mourisl / rascaf Goto Github PK

Hello,

I'm using Rascaf with sorted BAM files from HISAT2 alignments of multiple stranded RNA-Seq libraries. In each of the Rascaf .out files, there are several connections below the section 'WARNINGS:'. I was wondering if it's necessary to remove those lines from the .out files before using rascaf-join. Or perhaps run Rascaf with the -cs flag, use the '_cs.fa' files to search with BLASTN/BLASTX against RefSeq RNA or NR, and then run the FilterRascafConnection.pl script?

Any help is greatly appreciated.

Running rascaf directly from a clone of the master branch and downloading the v.1.0.0 source resulting in the following error:

Found 147832 exon blocks.
Found 113960 gene blocks.
Found 2281 non-trivial gene block components.
*** buffer overflow detected ***: /home/peter/bioinformatics/Rascaf-1.0.0/rascaf terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7338f)[0x7fbdc6b7a38f]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7fbdc6c11c9c]
/lib/x86_64-linux-gnu/libc.so.6(+0x109b60)[0x7fbdc6c10b60]
/lib/x86_64-linux-gnu/libc.so.6(+0x10a0f4)[0x7fbdc6c110f4]
/home/peter/bioinformatics/Rascaf-1.0.0/rascaf[0x403ae5]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7fbdc6b28ec5]
/home/peter/bioinformatics/Rascaf-1.0.0/rascaf[0x403f7f]

etc.

Running make didn't suggest any compilation errors. The OS is Ubuntu 14.04. Is there are a sample dataset that might be used to test the installation?

I have executed rascaf with a position-sorted bamfile, and it has generated a .out output. I fed that output file to rascaf-join and it ended in a segmentation fault. The only output from rascaf-join was "open: No such file or directory"

Thanks

rascaf-join uses the output from rascaf to determine whether the assembly was contig level and access the input assembly fasta file. It does this by searching for "-f" in the string that is obtained by searching for the line that begins with "command line:". The same approach is used to find the parameter provided to "-breakN" and "-b". This causes issues when file paths include hyphens followed by an f or a b. For example, if the path to the rascaf-join executable is "/home/username/blah-blah/rascaf/rascaf-join", the path to the bam file will be stored as "lah/rascaf/rascaf-join". This file will not be found and will result in a segmentation fault.

I was able to fix this problem for myself by altering the code to search for " -f", " -b", and " -breakN" (and incrementing the pointer increment by one). However, this fix is tenuous and is why I chose not to fork and make a pull request. More careful parsing would help, but another option would be to have the user provide the needed information at the command line (as a user- I would prefer this option). This would require a brief explanation in the README, but should be fairly simple for a user to understand. This is not super urgent (at least not for me), but I thought I'd throw the friendly suggestion out there.

I am trying to improve the scaffolding on a genome assembled using Supernova and Chromium 10x. I've aligned my reads to the genome using hisat2 and used samtools to sort/convert to bam.

I ran rascaf with
rascaf -b my.aligned.bam -f my.scaffolds -k30 -o rascaff1

I got the error message:
Unknown genome name: scaffold4,190040,f7622z26696k7a0m100_f134738Z163344

grep "scaffold1,184907,f53044Z184907" my.scaffolds

scaffold1,184907,f53044Z184907

grep "scaffold4,190040,f7622z26696k7a0m100_f134738Z163344" my.aligned.bam

Nothing.

It looks like rascaf is failing because a scaffold exists in the genome, but not in my bam file, which makes sense, right? How do I get past this hurdle. I'd really like to incorporate my RNA-seq data into improving my genome.

Thanks in advance for your help!

-genome size ~700k

Hello,

   In the manual it mentioned an optional step of validating proposed connections by mapping to a public protein database. I think this is really a great idea, but I don't seem to find the script for doing that in the repository.
  Is this function currently implemented or do the users have to come up with their own solutions?

Best Regards,
Rongfeng Cui
Max-Planck Institute for the Biology of Ageing.

Dear Rascaf Developer,

I got error messages when running the command below. Does that have anything to do with the fact I am using /dev/shm to store some data? I compiled the lasted version but still get issues.

Thanks for your time!

