpp
oneTBB-2021.5.0/test/tbbmalloc/test_malloc_used_by_lib.cpp
oneTBB-2021.5.0/test/tbbmalloc/test_malloc_whitebox.cpp
oneTBB-2021.5.0/test/tbbmalloc/test_scalable_allocator.cpp
oneTBB-2021.5.0/third-party-programs.txt
[ 3%] No update step for 'libtbb'
[ 4%] No patch step for 'libtbb'
[ 5%] Performing configure step for 'libtbb'
-- The CXX compiler identification is GNU 4.8.5
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - failed
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ - broken
CMake Error at /crex/proj/snic2020-15-201/anaconda3/envs/cmake/share/cmake-3.18/Modules/CMakeTestCXXCompiler.cmake:59 (message):
The C++ compiler
"/usr/bin/c++"
is not able to compile a simple test program.
It fails with the following output:
Change Dir: /home/kris/source/pufferfish/external/oneTBB-2021.5.0/CMakeFiles/CMakeTmp
Run Build Command(s):/usr/bin/gmake cmTC_599fb/fast && gmake[3]: Entering directory `/domus/h1/kris/source/pufferfish/external/oneTBB-2021.5.0/CMakeFiles/CMakeTmp'
/usr/bin/gmake -f CMakeFiles/cmTC_599fb.dir/build.make CMakeFiles/cmTC_599fb.dir/build
gmake[4]: Entering directory `/domus/h1/kris/source/pufferfish/external/oneTBB-2021.5.0/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_599fb.dir/testCXXCompiler.cxx.o
/usr/bin/c++ -std=c++14 -o CMakeFiles/cmTC_599fb.dir/testCXXCompiler.cxx.o -c /home/kris/source/pufferfish/external/oneTBB-2021.5.0/CMakeFiles/CMakeTmp/testCXXCompiler.cxx
c++: error: unrecognized command line option โ-std=c++14โ
gmake[4]: *** [CMakeFiles/cmTC_599fb.dir/testCXXCompiler.cxx.o] Error 1
gmake[4]: Leaving directory `/domus/h1/kris/source/pufferfish/external/oneTBB-2021.5.0/CMakeFiles/CMakeTmp'
gmake[3]: *** [cmTC_599fb/fast] Error 2
gmake[3]: Leaving directory `/domus/h1/kris/source/pufferfish/external/oneTBB-2021.5.0/CMakeFiles/CMakeTmp'
CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
CMakeLists.txt:57 (project)
-- Configuring incomplete, errors occurred!
See also "/home/kris/source/pufferfish/external/oneTBB-2021.5.0/CMakeFiles/CMakeOutput.log".
See also "/home/kris/source/pufferfish/external/oneTBB-2021.5.0/CMakeFiles/CMakeError.log".
make[2]: *** [libtbb-prefix/src/libtbb-stamp/libtbb-configure] Error 1
make[1]: *** [CMakeFiles/libtbb.dir/all] Error 2
make: *** [all] Error 2
Currently, the only way to get a bam file from puffalign is to write a sam and then convert it in a separate command. If puffalign could output to stdout it would be possible to pipe it into samtools to get a bam directly.
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