gatb / gatb-minia-pipeline Goto Github PK

right now we don't log any output, it would be good to

Is it possible to obtain GFA output from the assemblies created by this pipeline?

When trying to compile and test using make test, the compilation stops with an error related to samtools:

$ make test
...
(2016-05-25 13:57:31) Execution of 'python BESST/scripts/reads_to_ctg_map.py'. Command line:
python /home/pericard/programmes/gatb-minia-pipeline/BESST/scripts/reads_to_ctg_map.py --tmp_path /home/pericard/programmes/gatb-minia-pipeline/test/BESST_tmp --threads 4 assembly.lib0_1.fa assembly.lib0_2.fa assembly_k61.contigs.fa assembly.lib_0

pe1_path: assembly.lib0_1.fa
pe2_path: assembly.lib0_2.fa
genome_path: assembly_k61.contigs.fa
output_path: assembly.lib_0
tmp_path: /home/pericard/programmes/gatb-minia-pipeline/test/BESST_tmp
bwa path: bwa
number of threads: 4
Remove temp SAM and BAM files: No
Use bwa aln and sampe instead of bwa mem: No

Start processing.

Aligning with bwa mem.
Temp directory: /home/pericard/programmes/gatb-minia-pipeline/test/BESST_tmp
Output path: assembly.lib_0
Stderr file: assembly.lib_0.bwa.1
Make bwa index... Done.
Align with bwa mem... Done.
Time elapsed for bwa index and mem: 0:00:00.219248

Convert SAM to BAM... Done.
Time elapsed for SAM to BAM conversion: 0:00:00.109462

Sort BAM...Traceback (most recent call last):
File "/home/pericard/programmes/gatb-minia-pipeline/BESST/scripts/reads_to_ctg_map.py", line 317, in
tmp_path, args.bwa_path, args.clear)
File "/home/pericard/programmes/gatb-minia-pipeline/BESST/scripts/reads_to_ctg_map.py", line 184, in bwa_mem
pysam.sort(bwa_output + ".bam", output_path)
File "/usr/local/lib/python2.7/dist-packages/pysam/utils.py", line 65, in call
"\n".join(stderr)))
pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr=[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files\n\nUsage: samtools sort [options...] [in.bam]\n\nOptions:\n\n -l INT Set compression level, from 0 (uncompressed) to 9 (best)\n\n -m INT Set maximum memory per thread; suffix K/M/G recognized [768M]\n\n -n Sort by read name\n\n -o FILE Write final output to FILE rather than standard output\n\n -T PREFIX Write temporary files to PREFIX.nnnn.bam\n\n -@, --threads INT\n\n Set number of sorting and compression threads [1]\n\n --input-fmt-option OPT[=VAL]\n\n Specify a single input file format option in the form\n\n of OPTION or OPTION=VALUE\n\n -O, --output-fmt FORMAT[,OPT[=VAL]]...\n\n Specify output format (SAM, BAM, CRAM)\n\n --output-fmt-option OPT[=VAL]\n\n Specify a single output file format option in the form\n\n of OPTION or OPTION=VALUE\n\n --reference FILE\n\n Reference sequence FASTA FILE [null]\n'
(2016-05-25 13:57:31) Execution of 'python BESST/scripts/reads_to_ctg_map.py' failed. Command line:
python /home/pericard/programmes/gatb-minia-pipeline/BESST/scripts/reads_to_ctg_map.py --tmp_path /home/pericard/programmes/gatb-minia-pipeline/test/BESST_tmp --threads 4 assembly.lib0_1.fa assembly.lib0_2.fa assembly_k61.contigs.fa assembly.lib_0
make: *** [test] Erreur 1

I was thinking about a pb with samtools version so I tested with both samtools v0.1.19 and v1.3.1 without any change.

else BESST throws obscure error

Hi!

I'm using the gatb-minia pipeline to get the contigs for a couple of datasets that I have. The assembly runs fine until the kmer 121 (I have taken step 10).

When it jumps towards the kmer 131, I get an error: EXCEPTION: Failure because of unhandled kmer size 131

Are there any compile-time options that I can use to assemble at 131 and 141?

