Open TuoCai2000 opened 1 year ago
Hi, could you check whether "NM" or "nM" tag available in your bam files?
Yes,I checked my bam files and found NM tag available. How can I process it to apply Monopogen into my bam files? Thank you so much!!
So I wonder if such error is fine for me ? I persume I would only come up with this error when it processed to the chromsome like chrX,chrY,chrM,GL000008.2...So even with this error,I can still get my result,and it looks fine. I wonder if I comprehend it in the right way?
We have not tested monopogen on sex chromosomes. They have different imputation mode from reference panel. The preprocess step should be okay if you can generate the filtered bam files.
Hey , I met the same error.
[2023-09-14 10:54:04,148] INFO Monopogen.py Performing data preprocess before variant calling... [2023-09-14 10:54:04,148] INFO germline.py Parameters in effect: [2023-09-14 10:54:04,148] INFO germline.py --subcommand = [preProcess] [2023-09-14 10:54:04,148] INFO germline.py --bamFile = [bam_S7.lst] [2023-09-14 10:54:04,148] INFO germline.py --out = [S7_out] [2023-09-14 10:54:04,148] INFO germline.py --app_path = [/home/big/zheng/Monopogen/apps] [2023-09-14 10:54:04,148] INFO germline.py --max_mismatch = [3] [2023-09-14 10:54:04,148] INFO germline.py --nthreads = [16] [2023-09-14 10:54:04,165] DEBUG Monopogen.py PreProcessing sample S7 multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/zheng/anaconda3/envs/monopogen/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/home/zheng/anaconda3/envs/monopogen/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) File "/home/big/zheng/Monopogen/src/germline.py", line 206, in BamFilter if val < max_mismatch: UnboundLocalError: local variable 'val' referenced before assignment """
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/big/zheng/Monopogen/src/Monopogen.py", line 435, in
main() File "/home/big/zheng/Monopogen/src/Monopogen.py", line 428, in main args.func(args) File "/home/big/zheng/Monopogen/src/Monopogen.py", line 313, in preProcess result = pool.map(BamFilter, para_lst) File "/home/zheng/anaconda3/envs/monopogen/lib/python3.8/multiprocessing/pool.py", line 364, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/home/zheng/anaconda3/envs/monopogen/lib/python3.8/multiprocessing/pool.py", line 771, in get raise self._value UnboundLocalError: local variable 'val' referenced before assignment
I checked the 'NM' tag in the bam file using the command samtools view S7_final.bam
and the result shows
A00627:649:HFLL7DSX7:4:1443:26775:28917 165 chr1 10015 0 = 10015 0 ATTTATCTATGTACGCAAGTGGCCGATCATTCGCATCGGCGTACGACTTCTTCACAATCCACGTGCTTGAGACTGTGGTGGTATAC :FFFFFFFFFFFFFFFFF:F:FFFFF:::,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFFFFFFFFFF rl:i:0 MQ:i:0 MC:Z:14S92M1I43M ms:i:4140 A00627:649:HFLL7DSX7:4:1443:26775:28917 89 chr1 10015 0 14S92M1I43M = 10015 0 TTAACATTACACTTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC F,FF::FFF,,,F,FF:,F,:,,,FF,:F:F,F,F:F,F,:FFFF:,,F:F,,,FFF,F,FFF:,,FFF:::F,FFFFF:F:FFFF:,:FFFF,:F:FF:FFFF:F,,F,FFFFFF:FFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFF NM:i:2 AS:i:246 nn:i:0 tp:A:P cm:i:16 s1:i:123 s2:i:123 de:f:0.0147 rl:i:0 MC:Z: ms:i:3024 A00627:649:HFLL7DSX7:4:1356:25446:20979 