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simoncchu / GAPPadder

GAPPadder is tool for closing gaps on draft genomes with short sequencing data
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Problems running Collect #13

Open camillaln opened 3 years ago

camillaln commented 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

Traceback (most recent call last):

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