Also how does the pipeline chose the assembly to scaffold? Does it take the last kmer+contigs.fa as an input? Or do you employ other metrics as well (N50, median length etc)?

Hello minia group,

I wonder if it's possible to run scaffolding if I only have illumina pair end reads, without any mate pair reads?

It seems BESST needs mate pair reads, because "-orientation" is one of required fields, and commonly only mate pair reads provide this kind of information (If I did't understand wrongly). But for gatb-minia-pipeline, only raw fastq reads is required for inputs. Therefore, I am not sure whether mate pair reads is necessary for scaffolding in gatb-minia-pipeline?

Thank you,
Yuanwen

Hi,

consider specifying the preferred versions of needed software.

In particular: bwa, mathstats, scipy, networkx, pysam.

This would help tremendously when debugging the installation procedure.

Thanks
Johan

I was running gatb-minia-pipeline on my data set and get this error.

Traceback (most recent call last):
File "/home/apps/user_apps/piwczyn/mergi_apps/gatb-minia-pipeline/gatb", line 606, in
os.symlink(previous_contigs.rsplit("/", 1)[-1], prefix+"_final.contigs.fa") # create system link in same location as files
OSError: [Errno 17] File exists
~
What is the possible error and how to fix it?
thanks!

Hi,
There was an error as fllowed. I can not find the reason. could you help me?
(2019-05-25 03:32:29) Execution of 'perl tools/sga-deinterleave.pl'. Command line:
perl /home/emma/gatb-minia-pipeline/tools/sga-deinterleave.pl trim.fq assembly.lib0_1.fq assembly.lib0_2.fq
Found two consecutive /1 read headers, exiting; (last header: @rm2|S1|R22652116/1) at /home/emma/gatb-minia-pipeline/tools/sga-deinterleave.pl line 52, line 8.
(2019-05-25 03:32:30) Execution of 'perl tools/sga-deinterleave.pl' failed. Command line:
perl /home/emma/gatb-minia-pipeline/tools/sga-deinterleave.pl trim.fq assembly.lib0_1.fq assembly.lib0_2.fq

Best wishes,
Shirley

Hi,

I get the following error at the BESST part of the script, any ideas why?

(2018-05-30 06:24:22) Execution of 'python BESST/runBESST'. Command line:
/storage/raz/gatb-minia-pipeline/tools/memused python /storage/raz/gatb-minia-pipeline/BESST/runBESST -c assembly_k121.contigs.fa -f assembly.lib_0.bam -o assembly_besst -orientation fr --iter 10000
Number of initial contigs: 54117
Estimating insert size from 1000001 mappings with quality over --min_mapq 11.
Choosing mode: 470
mu_adjusted:562.118735931, sigma_adjusted:191.434136248, skewness_adjusted:0.825079377678
mode adj: 470
median adj 531
Creating contig graph with library: assembly.lib_0.bam
Traceback (most recent call last):
File "/storage/raz/gatb-minia-pipeline/BESST/runBESST", line 431, in
main(args)
File "/storage/raz/gatb-minia-pipeline/BESST/runBESST", line 182, in main
(G, G_prime) = CG.PE(Contigs, Scaffolds, Information, C_dict, param, small_contigs, small_scaffolds, bam_file) #Create graph, single out too short contigs/scaffolds and store them in F
File "/storage/raz/gatb-minia-pipeline/BESST/BESST/CreateGraph.py", line 202, in PE
CreateEdge(cont_obj1, cont_obj2, scaf_obj1, scaf_obj2, G_prime, param, alignedread, counter, contig1, contig2, save_obs=False)
File "/storage/raz/gatb-minia-pipeline/BESST/BESST/CreateGraph.py", line 844, in CreateEdge
G.edge[(scaf_obj1.name, scaf_side1)][(scaf_obj2.name, scaf_side2)]['obs_sq'] = (obs1 + obs2) ** 2
AttributeError: 'Graph' object has no attribute 'edge'
maximal memory used: 285 MB
(2018-05-30 06:24:40) Execution of 'python BESST/runBESST' failed. Command line:
/storage/raz/gatb-minia-pipeline/tools/memused python /storage/raz/gatb-minia-pipeline/BESST/runBESST -c assembly_k121.contigs.fa -f assembly.lib_0.bam -o assembly_besst -orientation fr --iter 10000