2121 chr1 10036 0 65H51M34H = 10036 0 CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA FFF:FFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFF:FFF NM:i:0 ms:i:102 AS:i:102 nn:i:0 tp:A:P cm:i:5 s1:i:45 s2:i:45 de:f:0 SA:Z:chr5,83515783,+,71M79S,60,0; rl:i:0 A00627:649:HFLL7DSX7:4:1663:14434:25958 65 chr1 10053 14 56M1I23M70S chr12 54151866 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAAACCCAAACCCTAACCCTAACCCAAAACCAAACCCAAACCCAAAACCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAAACAACCC FF,FFFFF:FF:FFFFFFFF,FFFFF,FF:FF:FFFFF,FFFFF,FF:FF,FF:FF,FFFFF,FFFFF,FF,FF,FFFFF,FF,FF:F:,FF,FF,FF,FF,FF,FFFFF,FFFF::F:,FF,FF:FF,FF,:F,:F,FF,F:FF,F,:F NM:i:2 AS:i:134 nn:i:0 tp:A:P cm:i:7 s1:i:54 s2:i:54 de:f:0.025 SA:Z:chr13,106450659,+,102S37M11S,10,0; rl:i:0 MQ:i:23 MC:Z:30S56M ms:i:2418 A00627:649:HFLL7DSX7:4:1511:12644:13150 163 chr1 10059 0 55S31M = 10156 181 CAAGCACGTGGATTACTTCGTAGTCGTACCCCGATGCTAAACATCGGCCACTCATCCTAACCCTAACCCTAACCCTAACCCTAACC FFFFFFFFFFFFFFFFFF,:,,F,F:,,,,FFFFFF,F,,FFFFF:FFF:FFFFFFFFFFF,,:FFFFFFF:FFFFFFFFFFFFFF NM:i:0 AS:i:62 nn:i:0 tp:A:P cm:i:1 s1:i:92 s2:i:91 de:f:0 rl:i:0 MQ:i:0 MC:Z:66S22M1I53M1D8M ms:i:3605 A00627:649:HFLL7DSX7:4:1129:3341:16172 165 chr1 10061 0 = 10061 0 GTCTGTCTTTACAGCAGAGTGGCCGATGTTTCGCATCGGCGTACGACTAGCACCTCATCCACGTGCTTGAGACTGTGGACTATTGC FFFFFFFFFFFFFFF:FFF,F:,FFF:::,F,FF,FFF:FF,,FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF rl:i:0 MQ:i:39 MC:Z:5S46M1I48M5D14M4D36M ms:i:4078 A00627:649:HFLL7DSX7:4:1129:3341:16172 89 chr1 10061 39 5S46M1I48M5D14M4D36M = 10061 0 AAACATAACCCTAACCCTAACCCTAACCATAACCCTAACCCTAACCCTAACACTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC ,F,:,:FF,FFFFF,:FFFF,::FF,F,,F:FF,,:F:,,:FFF,F,:FFF,,F:,FF,FF,,F,::,F,FF:FFF:,FF:,FFF:::,,:F,FFF:,FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFF,:F NM:i:12 AS:i:212 nn:i:0 tp:A:P cm:i:9 s1:i:95 s2:i:100 de:f:0.034 rl:i:0 MC:Z: ms:i:2839 A00627:649:HFLL7DSX7:4:1155:3974:23594 165 chr1 10068 0 = 10068 0 GGAATTAGCTGACAGTGCGTGGCCGATGTTTCGCATCGGCGTACGACTGACAGTGCATCCACGTGCTTGAGACTGTGGTCTGATCC FFF:FFFFFFFFFFFFFFF:FF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF rl:i:0 MQ:i:60 MC:Z:39M1I40M1D18M1I4M1I6M4D40M ms:i:4128 A00627:649:HFLL7DSX7:4:1155:3974:23594 89 chr1 10068 60 39M1I40M1D18M1I4M1I6M4D40M = 10068 0 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTAACCCTAACACTAATCCCTAAACCCTTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC :,,F,F::,:FFFF:::FFF,:,F:F,,FFF:,:FFFF,,FF:,:,FF:F::FFFF,:FFF::,FFF,,,FFFF:,FFF:,FFFFF,,FFF,,,,:,:,:FF:F,FFFFF,FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:11 AS:i:188 nn:i:0 tp:A:P cm:i:10 s1:i:97 s2:i:96 de:f:0.0526 rl:i:0 MC:Z: ms:i:3121 A00627:649:HFLL7DSX7:4:1362:9362:5869 65 chr1 10092 1 17M1I38M1D30M1I44M19S chr20 64287018 0 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAAACCCTAACCCTAACCCTAACCCTAACCCAAACCCTAACCCAAACCCTAACCCTAACCCTAACCCTAACCCGGGCGCTAAGCCTGGCCCG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF,,FFF:F,:FFFF,FFF:F:FF:F,::FF::,FFFFF,:F,F:,::,,:,,F,F:,,,,::,:,,,,,,:,:F,,,,,,,,,,,,,,,,,,, NM:i:6 AS:i:186 nn:i:0 tp:A:P cm:i:2 s1:i:42 s2:i:50 de:f:0.0455 rl:i:114 MQ:i:7 MC:Z:4M1D52M30S ms:i:2075
seems only some of the sequences are tagged with "NM".