./rascaf -b bwa_bh_C1_S7/sorted.mapM_PE_bh_C1_S7.bam -f k63_127.scafSeq -o rascaf_bh_C1_S7
*** Error in `/my/path/local_projects/software/rascaf/rascaf': munmap_chunk(): invalid pointer: 0x0000000004727be0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7ff3cc6777e5]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x1a8)[0x7ff3cc684698]
/my/path/local_projects/software/Rascaf-master/rascaf[0x406a93]
/my/path/local_projects/software/Rascaf-master/rascaf[0x40e6ea]
/my/path/local_projects/software/Rascaf-master/rascaf[0x403561]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7ff3cc620830]
/my/path/local_projects/software/Rascaf-master/rascaf[0x4041b9]
======= Memory map: ========
00400000-00435000 r-xp 00000000 00:2c 347975645 /my/path/local_projects/software/Rascaf-master/rascaf
00634000-00635000 r--p 00034000 00:2c 347975645 /my/path/local_projects/software/Rascaf-master/rascaf
00635000-00636000 rw-p 00035000 00:2c 347975645 /my/path/local_projects/software/Rascaf-master/rascaf
01408000-04733000 rw-p 00000000 00:00 0 [heap]
7ff3cb851000-7ff3cc600000 rw-p 00000000 00:00 0
7ff3cc600000-7ff3cc7c0000 r-xp 00000000 08:03 12321415 /lib/x86_64-linux-gnu/libc-2.23.so
7ff3cc7c0000-7ff3cc9c0000 ---p 001c0000 08:03 12321415 /lib/x86_64-linux-gnu/libc-2.23.so
7ff3cc9c0000-7ff3cc9c4000 r--p 001c0000 08:03 12321415 /lib/x86_64-linux-gnu/libc-2.23.so
7ff3cc9c4000-7ff3cc9c6000 rw-p 001c4000 08:03 12321415 /lib/x86_64-linux-gnu/libc-2.23.so
7ff3cc9c6000-7ff3cc9ca000 rw-p 00000000 00:00 0
7ff3cc9ca000-7ff3cc9e0000 r-xp 00000000 08:03 12320962 /lib/x86_64-linux-gnu/libgcc_s.so.1
7ff3cc9e0000-7ff3ccbdf000 ---p 00016000 08:03 12320962 /lib/x86_64-linux-gnu/libgcc_s.so.1
7ff3ccbdf000-7ff3ccbe0000 rw-p 00015000 08:03 12320962 /lib/x86_64-linux-gnu/libgcc_s.so.1
7ff3ccbe0000-7ff3ccce8000 r-xp 00000000 08:03 12321044 /lib/x86_64-linux-gnu/libm-2.23.so
7ff3ccce8000-7ff3ccee7000 ---p 00108000 08:03 12321044 /lib/x86_64-linux-gnu/libm-2.23.so
7ff3ccee7000-7ff3ccee8000 r--p 00107000 08:03 12321044 /lib/x86_64-linux-gnu/libm-2.23.so
7ff3ccee8000-7ff3ccee9000 rw-p 00108000 08:03 12321044 /lib/x86_64-linux-gnu/libm-2.23.so
7ff3ccee9000-7ff3cd05b000 r-xp 00000000 08:03 2884841 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7ff3cd05b000-7ff3cd25b000 ---p 00172000 08:03 2884841 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7ff3cd25b000-7ff3cd265000 r--p 00172000 08:03 2884841 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7ff3cd265000-7ff3cd267000 rw-p 0017c000 08:03 2884841 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7ff3cd267000-7ff3cd26b000 rw-p 00000000 00:00 0
7ff3cd26b000-7ff3cd283000 r-xp 00000000 08:03 12320927 /lib/x86_64-linux-gnu/libpthread-2.23.so
7ff3cd283000-7ff3cd482000 ---p 00018000 08:03 12320927 /lib/x86_64-linux-gnu/libpthread-2.23.so
7ff3cd482000-7ff3cd483000 r--p 00017000 08:03 12320927 /lib/x86_64-linux-gnu/libpthread-2.23.so
7ff3cd483000-7ff3cd484000 rw-p 00018000 08:03 12320927 /lib/x86_64-linux-gnu/libpthread-2.23.so
7ff3cd484000-7ff3cd488000 rw-p 00000000 00:00 0
7ff3cd488000-7ff3cd4a1000 r-xp 00000000 00:2d 73183823118 /users/lijing/usr/lib/libz.so.1.2.8
7ff3cd4a1000-7ff3cd6a0000 ---p 00019000 00:2d 73183823118 /users/lijing/usr/lib/libz.so.1.2.8
7ff3cd6a0000-7ff3cd6a1000 r--p 00018000 00:2d 73183823118 /users/lijing/usr/lib/libz.so.1.2.8
7ff3cd6a1000-7ff3cd6a2000 rw-p 00019000 00:2d 73183823118 /users/lijing/usr/lib/libz.so.1.2.8
7ff3cd6a2000-7ff3cd6c8000 r-xp 00000000 08:03 12320852 /lib/x86_64-linux-gnu/ld-2.23.so
7ff3cd6df000-7ff3cd8b7000 rw-p 00000000 00:00 0
7ff3cd8c4000-7ff3cd8c7000 rw-p 00000000 00:00 0
7ff3cd8c7000-7ff3cd8c8000 r--p 00025000 08:03 12320852 /lib/x86_64-linux-gnu/ld-2.23.so
7ff3cd8c8000-7ff3cd8c9000 rw-p 00026000 08:03 12320852 /lib/x86_64-linux-gnu/ld-2.23.so
7ff3cd8c9000-7ff3cd8ca000 rw-p 00000000 00:00 0
7ffffe8ce000-7ffffe8f0000 rw-p 00000000 00:00 0 [stack]
7ffffe9e3000-7ffffe9e5000 r--p 00000000 00:00 0 [vvar]
7ffffe9e5000-7ffffe9e7000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)