Thanks,

Hi,
I previously ran the gatb-minia-pipeline successfully on CentOS Linux 7.6 but when I switched to an Ubuntu 16.04 LTS, I ran into some trouble:

(2019-11-01 14:54:52) GATB-pipeline starting
(2019-11-01 14:54:52) Command line: /opt/gatb-minia-pipeline/gatb --nb-cores 6 -1 paired.1.fastq -2 paired.2.fastq -s single.fastq -o metafiles/assembly 


(2019-11-01 14:54:52) Setting maximum kmer length to: 150 bp
(2019-11-01 14:54:52) Multi-k values and cutoffs: [(21, 2), (41, 2), (61, 2), (81, 2), (101, 2), (121, 2), (141, 2)]


(2019-11-01 14:54:52) Minia assembling at k=21 min_abundance=2
(2019-11-01 14:54:52) Execution of 'minia/minia'. Command line: 
     /opt/gatb-minia-pipeline/tools/memused /opt/gatb-minia-pipeline/minia/minia -in metafiles/assembly.list_reads -kmer-size 21 -abundance-min 2 -out metafiles/assembly_k21
Minia 3, git commit 40f35ad
setting storage type to hdf5
HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 0:
  #000: /scratchdir/builds/workspace/gatb-minia/thirdparty/gatb-core/gatb-core/thirdparty/hdf5/src/H5F.c line 509 in H5Fopen(): unable to open file
    major: File accessibilty
    minor: Unable to open file

Has this been seen/solved before?
Thanks.

Greetings,

I've been using gatb-minima-pipeline for a while now for a de novo assembly software benchmark, available at Github. I've been running it so far without issue with real data, in this case, the ZymoBIOMICS Microbial Community Standard with even and log distribution.

Recently I've generated a mock community with the ZymoBIOMICS complete genomes and GATB-MINIA-PiPELINE is consistently failing on the samples without error model (perfect reads matching the reference). The mock read data is available here

I use the following command to run this assembler:

gatb -1 ${fastq_pair[0]} -2 ${fastq_pair[1]} --kmer-sizes ${kmer_list} -o ${sample_id}_GATBMiniaPipeline --no-error-correction (available here

the parameters used are

    gatbkmer = '21,61,101,141,181'
    gatb_besst_iter = 10000
    GATB_error_correction = false

This is the end of the stdout that I get while running gatb-minia-pipeline:

pe1_path: subENN_1.fq.gz
pe2_path: subENN_2.fq.gz
genome_path: subENN_GATBMiniaPipeline_k181.contigs.fa
output_path: subENN_GATBMiniaPipeline.lib_0
tmp_path: /mnt/beegfs/scratch/ONEIDA/cimendes/LMAS/work/18/993d693d0c79e5aef093045d4571d9/BESST_tmp
bwa path: bwa
number of threads: 8
Remove temp SAM and BAM files: No
Use bwa aln and sampe instead of bwa mem: No
Start processing.
Aligning with bwa mem.
Temp directory: /mnt/beegfs/scratch/ONEIDA/cimendes/LMAS/work/18/993d693d0c79e5aef093045d4571d9/BESST_tmp
Output path:    subENN_GATBMiniaPipeline.lib_0
Stderr file:    subENN_GATBMiniaPipeline.lib_0.bwa.1
Make bwa index... Done.
Align with bwa mem... Done.
Time elapsed for bwa index and mem:  0:02:10.200315
Convert SAM to BAM... Done.
Time elapsed for SAM to BAM conversion: 0:01:16.767939
Sort BAM... Done.
Time elapsed for BAM sorting: 0:01:08.141072
Index BAM... Done.
Time elapsed for BAM indexing: 0:00:03.765598
Remove temp files... Done.
Time elapsed for temp files removing: 0:00:00.008573
Processing is finished.
(2021-05-10 20:20:32) Execution of 'python BESST/runBESST'. Command line:
     /NGStools/gatb-minia-pipeline/tools/memused python /NGStools/gatb-minia-pipeline/BESST/runBESST -c subENN_GATBMiniaPipeline_k181.contigs.fa -f subENN_GATBMiniaPipeline.lib_0.bam -o subENN_GATBMiniaPipeline_besst --orientation fr --iter 10000
Number of initial contigs: 2028
Traceback (most recent call last):
  File "/NGStools/gatb-minia-pipeline/BESST/runBESST", line 401, in <module>
    main(args)
  File "/NGStools/gatb-minia-pipeline/BESST/runBESST", line 160, in main
    libmetrics.get_metrics(bam_file, param, Information)
  File "/NGStools/gatb-minia-pipeline/BESST/BESST/libmetrics.py", line 317, in get_metrics
    mean_isize = sum(filtered_list) / n
ZeroDivisionError: float division by zero
maximal memory used: 182 MB
(2021-05-10 20:20:40) Execution of 'python BESST/runBESST' failed. Command line:
     /NGStools/gatb-minia-pipeline/tools/memused python /NGStools/gatb-minia-pipeline/BESST/runBESST -c subENN_GATBMiniaPipeline_k181.contigs.fa -f subENN_GATBMiniaPipeline.lib_0.bam -o subENN_GATBMiniaPipeline_besst --orientation fr --iter 10000

This pipeline is being run in a dockerfile with the latest version in the master branch: cimendes/gatb-minia-pipeline:31.07.2020-1

Thank you for your assistance in understanding this error! Is there anything you suggest I do?

Best,

Inês

After installing all dependencies, downloading the GATB-pipeline and running make test , i got the following output:

Checking Python
scipy OK
numpy OK
mathstats OK
pysam OK
There is nothing to make. All programs are provided as binaries.
cd test ; rm -Rf assembly* ; ../gatb --12 small_test_reads.fa.gz #--no-error-correction
No debugging option
(2017-12-13 15:47:51) GATB-pipeline starting
(2017-12-13 15:47:51) Command line: ../gatb --12 small_test_reads.fa.gz 


(2017-12-13 15:47:51) Running bloocoo on 32 cores
(2017-12-13 15:47:51) Execution of 'bloocoo/Bloocoo'. Command line: 
     /home/john/gatb-minia-pipeline/bloocoo/Bloocoo -file assembly.list_reads -out assembly.corrected_with_bloocoo.fa -abundance-min 2 -kmer-size 31 -nb-cores 32 -slow -high-precision
(2017-12-13 15:47:51) Exception:[Errno 2] No such file or directory
(2017-12-13 15:47:51) Execution of 'bloocoo/Bloocoo' failed. Command line: 
     /home/john/gatb-minia-pipeline/bloocoo/Bloocoo -file assembly.list_reads -out assembly.corrected_with_bloocoo.fa -abundance-min 2 -kmer-size 31 -nb-cores 32 -slow -high-precision
make: *** [test] Error 1

The less important question here is, what this output might mean and how to fix it.

What scares me a lot more here though, is that the "bloocoo" step is simply using all available cores on my machine. I am ultimately planing to use this on my universities grid clusters, where using all available cores is definitely not an option.
Running ./gatb without arguments did not indicate any option for limiting the number of cores.

Does this mean the pipeline is really set to always use all available cores?

Hello!