And when I run Mnopogen preprocess, I can only get the following outputs: S7_chr10.filter.bam S7_chr13.filter.bam S7_chr15.filter.bam.bai S7_chr17.filter.bam.bai S7_chr1.filter.bam S7_chr22.filter.bam S7_chr3.filter.bam S7_chr5.filter.bam S7_chr7.filter.bam S7_chr10.filter.bam.bai S7_chr13.filter.bam.bai S7_chr16.filter.bam S7_chr18.filter.bam S7_chr20.filter.bam S7_chr22.filter.bam.bai S7_chr3.filter.bam.bai S7_chr5.filter.bam.bai S7_chr7.filter.bam.bai S7_chr11.filter.bam S7_chr14.filter.bam S7_chr16.filter.bam.bai S7_chr18.filter.bam.bai S7_chr21.filter.bam S7_chr2.filter.bam S7_chr4.filter.bam S7_chr6.filter.bam S7_chr8.filter.bam S7_chr12.filter.bam S7_chr15.filter.bam S7_chr17.filter.bam S7_chr19.filter.bam S7_chr21.filter.bam.bai S7_chr2.filter.bam.bai S7_chr4.filter.bam.bai S7_chr6.filter.bam.bai S7_chr9.filter.bam
some of them missed .bai and without .filter.bam.lst files.
could you please tell me how to solve this problem?
Hey , I met the same error.
[2023-09-14 10:54:04,148] INFO Monopogen.py Performing data preprocess before variant calling... [2023-09-14 10:54:04,148] INFO germline.py Parameters in effect: [2023-09-14 10:54:04,148] INFO germline.py --subcommand = [preProcess] [2023-09-14 10:54:04,148] INFO germline.py --bamFile = [bam_S7.lst] [2023-09-14 10:54:04,148] INFO germline.py --out = [S7_out] [2023-09-14 10:54:04,148] INFO germline.py --app_path = [/home/big/zheng/Monopogen/apps] [2023-09-14 10:54:04,148] INFO germline.py --max_mismatch = [3] [2023-09-14 10:54:04,148] INFO germline.py --nthreads = [16] [2023-09-14 10:54:04,165] DEBUG Monopogen.py PreProcessing sample S7 multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/zheng/anaconda3/envs/monopogen/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/home/zheng/anaconda3/envs/monopogen/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) File "/home/big/zheng/Monopogen/src/germline.py", line 206, in BamFilter if val < max_mismatch: UnboundLocalError: local variable 'val' referenced before assignment """ The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/big/zheng/Monopogen/src/Monopogen.py", line 435, in main() File "/home/big/zheng/Monopogen/src/Monopogen.py", line 428, in main args.func(args) File "/home/big/zheng/Monopogen/src/Monopogen.py", line 313, in preProcess result = pool.map(BamFilter, para_lst) File "/home/zheng/anaconda3/envs/monopogen/lib/python3.8/multiprocessing/pool.py", line 364, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/home/zheng/anaconda3/envs/monopogen/lib/python3.8/multiprocessing/pool.py", line 771, in get raise self._value UnboundLocalError: local variable 'val' referenced before assignment
I checked the 'NM' tag in the bam file using the command
samtools view S7_final.bam