Hi,
I tried to run rascaf using sorted bam file (which is generated by mapping trimmed RNA-Seq data to draft genome assembly scaffold) and draft genome assembly with cmd:
~/rascaf/rascaf -b ~/assembly_new/generate_bamfile/pgref_genome_sorted.bam -f ~/assembly_new/draft_genome/scaffolds.fasta -o rascaf_connection
However I ran into the following errors:
[bam_header_read] EOF marker is absent. The input is probably truncated.
*** glibc detected *** ~/rascaf/rascaf: double free or corruption (out): 0x000000001252cc00 ***
======= Backtrace: =========
/lib64/libc.so.6[0x39bc4750c6]
~/rascaf/rascaf[0x410c22]
~/rascaf/rascaf[0x414080]
~/rascaf/rascaf[0x403d53]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x39bc41ecdd]
~/rascaf/rascaf[0x4037b9]
======= Memory map: ========
00400000-00437000 r-xp 00000000 00:17 27052970
~/rascaf/rascaf
00636000-00638000 rw-p 00036000 00:17 27052970
~/rascaf/rascaf
00c83000-12578000 rw-p 00000000 00:00 0 [heap]
39bbc00000-39bbc20000 r-xp 00000000 08:06 914307 /lib64/ld-2.12.so
39bbe1f000-39bbe20000 r--p 0001f000 08:06 914307 /lib64/ld-2.12.so
39bbe20000-39bbe21000 rw-p 00020000 08:06 914307 /lib64/ld-2.12.so
39bbe21000-39bbe22000 rw-p 00000000 00:00 0
39bc400000-39bc597000 r-xp 00000000 08:06 914308 /lib64/libc-2.12.so
39bc597000-39bc797000 ---p 00197000 08:06 914308 /lib64/libc-2.12.so
39bc797000-39bc79b000 r--p 00197000 08:06 914308 /lib64/libc-2.12.so
39bc79b000-39bc79c000 rw-p 0019b000 08:06 914308 /lib64/libc-2.12.so
39bc79c000-39bc7a1000 rw-p 00000000 00:00 0
39bc800000-39bc817000 r-xp 00000000 08:06 914310 /lib64/libpthread-2.12.so
39bc817000-39bca16000 ---p 00017000 08:06 914310 /lib64/libpthread-2.12.so
39bca16000-39bca17000 r--p 00016000 08:06 914310 /lib64/libpthread-2.12.so
39bca17000-39bca18000 rw-p 00017000 08:06 914310 /lib64/libpthread-2.12.so
39bca18000-39bca1c000 rw-p 00000000 00:00 0
39bcc00000-39bcc83000 r-xp 00000000 08:06 914321 /lib64/libm-2.12.so
39bcc83000-39bce82000 ---p 00083000 08:06 914321 /lib64/libm-2.12.so
39bce82000-39bce83000 r--p 00082000 08:06 914321 /lib64/libm-2.12.so
39bce83000-39bce84000 rw-p 00083000 08:06 914321 /lib64/libm-2.12.so
2b46e6da2000-2b46e6da3000 rw-p 00000000 00:00 0
2b46e6da3000-2b46e6db9000 r-xp 00000000 00:17 7866957 ~/tools/hpclib/zlib128/lib/libz.so.1.2.8
2b46e6db9000-2b46e6fb8000 ---p 00016000 00:17 7866957 ~/tools/hpclib/zlib128/lib/libz.so.1.2.8
2b46e6fb8000-2b46e6fb9000 rw-p 00015000 00:17 7866957 ~/tools/hpclib/zlib128/lib/libz.so.1.2.8
2b46e6fc3000-2b46e6fc4000 rw-p 00000000 00:00 0
2b46e6fc4000-2b46e70b6000 r-xp 00000000 00:17 4085529
~/tools/gcc-4.9.1/lib64/libstdc++.so.6.0.20
2b46e70b6000-2b46e72b6000 ---p 000f2000 00:17 4085529
~/tools/gcc-4.9.1/lib64/libstdc++.so.6.0.20
2b46e72b6000-2b46e72bf000 r--p 000f2000 00:17 4085529
~/tools/gcc-4.9.1/lib64/libstdc++.so.6.0.20
2b46e72bf000-2b46e72c1000 rw-p 000fb000 00:17 4085529
~/tools/gcc-4.9.1/lib64/libstdc++.so.6.0.20
2b46e72c1000-2b46e72d7000 rw-p 00000000 00:00 0
2b46e72d7000-2b46e72ed000 r-xp 00000000 00:17 4084767
~/tools/gcc-4.9.1/lib64/libgcc_s.so.1
2b46e72ed000-2b46e74ec000 ---p 00016000 00:17 4084767
~/tools/gcc-4.9.1/lib64/libgcc_s.so.1
2b46e74ec000-2b46e74ed000 rw-p 00015000 00:17 4084767
~/tools/gcc-4.9.1/lib64/libgcc_s.so.1
2b46e74ed000-2b46ec94b000 rw-p 00000000 00:00 0
7fffdaf5b000-7fffdaf71000 rw-p 00000000 00:00 0 [stack]
7fffdaf72000-7fffdaf73000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
./rascaf.sh: line 1: 6287 Aborted (core dumped) ~/rascaf/rascaf -b ~/assembly_new/generate_bamfile/pgref_genome_sorted.bam -f ~/assembly_new/draft_genome/scaffolds.fasta -o rascaf_connection