I am trying to use GATB-minia-pipeline to assemble a genome. Because my storage is limited, I am not doing a multi-k but instead a k=41.

the assembly with minia works without issues, however when performing a scaffold with BESST I ran into the following issue:

(2021-08-10 11:41:36) Finished Multi-k GATB-Pipeline at k=41

(2021-08-10 11:41:38) Execution of 'python BESST/scripts/reads_to_ctg_map.py'. Command line:
python /home/sp1615/gatb-minia-pipeline/BESST/scripts/reads_to_ctg_map.py --tmp_path /home/sp1615/Desktop/T51_genome_assembly/BESST_tmp --threads 40 T51_S8_R1_001.fastq.gz T51_S8_R2_001.fastq.gz assembly_k41.contigs.fa assembly.lib_0

pe1_path: T51_S8_R1_001.fastq.gz
pe2_path: T51_S8_R2_001.fastq.gz
genome_path: assembly_k41.contigs.fa
output_path: assembly.lib_0
tmp_path: /home/sp1615/Desktop/T51_genome_assembly/BESST_tmp
bwa path: bwa
number of threads: 40
Remove temp SAM and BAM files: No
Use bwa aln and sampe instead of bwa mem: No
Do not rebuild bwa index if already exists in tmp dir: No

Start processing.

Aligning with bwa mem.
Temp directory: /home/sp1615/Desktop/T51_genome_assembly/BESST_tmp
Output path: assembly.lib_0
Stderr file: assembly.lib_0.bwa.1
Make bwa index... Done.
Align with bwa mem... Done.
Time elapsed for bwa index and mem: 5:43:13.571824

Convert SAM to BAM... Done.
Time elapsed for SAM to BAM conversion: 2:09:30.058622

Sort BAM... Done.
Time elapsed for BAM sorting: 4:17:52.790747

Index BAM... Done.
Time elapsed for BAM indexing: 0:14:52.160132

Remove temp files... Done.
Time elapsed for temp files removing: 0:00:16.807376

Processing is finished.
(2021-08-11 00:07:30) Execution of 'python BESST/runBESST'. Command line:
/home/sp1615/gatb-minia-pipeline/tools/memused python /home/sp1615/gatb-minia-pipeline/BESST/runBESST -c assembly_k41.contigs.fa -f assembly.lib_0.bam -o assembly_besst --orientation fr --iter 10000
usage: BESST [-h] -c CONTIGFILE -f BAMFILES [BAMFILES ...] -orientation
ORIENTATION [ORIENTATION ...] [-r READLEN [READLEN ...]]
[-m MEAN [MEAN ...]] [-s STDDEV [STDDEV ...]] [-z COVCUTOFF]
[-z_min LOWER_COVCUTOFF] [-T THRESHOLD [THRESHOLD ...]]
[-e EDGESUPPORT [EDGESUPPORT ...]] [-k MINSIZE [MINSIZE ...]]
[-filter_contigs CONTIG_FILTER_LENGTH] [--min_mapq MIN_MAPQ]
[--iter PATH_THRESHOLD] [--score_cutoff SCORE_CUTOFF]
[--max_extensions MAX_EXTENSIONS] [-a HAPLRATIO]
[-b HAPLTHRESHOLD] [-K KMER] [-M MMER] [-g] [-o OUTPUT] [-d] [-y]
[-q] [--no_score] [-devel] [-plots] [--separate_repeats]
[--NO_ILP] [--FASTER_ILP] [--print_scores] [--dfs_traversal]
[--bfs_traversal] [-max_contig_overlap MAX_CONTIG_OVERLAP]
[--version]
BESST: error: argument -orientation is required
maximal memory used: 6 MB
(2021-08-11 00:07:31) Execution of 'python BESST/runBESST' failed. Command line:
/home/sp1615/gatb-minia-pipeline/tools/memused python /home/sp1615/gatb-minia-pipeline/BESST/runBESST -c assembly_k41.contigs.fa -f assembly.lib_0.bam -o assembly_besst --orientation fr --iter 10000

I noticed here #25 that there seems to be an issue with how the gatb script calls BESST which can be fixed by changing line 469 from -orientation to --orientation.

however, this is the gatb script version I have at line 469:

cmd = ['-c', contigs, '-f'] + bam_files + ['-o', prefix + '_besst'] + ['--orientation'] + orientations + ['--iter', besst_iter]

which already has the change from -orientation to --orientation.

should I change it back to -orientation?

thank you for your help!
S

Hello,

Is there a flag/option to remove intermediate files (SAM, and the .glue files specifically) during a run of the pipeline? I'm running a large assembly and the folder is > 5 TB at the moment. I didn't see any options in the help or in this repo.

