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Ecogenomics / BamM

Metagenomics-focused BAM file manipulation
http://ecogenomics.github.io/BamM/
GNU Lesser General Public License v3.0
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bamm filter #57

Closed liaohu1231 closed 4 years ago

liaohu1231 commented 4 years ago

when we run the bamm filter, there have a error samtools index: failed to create index for "/hwfssz1/ST_CANCER/CGR/USER/liaohu/metagenome/bamm_filter/ERR1190801_filtered.bam" Traceback (most recent call last): File "/home/liaohu/.conda/envs/gtdbtk/bin/bamm", line 660, in doWork(args) File "/home/liaohu/.conda/envs/gtdbtk/bin/bamm", line 292, in doWork useSecondaryAlignments=args.use_secondary File "/home/liaohu/.conda/envs/gtdbtk/lib/python2.7/site-packages/bamm/bamFilter.py", line 174, in filter self.samtoolsIndex(outputFile) File "/home/liaohu/.conda/envs/gtdbtk/lib/python2.7/site-packages/bamm/bamFilter.py", line 214, in samtoolsIndex self._run_cmd(cmd) File "/home/liaohu/.conda/envs/gtdbtk/lib/python2.7/site-packages/bamm/bamFilter.py", line 196, in _run_cmd subprocess.check_call(cmd, shell=True) File "/home/liaohu/.conda/envs/gtdbtk/lib/python2.7/subprocess.py", line 190, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'samtools index /hwfssz1/ST_CANCER/CGR/USER/liaohu/metagenome/bamm_filter/ERR1190801_filtered.bam ' returned non-zero exit status 1

wwood commented 4 years ago

Hi. BamM is now deprecated - try using CoverM instead. https://github.com/wwood/CoverM