Could you please help me with this problem?
Thank you!

Hi,
I'm trying to apply Rascaf to an assembly that is unpolished and has high base level errors. I still want to try out Rascaf, and I was wondering if there are parameters we could tune to accept higher mismatch rates.

Thanks!

Good afternoon,

I am trying to run rascaf to improve a draft genome that I am working with.
However when I try to use it I get the following error

Unknown genome name: k141_3

k141_3 is the name of the first contig on my assembly.

Can you help me, if I am doing something wrong?

Thanks

When running rascaf, if an option argument is empty string (e.g., '-b ""' or '-f ""') or missing (e.g., '-b -f somefile.fa', the program seg faults. Additional argument validation would be helpful.

Hi,

I used rascaf like this:

rascaf -b Aligned.sortedByCoord.out.bam -f draft.fa
but I got the following error:

Found 135172 exon blocks.
Assertion failed: (readCnt > 30), function GetAlignmentsInfo, file ./blocks.hpp, line 554.
[1]    76830 abort      rascaf -b  -f

Can you help me solve this problem, please?

Cheers.

Dear developper
I'm trying to use rascaf on my genome with the following command
rascaf -b /scratch/fr2424/sib/corre/my.bam -o ind2_0 -f /scratch/fr2424/sib/corre/mygenome.fasta
-o /scratch/fr2424/sib/corre/rascaf_out

My job end with the following error

Found 232107 exon blocks.
rascaf: blocks.hpp:554: void Blocks::GetAlignmentsInfo(Alignments&): Assertion `readCnt > 30' failed.
rascaf failed.