Morning,

I am on a Intel Core i& (64bit) Mac running OSX 10.11.6 with Xcode and Anaconda installed. When I run the make test or gatb directly I get the following error:
gatb-pipeline requires a Linux 64 bits system

I do have bcalm and bloocoo install individually and they are running fine. I was wondering if there is a work around for this?

Thanks!
ara

Hi!

I have a couple of older Illumina datasets (both PE and MP) split across multiple insert sizes and libraries.

Is it possible to pass them as a single argument, as I think that'd make life easy.

Would a FIFO sort of approach work? Or should I give a file of files (FOF) ? I believe that the FOF approach works only for SE-Reads rather than PE.

If needed I can pass MP libraries later to scaffold only.

What would you suggest?

(2019-12-24 19:56:17) Minia assembling at k=21 min_abundance=2
(2019-12-24 19:56:17) Execution of 'minia/minia'. Command line:
/NGStools/gatb-minia-pipeline/tools/memused /NGStools/gatb-minia-pipeline/minia/minia -in assembly.list_reads -kmer-size 21 -abundance-min 2 -out assembly_k21
Minia 3, git commit 40f35ad
setting storage type to hdf5
[Approximating frequencies of minimizers ] 0 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 22, 22, 22] MB /NGStools/gatb-minia-pipeline/tools/memused: line 13: 22872
920: syntax error in expression (error token is "920")
[Approximating frequencies of minimizers ] 100 % elapsed: 0 min 29 sec remaining: 0 min 0 sec cpu: 93.9 % mem: [ 22, 22, 22] MB
[DSK: Pass 1/1, Step 1: partitioning ] 0 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 76, 76, 91] MB

Hi,

Following the installation instructions, make test fails with an Error (from runBESST). Is the test correctly designed?

To reproduce:

• Ubuntu 18.04.3 LTS
• python version 2.7.15+
• pip 9.0.1 from /usr/lib/python2.7/dist-packages (python 2.7)
• mathstats version 0.2.6.5
• networkx version 2.2
• scipy version 1.2.2
• pyfasta version 0.5.2
• pysam version 0.8.3
• bwa version 0.7.17-r1188
• samtools version 1.7 (using htslib 1.7-2)

$ make test
...
Processing is finished.
(2019-12-16 08:32:42) Execution of 'python BESST/runBESST'. Command line: 
     gatb-minia-pipeline/tools/memused python gatb-minia-pipeline/BESST/runBESST -c assembly_k61.contigs.fa -f assembly.lib_0.bam -o assembly_besst -orientation fr --iter 10000
Number of initial contigs: 1
Estimating insert size from 10001 mappings with quality over --min_mapq 11.
Choosing mode: 495
mu_adjusted:499.4076, sigma_adjusted:49.8135148553, skewness_adjusted:-0.0259150237889
Creating contig graph with library:  assembly.lib_0.bam
Too few contigs to calculate coverage on. Got: 1 contigs. If you have specified  -z_min or --min_mapq, consider lower them. If not, check the BAM file for proper alignments. Exiting here before scaffolding...
maximal memory used: 84 MB
(2019-12-16 08:32:44) Execution of 'python BESST/runBESST' failed. Command line: 
     gatb-minia-pipeline/tools/memused python gatb-minia-pipeline/BESST/runBESST -c assembly_k61.contigs.fa -f assembly.lib_0.bam -o assembly_besst -orientation fr --iter 10000
Makefile:14: recipe for target 'test' failed
make: *** [test] Error 1
Processing is finished.
(2019-12-16 08:32:42) Execution of 'python BESST/runBESST'. Command line: 
     gatb-minia-pipeline/tools/memused python gatb-minia-pipeline/BESST/runBESST -c assembly_k61.contigs.fa -f assembly.lib_0.bam -o assembly_besst -orientation fr --iter 10000
Number of initial contigs: 1
Estimating insert size from 10001 mappings with quality over --min_mapq 11.
Choosing mode: 495
mu_adjusted:499.4076, sigma_adjusted:49.8135148553, skewness_adjusted:-0.0259150237889
Creating contig graph with library:  assembly.lib_0.bam
Too few contigs to calculate coverage on. Got: 1 contigs. If you have specified  -z_min or --min_mapq, consider lower them. If not, check the BAM file for proper alignments. Exiting here before scaffolding...
maximal memory used: 84 MB
(2019-12-16 08:32:44) Execution of 'python BESST/runBESST' failed. Command line: 
     gatb-minia-pipeline/tools/memused python gatb-minia-pipeline/BESST/runBESST -c assembly_k61.contigs.fa -f assembly.lib_0.bam -o assembly_besst -orientation fr --iter 10000
Makefile:14: recipe for target 'test' failed
make: *** [test] Error 1

