rchikhi
commented
8 years ago Thanks for letting us know! This is an error with Pysam 0.9.0 it seems. Until it is resolved, we'll support pysam <=0.8.3 only. You can install it via the command:
pip install pysam==0.8.3 --user
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.