and the result showsA00627:649:HFLL7DSX7:4:1443:26775:28917 165 chr1 10015 0 = 10015 0 ATTTATCTATGTACGCAAGTGGCCGATCATTCGCATCGGCGTACGACTTCTTCACAATCCACGTGCTTGAGACTGTGGTGGTATAC :FFFFFFFFFFFFFFFFF:F:FFFFF:::,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFFFFFFFFFF rl:i:0 MQ:i:0 MC:Z:14S92M1I43M ms:i:4140 A00627:649:HFLL7DSX7:4:1443:26775:28917 89 chr1 10015 0 14S92M1I43M = 10015 0 TTAACATTACACTTACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC F,FF::FFF,,,F,FF:,F,:,,,FF,:F:F,F,F:F,F,:FFFF:,,F:F,,,FFF,F,FFF:,,FFF:::F,FFFFF:F:FFFF:,:FFFF,:F:FF:FFFF:F,,F,FFFFFF:FFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFF NM:i:2 AS:i:246 nn:i:0 tp:A:P cm:i:16 s1:i:123 s2:i:123 de:f:0.0147 rl:i:0 MC:Z: ms:i:3024 A00627:649:HFLL7DSX7:4:1356:25446:20979 2121 chr1 10036 0 65H51M34H = 10036 0 CTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA FFF:FFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFF:FFF NM:i:0 ms:i:102 AS:i:102 nn:i:0 tp:A:P cm:i:5 s1:i:45 s2:i:45 de:f:0 SA:Z:chr5,83515783,+,71M79S,60,0; rl:i:0 A00627:649:HFLL7DSX7:4:1663:14434:25958 65 chr1 10053 14 56M1I23M70S chr12 54151866 0 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAAACCCAAACCCTAACCCTAACCCAAAACCAAACCCAAACCCAAAACCAAACCCAAACCCAAACCCAAACCCAAACCCAAACCCAAAACAACCC FF,FFFFF:FF:FFFFFFFF,FFFFF,FF:FF:FFFFF,FFFFF,FF:FF,FF:FF,FFFFF,FFFFF,FF,FF,FFFFF,FF,FF:F:,FF,FF,FF,FF,FF,FFFFF,FFFF::F:,FF,FF:FF,FF,:F,:F,FF,F:FF,F,:F NM:i:2 AS:i:134 nn:i:0 tp:A:P cm:i:7 s1:i:54 s2:i:54 de:f:0.025 SA:Z:chr13,106450659,+,102S37M11S,10,0; rl:i:0 MQ:i:23 MC:Z:30S56M ms:i:2418 A00627:649:HFLL7DSX7:4:1511:12644:13150 163 chr1 10059 0 55S31M = 10156 181 CAAGCACGTGGATTACTTCGTAGTCGTACCCCGATGCTAAACATCGGCCACTCATCCTAACCCTAACCCTAACCCTAACCCTAACC FFFFFFFFFFFFFFFFFF,:,,F,F:,,,,FFFFFF,F,,FFFFF:FFF:FFFFFFFFFFF,,:FFFFFFF:FFFFFFFFFFFFFF NM:i:0 AS:i:62 nn:i:0 tp:A:P cm:i:1 s1:i:92 s2:i:91 de:f:0 rl:i:0 MQ:i:0 MC:Z:66S22M1I53M1D8M ms:i:3605 A00627:649:HFLL7DSX7:4:1129:3341:16172 165 chr1 10061 0 = 10061 0 GTCTGTCTTTACAGCAGAGTGGCCGATGTTTCGCATCGGCGTACGACTAGCACCTCATCCACGTGCTTGAGACTGTGGACTATTGC FFFFFFFFFFFFFFF:FFF,F:,FFF:::,F,FF,FFF:FF,,FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF rl:i:0 MQ:i:39 MC:Z:5S46M1I48M5D14M4D36M ms:i:4078 A00627:649:HFLL7DSX7:4:1129:3341:16172 89 chr1 10061 39 5S46M1I48M5D14M4D36M = 10061 0 AAACATAACCCTAACCCTAACCCTAACCATAACCCTAACCCTAACCCTAACACTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC ,F,:,:FF,FFFFF,:FFFF,::FF,F,,F:FF,,:F:,,:FFF,F,:FFF,,F:,FF,FF,,F,::,F,FF:FFF:,FF:,FFF:::,,:F,FFF:,FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFF,:F NM:i:12 AS:i:212 nn:i:0 tp:A:P cm:i:9 s1:i:95 s2:i:100 de:f:0.034 rl:i:0 MC:Z: ms:i:2839 A00627:649:HFLL7DSX7:4:1155:3974:23594 165 chr1 10068 0 = 10068 0 GGAATTAGCTGACAGTGCGTGGCCGATGTTTCGCATCGGCGTACGACTGACAGTGCATCCACGTGCTTGAGACTGTGGTCTGATCC FFF:FFFFFFFFFFFFFFF:FF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF rl:i:0 MQ:i:60 MC:Z:39M1I40M1D18M1I4M1I6M4D40M ms:i:4128 A00627:649:HFLL7DSX7:4:1155:3974:23594 89 chr1 10068 60 39M1I40M1D18M1I4M1I6M4D40M = 10068 0 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTAACCCTAACCCTAACCCTAACCCTAACACTAACCCTAACCCTAACACTAATCCCTAAACCCTTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC :,,F,F::,:FFFF:::FFF,:,F:F,,FFF:,:FFFF,,FF:,:,FF:F::FFFF,:FFF::,FFF,,,FFFF:,FFF:,FFFFF,,FFF,,,,:,:,:FF:F,FFFFF,FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NM:i:11 AS:i:188 nn:i:0 tp:A:P cm:i:10 s1:i:97 