File assembly_k61.contigs.fa:

Nseqs Min.len Max.len Avg.len
1         9985     9985     9985

File assembly.lib_0.bam:

$ samtools flagstat assembly.lib_0.bam
20000 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
20000 + 0 mapped (100.00% : N/A)
20000 + 0 paired in sequencing
10000 + 0 read1
10000 + 0 read2
20000 + 0 properly paired (100.00% : N/A)
20000 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

It would be good to have this as a binary/source release package like other members of the suite.

Hello!

I've been trying to run gatb-minia-pipeline and although it seems to be producing an assembly (a file called `*_final.contigs.fa), i've been getting the following error right at the end of the pipeline. As the error is not something that is controlled by the user, but rather defined in your python script/pipeline, I thought I should share it here.

I'm running the pipeline with the following command: gatb -1 ${fastq_pair[0]} -2 ${fastq_pair[1]} --kmer-sizes ${kmer_list} -o ${sample_id}_GATBMiniaPipeline --no-error-correction

And this is the error that I have:

Remove temp files... Done.
Time elapsed for temp files removing: 0:00:00.009432

Processing is finished.
(2020-07-22 08:32:20) Execution of 'python BESST/runBESST'. Command line:
     /NGStools/gatb-minia-pipeline/tools/memused python /NGStools/gatb-minia-pipeline/BESST/runBESST -c ERR2984773_GATBMiniaPipeline_k181.contigs.fa -f ERR2984773_GATBMiniaPipeline.lib_0.bam -o ERR2984773_GATBMiniaPipeline_besst -orientation fr --iter 10000
usage: BESST [-h] -c CONTIGFILE -f BAMFILES [BAMFILES ...]
             [-r READLEN [READLEN ...]] [-m MEAN [MEAN ...]]
             [-s STDDEV [STDDEV ...]] [-z COVCUTOFF [COVCUTOFF ...]]
             [-T THRESHOLD [THRESHOLD ...]] [-e EDGESUPPORT [EDGESUPPORT ...]]
             [-k MINSIZE [MINSIZE ...]] [-filter_contigs CONTIG_FILTER_LENGTH]
             [--min_mapq MIN_MAPQ] [--iter PATH_THRESHOLD]
             [--score_cutoff SCORE_CUTOFF] [--max_extensions MAX_EXTENSIONS]
             [--bfs_traversal] [-a HAPLRATIO] [-b HAPLTHRESHOLD] [-K KMER]
             [-M MMER] [-g] [--orientation ORIENTATION [ORIENTATION ...]]
             [-o OUTPUT] [-d] [-y] [-q] [--no_score] [-devel] [-plots]
             [--separate_repeats] [--NO_ILP] [--FASTER_ILP] [--print_scores]
             [--version]
BESST: error: unrecognized arguments: fr
maximal memory used: 0 MB
(2020-07-22 08:32:21) Execution of 'python BESST/runBESST' failed. Command line:
     /NGStools/gatb-minia-pipeline/tools/memused python /NGStools/gatb-minia-pipeline/BESST/runBESST -c ERR2984773_GATBMiniaPipeline_k181.contigs.fa -f ERR2984773_GATBMiniaPipeline.lib_0.bam -o ERR2984773_GATBMiniaPipeline_besst -orientation fr --iter 10000

Any help overcoming this problem is highly appreciated!

Best,

Inês