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simoncchu / GAPPadder

GAPPadder is tool for closing gaps on draft genomes with short sequencing data
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Error during pipeline - returned non-zero exit status 1 #9

Open DomeJoyce opened 3 years ago

DomeJoyce commented 3 years ago

I get several errors during the complete run (-c All) as well as using -c Collect, as you can see below.

Can you please help to fix it, or to understaind what is creating the issue?

`python2.7 ./main.py -c Collect -g configuration.json samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chr1A" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 - samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chr2A" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 -samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chr4A" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 -

samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chr3A" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 - samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chr5A" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 - samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chr6A" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 - samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chr7A" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 - samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chrM" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 - samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chrRA" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 - 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 193, in parse_reads_fall_in_gaps_one_scaffold_short_is focal_region, gap_pos=self.get_focal_region_of_scaffold_v2(sf_gap_pos,ref) File "collect_reads_for_gaps.py", line 49, in get_focal_region_of_scaffold_v2 if focal_region.has_key(start-i)==False: AttributeError: 'dict' object has no attribute 'has_key' 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 193, in parse_reads_fall_in_gaps_one_scaffold_short_is focal_region, gap_pos=self.get_focal_region_of_scaffold_v2(sf_gap_pos,ref) File "collect_reads_for_gaps.py", line 49, in get_focal_region_of_scaffold_v2 if focal_region.has_key(start-i)==False: AttributeError: 'dict' object has no attribute 'has_key' samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 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 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 193, in parse_reads_fall_in_gaps_one_scaffold_short_is focal_region, gap_pos=self.get_focal_region_of_scaffold_v2(sf_gap_pos,ref) File "collect_reads_for_gaps.py", line 49, in get_focal_region_of_scaffold_v2 main_func(scommand,sfconfig) if focal_region.has_key(start-i)==False: AttributeError: 'dict' object has no attribute 'has_key' File "./main.py", line 244, in main_func mtrc.dispath_collect_jobs(nthreads, samtools_path, insert_size, derivation, clip_dist, folder) File "/home/software/GAPPadder/run_multi_threads_collect_reads.py", line 36, in dispath_collect_jobs pool.map(run_cmd_reads_collect, cmd_list) File "/usr/lib/python2.7/multiprocessing/pool.py", line 253, in map return self.map_async(func, iterable, chunksize).get() File "/usr/lib/python2.7/multiprocessing/pool.py", line 572, in get 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 193, in parse_reads_fall_in_gaps_one_scaffold_short_is raise self._value subprocess.CalledProcessError: Command 'samtools view /home/user/tmp_proj/EN_Caf/PILON_runs/SR_as_ref_CBS.bam "CBS_chr2A" | python collect_reads_for_gaps.py /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/gap_positions.txt 30 /home/user/tmp_proj/EN_Caf/PILON_runs/GAPPadder_out/1_is460/ 460 80 250 -' returned non-zero exit status 1 focal_region, gap_pos=self.get_focal_region_of_scaffold_v2(sf_gap_pos,ref) File "collect_reads_for_gaps.py", line 49, in get_focal_region_of_scaffold_v2

if focal_region.has_key(start-i)==False:

AttributeError: 'dict' object has no attribute 'has_key' samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 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 193, in parse_reads_fall_in_gaps_one_scaffold_short_is focal_region, gap_pos=self.get_focal_region_of_scaffold_v2(sf_gap_pos,ref) File "collect_reads_for_gaps.py", line 49, in get_focal_region_of_scaffold_v2 if focal_region.has_key(start-i)==False: AttributeError: 'dict' object has no attribute 'has_key' 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 193, in parse_reads_fall_in_gaps_one_scaffold_short_is focal_region, gap_pos=self.get_focal_region_of_scaffold_v2(sf_gap_pos,ref) File "collect_reads_for_gaps.py", line 49, in get_focal_region_of_scaffold_v2 if focal_region.has_key(start-i)==False: samtools view: AttributeError: 'dict' object has no attribute 'has_key' writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 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 193, in parse_reads_fall_in_gaps_one_scaffold_short_is focal_region, gap_pos=self.get_focal_region_of_scaffold_v2(sf_gap_pos,ref) File "collect_reads_for_gaps.py", line 49, in get_focal_region_of_scaffold_v2 if focal_region.has_key(start-i)==False: AttributeError: 'dict' object has no attribute 'has_key' 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 193, in parse_reads_fall_in_gaps_one_scaffold_short_is focal_region, gap_pos=self.get_focal_region_of_scaffold_v2(sf_gap_pos,ref) File "collect_reads_for_gaps.py", line 49, in get_focal_region_of_scaffold_v2 if focal_region.has_key(start-i)==False: AttributeError: 'dict' object has no attribute 'has_key' samtools view: writing to standard output failed: Broken pipe samtools view: Traceback (most recent call last): error closing standard output: -1 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 193, in parse_reads_fall_in_gaps_one_scaffold_short_is focal_region, gap_pos=self.get_focal_region_of_scaffold_v2(sf_gap_pos,ref) File "collect_reads_for_gaps.py", line 49, in get_focal_region_of_scaffold_v2 if focal_region.has_key(start-i)==False: AttributeError: 'dict' object has no attribute 'has_key' samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 `