search

KChen-lab / Monopogen

SNV calling from single cell sequencing
GNU General Public License v3.0
71 stars 17 forks source link

Error about data preprocess #13

Open TuoCai2000 opened 1 year ago

TuoCai2000 commented 1 year ago

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!

jinzhuangdou commented 1 year ago

Hi, could you check whether "NM" or "nM" tag available in your bam files?

TuoCai2000 commented 1 year ago

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!!

TuoCai2000 commented 1 year ago

Hi ,thank you for quickly answering my question! I just found my bam files sorted by the chromsome:chr1,chr2...chrX,chrY,chrM,GL000008.2... And if I run the code ,I can get the output like this even if it errors:

total 361052 -rw-r--r-- 1 caituo zhulab 41 Sep 6 18:34 chr10.filter.bam.lst -rw-r--r-- 1 caituo zhulab 41 Sep 6 18:34 chr11.filter.bam.lst -rw-r--r-- 1 caituo zhulab 41 Sep 6 18:34 chr12.filter.bam.lst -rw-r--r-- 1 caituo zhulab 41 Sep 6 18:34 chr13.filter.bam.lst -rw-r--r-- 1 caituo zhulab 41 Sep 6 18:34 chr14.filter.bam.lst -rw-r--r-- 1 caituo zhulab 41 Sep 6 18:34 chr15.filter.bam.lst -rw-r--r-- 1 caituo zhulab 41 Sep 6 18:34 chr16.filter.bam.lst -rw-r--r-- 1 caituo zhulab 41 Sep 6 18:34 chr17.filter.bam.lst -rw-r--r-- 1 caituo zhulab 41 Sep 6 18:34 chr18.filter.bam.lst -rw-r--r-- 1 caituo zhulab 41 Sep 6 18:34 chr19.filter.bam.lst -rw-r--r-- 1 caituo zhulab 40 Sep 6 18:34 chr1.filter.bam.lst -rw-r--r-- 1 caituo zhulab 41 Sep 6 18:34 chr20.filter.bam.lst -rw-r--r-- 1 caituo zhulab 41 Sep 6 18:34 chr21.filter.bam.lst -rw-r--r-- 1 caituo zhulab 41 Sep 6 18:34 chr22.filter.bam.lst -rw-r--r-- 1 caituo zhulab 40 Sep 6 18:34 chr2.filter.bam.lst -rw-r--r-- 1 caituo zhulab 40 Sep 6 18:34 chr3.filter.bam.lst -rw-r--r-- 1 caituo zhulab 40 Sep 6 18:34 chr4.filter.bam.lst -rw-r--r-- 1 caituo zhulab 40 Sep 6 18:34 chr5.filter.bam.lst -rw-r--r-- 1 caituo zhulab 40 Sep 6 18:34 chr6.filter.bam.lst -rw-r--r-- 1 caituo zhulab 40 Sep 6 18:34 chr7.filter.bam.lst -rw-r--r-- 1 caituo zhulab 40 Sep 6 18:34 chr8.filter.bam.lst -rw-r--r-- 1 caituo zhulab 40 Sep 6 18:34 chr9.filter.bam.lst -rw-r--r-- 1 caituo zhulab 5875414 Sep 6 18:46 LGDR1-10_chr10.filter.bam -rw-r--r-- 1 caituo zhulab 87752 Sep 6 18:46 LGDR1-10_chr10.filter.bam.bai -rw-r--r-- 1 caituo zhulab 21532825 Sep 6 18:46 LGDR1-10_chr11.filter.bam -rw-r--r-- 1 caituo zhulab 90712 Sep 6 18:46 LGDR1-10_chr11.filter.bam.bai -rw-r--r-- 1 caituo zhulab 12284703 Sep 6 18:47 LGDR1-10_chr12.filter.bam -rw-r--r-- 1 caituo zhulab 88984 Sep 6 18:47 LGDR1-10_chr12.filter.bam.bai -rw-r--r-- 1 caituo zhulab 5181496 Sep 6 18:46 LGDR1-10_chr13.filter.bam -rw-r--r-- 1 caituo zhulab 70912 Sep 6 18:46 LGDR1-10_chr13.filter.bam.bai -rw-r--r-- 1 caituo zhulab 3862777 Sep 6 18:46 LGDR1-10_chr14.filter.bam -rw-r--r-- 1 caituo zhulab 68344 Sep 6 18:46 LGDR1-10_chr14.filter.bam.bai -rw-r--r-- 1 caituo zhulab 7412 Sep 6 18:46 LGDR1-10_chr15.filter.bam -rw-r--r-- 1 caituo zhulab 4456 Sep 6 18:34 LGDR1-10_chr15.filter.bam.bai -rw-r--r-- 1 caituo zhulab 7426 Sep 6 18:34 LGDR1-10_chr16.filter.bam -rw-r--r-- 1 caituo zhulab 4456 Sep 6 18:34 LGDR1-10_chr16.filter.bam.bai -rw-r--r-- 1 caituo zhulab 13331062 Sep 6 18:46 LGDR1-10_chr17.filter.bam -rw-r--r-- 1 caituo zhulab 62200 Sep 6 18:46 LGDR1-10_chr17.filter.bam.bai -rw-r--r-- 1 caituo zhulab 2809370 Sep 6 18:46 LGDR1-10_chr18.filter.bam -rw-r--r-- 1 caituo zhulab 51400 Sep 6 18:46 LGDR1-10_chr18.filter.bam.bai -rw-r--r-- 1 caituo zhulab 19726554 Sep 6 18:46 LGDR1-10_chr19.filter.bam -rw-r--r-- 1 caituo zhulab 48728 Sep 6 18:46 LGDR1-10_chr19.filter.bam.bai -rw-r--r-- 1 caituo zhulab 24781345 Sep 6 18:46 LGDR1-10_chr1.filter.bam -rw-r--r-- 1 caituo zhulab 161440 Sep 6 18:46 LGDR1-10_chr1.filter.bam.bai -rw-r--r-- 1 caituo zhulab 5866005 Sep 6 18:47 LGDR1-10_chr20.filter.bam -rw-r--r-- 1 caituo zhulab 45016 Sep 6 18:47 LGDR1-10_chr20.filter.bam.bai -rw-r--r-- 1 caituo zhulab 178118080 Sep 6 18:47 LGDR1-10_chr21.filter.bam -rw-r--r-- 1 caituo zhulab 70712 Sep 6 18:47 LGDR1-10_chr21.filter.bam.bai -rw-r--r-- 1 caituo zhulab 4883524 Sep 6 18:47 LGDR1-10_chr22.filter.bam -rw-r--r-- 1 caituo zhulab 37136 Sep 6 18:47 LGDR1-10_chr22.filter.bam.bai -rw-r--r-- 1 caituo zhulab 15516960 Sep 6 18:46 LGDR1-10_chr2.filter.bam -rw-r--r-- 1 caituo zhulab 151872 Sep 6 18:46 LGDR1-10_chr2.filter.bam.bai -rw-r--r-- 1 caituo zhulab 7412 Sep 6 18:46 LGDR1-10_chr3.filter.bam -rw-r--r-- 1 caituo zhulab 4456 Sep 6 18:34 LGDR1-10_chr3.filter.bam.bai -rw-r--r-- 1 caituo zhulab 7426 Sep 6 18:34 LGDR1-10_chr4.filter.bam -rw-r--r-- 1 caituo zhulab 4456 Sep 6 18:34 LGDR1-10_chr4.filter.bam.bai -rw-r--r-- 1 caituo zhulab 15036108 Sep 6 18:46 LGDR1-10_chr5.filter.bam -rw-r--r-- 1 caituo zhulab 117640 Sep 6 18:46 LGDR1-10_chr5.filter.bam.bai -rw-r--r-- 1 caituo zhulab 10952824 Sep 6 18:46 LGDR1-10_chr6.filter.bam -rw-r--r-- 1 caituo zhulab 109880 Sep 6 18:46 LGDR1-10_chr6.filter.bam.bai -rw-r--r-- 1 caituo zhulab 14526624 Sep 6 18:46 LGDR1-10_chr7.filter.bam -rw-r--r-- 1 caituo zhulab 103976 Sep 6 18:46 LGDR1-10_chr7.filter.bam.bai -rw-r--r-- 1 caituo zhulab 6764889 Sep 6 18:46 LGDR1-10_chr8.filter.bam -rw-r--r-- 1 caituo zhulab 92160 Sep 6 18:46 LGDR1-10_chr8.filter.bam.bai -rw-r--r-- 1 caituo zhulab 6879066 Sep 6 18:46 LGDR1-10_chr9.filter.bam -rw-r--r-- 1 caituo zhulab 88448 Sep 6 18:46 LGDR1-10_chr9.filter.bam.bai

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?

jinzhuangdou commented 1 year ago

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.

zheng-sc commented 11 months ago

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?

zheng-sc commented 11 months ago

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?

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?.