Open camillaln opened 3 years ago
Hi,
I am trying to run your GAPPadder software. However, I get an error that we can not figure out. Could you please give some advice? Do we need a specific version of samtools?
(py27) nesbocam@silicon:~/GAPPadder-master$ python ./main.py -c Collect -g configuration_bathy1.json
samtools view /nfs/homes/nesbocam/ReAssemble-0.6/ctbRA/MWAHD1170726bathy_rMAG1/MWAHD1170726pbOP_mb_MAG_00021V2_16S_corrected.curated/BBmap/MWAHD1170726pbOP_mb_MAG_00021V2_16S_corrected_Ra_sorted.bam "MWAHD1170726pbOP_mb_MAG_00021V2_16S" | python collect_reads_for_gaps.py MWAHD1170726bathy_rMAG1Gappadder/gap_positions.txt 30 MWAHD1170726bathy_rMAG1Gappadder/1_is500/ 500 50 250 -
Traceback (most recent call last):
File "collect_reads_for_gaps.py", line 278, in
grc.parse_reads_fall_in_gaps_one_scaffold_short_is(sf_gap_pos, anchor_mapq, working_folder)
File "collect_reads_for_gaps.py", line 178, in parse_reads_fall_in_gaps_one_scaffold_short_is
flag=int(sam_fields[1])
ValueError: invalid literal for int() with base 10: '1:N:0:0'
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
File "./main.py", line 283, in
main_func(scommand,sfconfig)
File "./main.py", line 244, in main_func
mtrc.dispath_collect_jobs(nthreads, samtools_path, insert_size, derivation, clip_dist, folder)
File "/nfs/homes/nesbocam/GAPPadder-master/run_multi_threads_collect_reads.py", line 36, in dispath_collect_jobs
pool.map(run_cmd_reads_collect, cmd_list)
File "/nfs/homes/nesbocam/miniconda3/envs/py27/lib/python2.7/multiprocessing/pool.py", line 253, in map
return self.map_async(func, iterable, chunksize).get()
File "/nfs/homes/nesbocam/miniconda3/envs/py27/lib/python2.7/multiprocessing/pool.py", line 572, in get
raise self._value
subprocess.CalledProcessError: Command 'samtools view /nfs/homes/nesbocam/ReAssemble-0.6/ctbRA/MWAHD1170726bathy_rMAG1/MWAHD1170726pbOP_mb_MAG_00021V2_16S_corrected.curated/BBmap/MWAHD1170726pbOP_mb_MAG_00021V2_16S_corrected_Ra_sorted.bam "MWAHD1170726pbOP_mb_MAG_00021V2_16S" | python collect_reads_for_gaps.py MWAHD1170726bathy_rMAG1Gappadder/gap_positions.txt 30 MWAHD1170726bathy_rMAG1Gappadder/1_is500/ 500 50 250 -' returned non-zero exit status 1
Hi,
I am trying to run your GAPPadder software. However, I get an error that we can not figure out. Could you please give some advice? Do we need a specific version of samtools?
(py27) nesbocam@silicon:~/GAPPadder-master$ python ./main.py -c Collect -g configuration_bathy1.json
samtools view /nfs/homes/nesbocam/ReAssemble-0.6/ctbRA/MWAHD1170726bathy_rMAG1/MWAHD1170726pbOP_mb_MAG_00021V2_16S_corrected.curated/BBmap/MWAHD1170726pbOP_mb_MAG_00021V2_16S_corrected_Ra_sorted.bam "MWAHD1170726pbOP_mb_MAG_00021V2_16S" | python collect_reads_for_gaps.py MWAHD1170726bathy_rMAG1Gappadder/gap_positions.txt 30 MWAHD1170726bathy_rMAG1Gappadder/1_is500/ 500 50 250 -
Traceback (most recent call last):
File "collect_reads_for_gaps.py", line 278, in
File "collect_reads_for_gaps.py", line 178, in parse_reads_fall_in_gaps_one_scaffold_short_is
ValueError: invalid literal for int() with base 10: '1:N:0:0'
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
Traceback (most recent call last):
File "./main.py", line 283, in
File "./main.py", line 244, in main_func
File "/nfs/homes/nesbocam/GAPPadder-master/run_multi_threads_collect_reads.py", line 36, in dispath_collect_jobs
File "/nfs/homes/nesbocam/miniconda3/envs/py27/lib/python2.7/multiprocessing/pool.py", line 253, in map
File "/nfs/homes/nesbocam/miniconda3/envs/py27/lib/python2.7/multiprocessing/pool.py", line 572, in get
subprocess.CalledProcessError: Command 'samtools view /nfs/homes/nesbocam/ReAssemble-0.6/ctbRA/MWAHD1170726bathy_rMAG1/MWAHD1170726pbOP_mb_MAG_00021V2_16S_corrected.curated/BBmap/MWAHD1170726pbOP_mb_MAG_00021V2_16S_corrected_Ra_sorted.bam "MWAHD1170726pbOP_mb_MAG_00021V2_16S" | python collect_reads_for_gaps.py MWAHD1170726bathy_rMAG1Gappadder/gap_positions.txt 30 MWAHD1170726bathy_rMAG1Gappadder/1_is500/ 500 50 250 -' returned non-zero exit status 1