and this output file

head rascaf_out.out

Contigs
0: opera_scaffold_35 1 21160
1: opera_scaffold_35 21162 30042
2: opera_scaffold_35 30044 44257
3: opera_scaffold_35 44259 49471
4: opera_scaffold_35 49473 51592
5: opera_scaffold_35 51594 54391
6: opera_scaffold_35 54393 56418
7: opera_scaffold_35 56420 65899
8: opera_scaffold_35 65901 67093
9: opera_scaffold_35 67095 68230
10: opera_scaffold_35 68232 69045
11: opera_scaffold_35 69047 85263
12: opera_scaffold_35 85265 91369
13: opera_scaffold_35 91371 95685
14: opera_scaffold_35 95687 106381
15: opera_scaffold_35 106383 106886
16: opera_scaffold_35 106888 107071
17: opera_scaffold_35 107073 111205
18: opera_scaffold_35 111207 136990
19: opera_scaffold_35 136992 144728
20: opera_scaffold_35 144730 147483

Do you have any ideas about how to solve this error?

Regards Erwan

Hai,

I am working to improve my draft genome assembly with PE-RNA sequences. I was able to scaffold my data with
./rascaf -b *.bam -f assm1kb.fa -o outtestfile.

I have problem with rascaf-join (command below)
./rascaf-join -r outtestfile -o assembly_scaftest

after i submit this command nothing happens, just remains forever as
Found raw assembly file: ../../../*-sort.bam

I have also run the sample data to check if rascaf-join, i still have the same issue

Found raw assembly file: omitopsis/rna_geno/rascaf/sample/sample-sort.bam
(remains forever without any further error or output). i have read the previous queries, that was suggested to sort out *bam file, i have tired it but still with no progress.

could you please help me with the issue?

thank you
Prakash

Hi,

I mapped several RNAseq libraries to my reference genome using BWA mem and sorted the BAM file for coordinate with samtools sort (I checked that it is really is coordinate sorted).
I then executed Rascaf like this:

rascaf-wrapper.pl -b mapping.sorted.bam -f reference.fasta -o reference.consensus.rascaf

The log file contains the following:

rascaf -b mapping.sorted.bam -o mapping.sorted_0 -f reference.fasta -o reference.rascaf
Found 8273702 exon blocks.
Found 4555833 gene blocks.
Found 58394 non-trivial gene block components.
rascaf-join -r reference.sorted_0.out -o reference.rascaf
rascaf-join failed.

The file reference.rascaf.out start with

Contigs
0: Consensus_utg000001l 1 23842
1: Consensus_utg000002l 1 28081
...

and continues with a lot of entries like these:

Contig 105247 is misassembled. (Consensus_utg105248l 1-20821): (7197-7854) (5169-6053): Found deletion between.

3: (Consensus_utg000005l 45898 4 -) (Consensus_utg059814l 54357 59813 +) (Consensus_utg025230l 58213 25229 -)

WARNINGS:
71: (Consensus_utg044293l:12054-12178 44292 +) (Consensus_utg050357l:31186-33007 50356 +)

Do you have an idea what could have been gone wrong?
Chris

Hi,
I used TopHat to align my RNAseq PE reads. I'm getting absolutely no improvements on the final assembly, and I'm suspicious that I'm doing something wrong, because I did get decent improvements with L_RNA_scaffolder.
rascaf -b $workDir/tophat_out/accepted_hits.bam -f $sourceDir/$sourceName -o "$descriptor"_rascafOut -v -ms 1
Output:
Found 355447 exon blocks.
Found 212574 gene blocks.
Found 0 non-trivial gene block components.

rascaf-join -ignoreGap -r "$descriptor"_rascafOut.out -o "$descriptor"_rascafJoinOut.ignoreGap -ms 1
Output
Found raw assembly file: (...assembly.fasta)
Finish reading the rascaf output files.
Finish removing cycles in the graph.
Finish ordering the scaffolds.
There is no change to the number of contigs, scaffolds, N50, etc.
Could you please help me out?

Thanks!

Hi Li Song,

I enconter a problem when run rascaf-join. (See bellow)

The genome is approxmately 1G, bam file 2 G.

How to adjust it?