s2:i:96 de:f:0.0526 rl:i:0 MC:Z: ms:i:3121 A00627:649:HFLL7DSX7:4:1362:9362:5869 65 chr1 10092 1 17M1I38M1D30M1I44M19S chr20 64287018 0 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCAAACCCTAACCCTAACCCTAACCCTAACCCAAACCCTAACCCAAACCCTAACCCTAACCCTAACCCTAACCCGGGCGCTAAGCCTGGCCCG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF,,FFF:F,:FFFF,FFF:F:FF:F,::FF::,FFFFF,:F,F:,::,,:,,F,F:,,,,::,:,,,,,,:,:F,,,,,,,,,,,,,,,,,,, NM:i:6 AS:i:186 nn:i:0 tp:A:P cm:i:2 s1:i:42 s2:i:50 de:f:0.0455 rl:i:114 MQ:i:7 MC:Z:4M1D52M30S ms:i:2075
seems only some of the sequences are tagged with "NM".
And when I run Mnopogen preprocess, I can only get the following outputs: S7_chr10.filter.bam S7_chr13.filter.bam S7_chr15.filter.bam.bai S7_chr17.filter.bam.bai S7_chr1.filter.bam S7_chr22.filter.bam S7_chr3.filter.bam S7_chr5.filter.bam S7_chr7.filter.bam S7_chr10.filter.bam.bai S7_chr13.filter.bam.bai S7_chr16.filter.bam S7_chr18.filter.bam S7_chr20.filter.bam S7_chr22.filter.bam.bai S7_chr3.filter.bam.bai S7_chr5.filter.bam.bai S7_chr7.filter.bam.bai S7_chr11.filter.bam S7_chr14.filter.bam S7_chr16.filter.bam.bai S7_chr18.filter.bam.bai S7_chr21.filter.bam S7_chr2.filter.bam S7_chr4.filter.bam S7_chr6.filter.bam S7_chr8.filter.bam S7_chr12.filter.bam S7_chr15.filter.bam S7_chr17.filter.bam S7_chr19.filter.bam S7_chr21.filter.bam.bai S7_chr2.filter.bam.bai S7_chr4.filter.bam.bai S7_chr6.filter.bam.bai S7_chr9.filter.bam
some of them missed .bai and without .filter.bam.lst files.
could you please tell me how to solve this problem?
I think the problem is that I failed to integrate the cell barcode(read1_fq.gz) and the cDNA(read2.fq.gz) may I ask which tool are you using to generate the bam file?.
Hello!Thank you for developing monopogen! I run the code:python ${path}/src/Monopogen.py preProcess -b test.lst -o 01.test -a ${path}/apps,but got error like this:
multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/public/home/user/program/miniconda3/envs/monopogen/lib/python3.7/multiprocessing/pool.py", line 121, in worker result = (True, func(*args, *kwds)) File "/public/home/user/program/miniconda3/envs/monopogen/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar return list(map(args)) File "/public/home/user/program/Monopogen/src/germline.py", line 206, in BamFilter if val < max_mismatch: UnboundLocalError: local variable 'val' referenced before assignment """
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/public/home/user/program/Monopogen/src/Monopogen.py", line 435, in
main()
File "/public/home/user/program/Monopogen/src/Monopogen.py", line 428, in main
args.func(args)
File "/public/home/user/program/Monopogen/src/Monopogen.py", line 313, in preProcess
result = pool.map(BamFilter, para_lst)
File "/public/home/user/program/miniconda3/envs/monopogen/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/public/home/user/program/miniconda3/envs/monopogen/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
UnboundLocalError: local variable 'val' referenced before assignment
I would appreciate if you can help me. Thank you very much!