Closed DNA-language closed 8 years ago
mducar
commented
8 years ago Hi,
Based on the error messages, you are using the code from the master branch. As mentioned in the Readme, this is development code and is not supported.
If you look in the "releases" section, there is a release tagged for version 0.0.6 of the software. Please use that version: https://github.com/ccgd-profile/BreaKmer/releases
Best, Matt
Tinalxt
commented
7 years ago Hi~ I had the same problem, but when I run the example_data with version 0.0.6, I got a new problem, just like below:
1 Traceback (most recent call last):
2 File "/Workspace/home/difanglei/pipeline/ctDNA/software/BreaKmer-0.0.6/breakmer.py", line 96, in
I wonder if it is a new bug? And how can I fix it. Thank you~
err info :
`Traceback (most recent call last): File "../BreaKmer-master/breakmer.py", line 72, in
RUN_TRACKER.run()
File "/ifs/TJPROJ3/RD/shanguangyu/project/BreaKmer-master/breakmer/processor/analysis.py", line 143, in run
aggResults = analyze_targets(targetAnalysisList)
File "/ifs/TJPROJ3/RD/shanguangyu/project/BreaKmer-master/breakmer/processor/analysis.py", line 79, in analyze_targets
if not targetRegion.find_sv_reads(): # No SV reads extracted. Exiting.
File "/ifs/TJPROJ3/RD/shanguangyu/project/BreaKmer-master/breakmer/processor/target.py", line 552, in find_sv_reads
self.extract_bam_reads('sv') # Extract variant reads.
File "/ifs/TJPROJ3/RD/shanguangyu/project/BreaKmer-master/breakmer/processor/target.py", line 578, in extract_bam_reads
self.variation.set_var_reads(sampleType, bamFile, self.chrom, self.start, self.end, self.regionBuffer)
File "/ifs/TJPROJ3/RD/shanguangyu/project/BreaKmer-master/breakmer/processor/target.py", line 165, in set_var_reads
pysam.sort(self.files['sv_bam'], self.files['sv_bam_sorted'].replace('.bam', ''))
File "/ifs/TJPROJ3/RD/shanguangyu/software/python27/lib/python2.7/site-packages/pysam-0.9.1.4-py2.7-linux-x86_64.egg/pysam/utils.py", line 75, in call
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\nUsage: samtools sort [options...] [in.bam]\nOptions:\n -l INT Set compression level, from 0 (uncompressed) to 9 (best)\n -m INT Set maximum memory per thread; suffix K/M/G recognized [768M]\n -n Sort by read name\n -o FILE Write final output to FILE rather than standard output\n -T PREFIX Write temporary files to PREFIX.nnnn.bam\n -@, --threads INT\n Set number of sorting and compression threads [1]\n --input-fmt-option OPT[=VAL]\n Specify a single input file format option in the form\n of OPTION or OPTION=VALUE\n -O, --output-fmt FORMAT[,OPT[=VAL]]...\n Specify output format (SAM, BAM, CRAM)\n --output-fmt-option OPT[=VAL]\n Specify a single output file format option in the form\n of OPTION or OPTION=VALUE\n --reference FILE\n Reference sequence FASTA FILE [null]\n'
it seems get stuck when it invoke 'pysam' package which sort bam file, does anyone tells some usefull info . any opinoin is appreciate.