Thanks

[lzc@localhost lotusbam]$ /home/lzc/CJM_reseq/rascaf/rascaf-join -r SRR2052526_0.out -o SRR2052526ras -ms 50
Found raw assembly file: /home/lzc/CJM_reseq/rascaf/lotusbam/Lotus_mega_gap1M.fa
Segmentation fault (core dumped)

hello, i also seem to have similar problem
Found 432405 exon blocks.
rascaf: blocks.hpp:556: void Blocks::GetAlignmentsInfo(Alignments&): Assertion `readCnt > 30' failed.
/job_scripts/3643772: line 33: 55796 Aborted (core dumped) ${RASCAF}/rascaf -b ${READS}/..unfilt_RNA.bam -f ${FASTA}/20190319.._001_001_1st_assembly_minION.ctn.fa -o ${TARGET}/rascaf_1st

SRR3453110.85720556 163 ctg1 18931 40 9M3I89M = 18980 150 ATTTATGATAAAAAAAAAGAATTTAATAGATGGGCACACTACTAGGCACACTTATTCAAAGTAAATAAGATTTAGGAGCATATATGTATGAATTTCAATTA ?@BFFFFDHHHFHIJJGGFFFGIJIGGDHIGGGGHHGHIJJIJIJJIJGGGCHHHHEEHBDBDFCCDEEECED>CCDD?BDDDEEECCFEDDEDCACCDDD AS:i:-24 XN:i:0 XM:i:2 XO:i:1 XG:i:3 NM:i:5 MD:Z:16C60C20 YS:i:-7 YT:Z:CP
SRR3453110.89338447 163 ctg1 18940 42 101M = 18986 147 AAAAAAGAATTTAATAGATGGGCACACTACTAGGCACACTTATTCAAAGTAAATAAGATTTAGGAGCATATATGTATGAATTTCAATTAATTGAAACTGAG CCCFFFFFHHHHHJJJJJJJJJIJJJJJJJJJIJJJJJJJJJJJJJJJJGFHIJJJJIJJJJJJJJIGJHHHHHFHHFFFFFFFEEDEEDEEDDDDDCCCC AS:i:-11 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7C60C32 YS:i:-5 YT:Z:CP
SRR3453110.90544994 163 ctg1 18960 42 101M = 19116 256 GGCACACTACTAGGCACACTTATTCAAAGTAAATAAGATTTAGGAGCATATATGTATGAATTTCAATTAATTGAAACTGAGTTGGTATTTGGGTGATTTGT @@@DFDFFHFFBFEGGIJJHIEHIHFEE>HHGGIGDCBFHGEIB4?D?DB??BDGHEGCEHHHGC=BFGFDHHGFC@EGCGHGFFCE?CBDBB=AA;A@@> AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:48C52 YS:i:-8 YT:Z:CP
SRR3453110.89452103 99 ctg1 18970 42 101M = 19010 141 TAGGCACACTTATTCAAAGTAAATAAGATTTAGGAGCATATATGTATGAATTTCAATTAATTGAAACTGAGTTGGTATTTGGGTGATTTGTCAGGATTGAA @@CFFFDFHGFFHGGHIIIFHIGGJGIHIEHIGGGHIIIHIIIGBHGEGEFHGHGHIIJIIGGGICJEE>HCHIIIHGIIGF@;A=EBCDEFFFA;AEEDD AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:38C62 YS:i:-4 YT:Z:CP
SRR3453110.85720556 83 ctg1 18980 40 101M = 18931 -150 TATTCAAAGTAAATAAGATTTAGGAGCATATATGTATGAATTTCAATTAATTGAAACTGAGTTTGTATTTGGGTGATTTGTCAGGATTGAAGAGACCAAAA @3;CCEDEDFFDDFCFHHHHFFGGDDGCHEGIEJGGBCDIHGIIIGEHDFBGEGGHGFDHGFC*GJJJIGHFHFGIJJJHDJJIHIGIHHHHHDDFFF@@C AS:i:-7 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:28C34G3YS:i:-24 YT:Z:CP
SRR3453110.89338447 83 ctg1 18986 42 101M = 18940 -147 AAGTAAATAAGATTTAGGAGCATATATGTATGAATTTCAATTAATTGAAACTGAGTTGGTATTTGGGTGATTTGTCAGGATTGAAGAGACCAAAATGTCGC CCDDEDDDCCEDEFEEDFEGGHHFFGIJJIIIIJJJJIJJJJJIJJJJIIIIJJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJIHIFHHHHFFFFFCCC AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:22C78 YS:i:-11 YT:Z:CP
SRR3453110.74320311 99 ctg1 19002 42 101M = 19034 132 GGAGCATATATGTATGAATTTCAATTAATTGAAACTGAGTTGGTATTTGGGTGATTTGTCAGGATTGAAGAGACCAAAATGTCGCTCAGTTTCGGCACCCT @@@DFFDDDHFHCEGHD>DHGEHEHIIBGFEFCHIGE?EB@C@::CDGFHA?68?D?BFHIIC>FGGII@GGII;=@6ch?7=2;/?ACCDEDB:?==?BA AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6C94 YS:i:-8 YT:Z:CP
SRR3453110.89452103 147 ctg1 19010 42 101M = 18970 -141 TATGTATGAATTTCAATTAATTGAAACTGAGTTGGTATTTGGGTGATTTGTCAGGGTTGAAGAGACCAAAATGTCGCTCAGTTTCGGCACCCTGTTTCTGG DDCDDEDCDCCCCCEEDDCA>FDEFCDDCDDDECECCA?;FHHEHEEHGGHIHB@=GGGGGGIGHGIJJJIIIIGJIEFJIIIIJIHFAFGHFFFFDD@@@ AS:i:-4 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:55A45 YS:i:-6 YT:Z:CP
SRR3453110.74320311 147 ctg1 19034 42 77M1I23M = 19002 -132 AACTGAGTTGGTATTTGGGTGATTTGTCAGGATTGAAGAGACCAAAATGTCGCTCAGTTTCGGCACCCTGTTTCTGGTTTTCGTCGAACATGGCAAACAAG >:CCCC@>CCCAAABBB?@>@><>@ccccACCCAACCBBCDDCCD>A:>GGIHGGEGHGFB9IGBC@FIGGEGGBGDBGGGGFCCDFF??DDDBD??@ AS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:100 YS:i:-5 YT:Z:CP
SRR3453110.84141312 99 ctg1 19042 42 69M1I31M = 19116 174 TGGTATTTGGGTGATTTGTCAGGATTGAAGAGACCAAAATGTCGCTCAGTTTCGGCACCCTGTTTCTGGTTTTCGTCGAACATGGCAAACAAGAAGGTTTC B@CADDFFHHHFFHIJJJHIJJJIJIIJJIJJGIIJJJJIJHIJIJIFIIJIIIJJJIJJIHHHHHHFDBEFDECDBD??BDDCDDDDDDDDDCDDD?CDD AS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:100 YS:i:-8 YT:Z:CP

HI,
I am working on a hybrid assembly for a 3.2G allotetraploid plant genome:

1. Illumina assembly with w2rap-contigger.
2. DBG2OLC to combine Illumina assembly with PacBio reads
3. PBjelly gap closing with PacBio reads.

Q1. After which above steps do you recommend to run your tool?
Q2. Do you recommend to prepare the RNAseq data e.g. with afterqc and any khmer recipes before running your tool?
Q3. We have few datasets of different RNA-seq experiments do you think I should combine all or run your tool each time with a different RNA-seq experiments?

Thank you in advance,

Michal

A simple addition to the README might be helpful. When I ran the sample test, it appeared to overwrite the original fasta file. Upon delving into the code, I realized that the parameter provided to rascaf-join with "-o" simply had ".fa" and ".info" appended to it to create the two output files. It just so happened that "-o sample/sample" will cause the original "sample/sample.fa" to be overwritten. I see nothing wrong with the approach, but it would be nice to have known what to expect from the README. It would be a bummer for someone to have their initial assembly fasta file lost forever by being overwritten.

Hello, I am running rascaf but in rascaf-join it stays for ever and no output is generated. I can see with top that it is running.

this is the run status:

Found raw assembly file: mejora1sorted.bam
Finish reading the rascaf output files.
b

any idea?

thanks in advance

I am very interested in using "Rascaf" to improve my genome assembly. However, after I clone GitHub repo to my terminal and run "make" in Rascaf dir, I cannot find the two executable files, "rascaf" and "rascaf-join". Could you please help me with this? Thanks.

Hello,

I need to run all my jobs in a scheduler, however when I try to run rascaf-join it gives me the following error:

Found raw assembly file: /panfs/panfs.cluster/scratch/ch1005/genomes/D_maidis_final.contigs.fa
Failed to resolve the path of file PBS_QUEUE=batch.

I don't know why it is trying to resolve the path of the scheduler queue.

Please can you help me with that?