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SdeBlank / NanoFG

Third-generation fusion gene detection
GNU General Public License v3.0
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Errors with -b command #25

Open Lalitha611 opened 1 year ago

Lalitha611 commented 1 year ago

I attempted to use the tool with the BAM file generated from demo data and encountered an error. Could you kindly provide assistance with this?

(venv) (base) kamada@Lalithas-MacBook-Pro NanoFG % bash NanoFG.sh -b /Users/kamada/Downloads/NanoFG/demo.bam
Tue Jul  4 11:58:26 CEST 2023    Running on Lalithas-MacBook-Pro.local
### bam (-b) already provided. Skipping minimap2 mapping
### No selection parameter (-s) provided. Using all mapped reads
Tue Jul  4 11:58:26 CEST 2023    SV calling...
Tue Jul  4 11:58:26 2023 Busy with parsing bam file...
Process Process-1:
Traceback (most recent call last):
  File "/Users/kamada/anaconda3/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/Users/kamada/anaconda3/lib/python3.10/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/kamada/Downloads/NanoFG/venv/lib/python3.10/site-packages/nanosv/utils/../utils/parse_bam.py", line 112, in parse_chr_bam
    for item in header["SQ"]:
NameError: name 'header' is not defined

^CTraceback (most recent call last):
  File "/Users/kamada/Downloads/NanoFG/venv/bin/nanosv", line 8, in <module>
    sys.exit(main())
  File "/Users/kamada/Downloads/NanoFG/venv/lib/python3.10/site-packages/nanosv/NanoSV.py", line 71, in main
    utils.parse_bam.parse_bam()
  File "/Users/kamada/Downloads/NanoFG/venv/lib/python3.10/site-packages/nanosv/utils/../utils/parse_bam.py", line 70, in parse_bam
    time.sleep(5)    # Give tasks a chance to put more data in
KeyboardInterrupt

Also, I also tried running the tool with my own bam file and encountered the error below:

(venv) (base) kamada@Lalithas-MacBook-Pro NanoFG % bash NanoFG.sh -b /Users/kamada/Downloads/NanoFG/demo/demo_bamdir/output.bam
Tue Jul  4 12:20:13 CEST 2023    Running on Lalithas-MacBook-Pro.local
### bam (-b) already provided. Skipping minimap2 mapping
### No selection parameter (-s) provided. Using all mapped reads
Tue Jul  4 12:20:13 CEST 2023    SV calling...
Tue Jul  4 12:20:14 2023 Busy with parsing bam file...
Process Process-1:
Traceback (most recent call last):
  File "/Users/kamada/anaconda3/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/Users/kamada/anaconda3/lib/python3.10/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/Users/kamada/Downloads/NanoFG/venv/lib/python3.10/site-packages/nanosv/utils/../utils/parse_bam.py", line 112, in parse_chr_bam
    for item in header["SQ"]:
NameError: name 'header' is not defined
^CTraceback (most recent call last):
  File "/Users/kamada/Downloads/NanoFG/venv/bin/nanosv", line 8, in <module>
    sys.exit(main())
  File "/Users/kamada/Downloads/NanoFG/venv/lib/python3.10/site-packages/nanosv/NanoSV.py", line 71, in main
    utils.parse_bam.parse_bam()
  File "/Users/kamada/Downloads/NanoFG/venv/lib/python3.10/site-packages/nanosv/utils/../utils/parse_bam.py", line 70, in parse_bam
    time.sleep(5)    # Give tasks a chance to put more data in
KeyboardInterrupt

The header of output.bam is:

(base) kamada@Lalithas-MacBook-Pro demo_bamdir % samtools view -H output.bam
@HD VN:1.6  SO:coordinate
@SQ SN:chr1 LN:249250621
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr7 LN:159138663
@SQ SN:chrX LN:155270560
@SQ SN:chr8 LN:146364022
@SQ SN:chr9 LN:141213431
@SQ SN:chr10    LN:135534747
@SQ SN:chr11    LN:135006516
@SQ SN:chr12    LN:133851895
@SQ SN:chr13    LN:115169878
@SQ SN:chr14    LN:107349540
@SQ SN:chr15    LN:102531392
@SQ SN:chr16    LN:90354753
@SQ SN:chr17    LN:81195210
@SQ SN:chr18    LN:78077248
@SQ SN:chr20    LN:63025520
@SQ SN:chrY LN:59373566
@SQ SN:chr19    LN:59128983
@SQ SN:chr22    LN:51304566
@SQ SN:chr21    LN:48129895
@SQ SN:chr6_ssto_hap7   LN:4928567
@SQ SN:chr6_mcf_hap5    LN:4833398
@SQ SN:chr6_cox_hap2    LN:4795371
@SQ SN:chr6_mann_hap4   LN:4683263
@SQ SN:chr6_apd_hap1    LN:4622290
@SQ SN:chr6_qbl_hap6    LN:4611984
@SQ SN:chr6_dbb_hap3    LN:4610396
@SQ SN:chr17_ctg5_hap1  LN:1680828
@SQ SN:chr4_ctg9_hap1   LN:590426
@SQ SN:chr1_gl000192_random LN:547496
@SQ SN:chrUn_gl000225   LN:211173
@SQ SN:chr4_gl000194_random LN:191469
@SQ SN:chr4_gl000193_random LN:189789
@SQ SN:chr9_gl000200_random LN:187035
@SQ SN:chrUn_gl000222   LN:186861
@SQ SN:chrUn_gl000212   LN:186858
@SQ SN:chr7_gl000195_random LN:182896
@SQ SN:chrUn_gl000223   LN:180455
@SQ SN:chrUn_gl000224   LN:179693
@SQ SN:chrUn_gl000219   LN:179198
@SQ SN:chr17_gl000205_random    LN:174588
@SQ SN:chrUn_gl000215   LN:172545
@SQ SN:chrUn_gl000216   LN:172294
@SQ SN:chrUn_gl000217   LN:172149
@SQ SN:chr9_gl000199_random LN:169874
@SQ SN:chrUn_gl000211   LN:166566
@SQ SN:chrUn_gl000213   LN:164239
@SQ SN:chrUn_gl000220   LN:161802
@SQ SN:chrUn_gl000218   LN:161147
@SQ SN:chr19_gl000209_random    LN:159169
@SQ SN:chrUn_gl000221   LN:155397
@SQ SN:chrUn_gl000214   LN:137718
@SQ SN:chrUn_gl000228   LN:129120
@SQ SN:chrUn_gl000227   LN:128374
@SQ SN:chr1_gl000191_random LN:106433
@SQ SN:chr19_gl000208_random    LN:92689
@SQ SN:chr9_gl000198_random LN:90085
@SQ SN:chr17_gl000204_random    LN:81310
@SQ SN:chrUn_gl000233   LN:45941
@SQ SN:chrUn_gl000237   LN:45867
@SQ SN:chrUn_gl000230   LN:43691
@SQ SN:chrUn_gl000242   LN:43523
@SQ SN:chrUn_gl000243   LN:43341
@SQ SN:chrUn_gl000241   LN:42152
@SQ SN:chrUn_gl000236   LN:41934
@SQ SN:chrUn_gl000240   LN:41933
@SQ SN:chr17_gl000206_random    LN:41001
@SQ SN:chrUn_gl000232   LN:40652
@SQ SN:chrUn_gl000234   LN:40531
@SQ SN:chr11_gl000202_random    LN:40103
@SQ SN:chrUn_gl000238   LN:39939
@SQ SN:chrUn_gl000244   LN:39929
@SQ SN:chrUn_gl000248   LN:39786
@SQ SN:chr8_gl000196_random LN:38914
@SQ SN:chrUn_gl000249   LN:38502
@SQ SN:chrUn_gl000246   LN:38154
@SQ SN:chr17_gl000203_random    LN:37498
@SQ SN:chr8_gl000197_random LN:37175
@SQ SN:chrUn_gl000245   LN:36651
@SQ SN:chrUn_gl000247   LN:36422
@SQ SN:chr9_gl000201_random LN:36148
@SQ SN:chrUn_gl000235   LN:34474
@SQ SN:chrUn_gl000239   LN:33824
@SQ SN:chr21_gl000210_random    LN:27682
@SQ SN:chrUn_gl000231   LN:27386
@SQ SN:chrUn_gl000229   LN:19913
@SQ SN:chrM LN:16571
@SQ SN:chrUn_gl000226   LN:15008
@SQ SN:chr18_gl000207_random    LN:4262
@PG ID:aligner  PN:minimap2 VN:2.24-r1122
@PG ID:basecaller   PN:guppy    VN:6.5.7+ca6d6af    CL:guppy_basecaller --input_path ./ --save_path ../results_newbasecalling --num_callers 64 --flowcell FLO-MIN106 --kit SQK-CS9109 --compress_fastq --align_ref /gpfs/project/dik09gax/nanopore_seq/hg19.fa --bam_out --index
@RG ID:2eed4e4350523f2b62a858234c2335f032d35e00_2021-05-17_dna_r9.4.1_minion_384_d37a2ab9   SM:test_run DT:2023-06-20T14:16:17.080919+02:00 DS:runid=2eed4e4350523f2b62a858234c2335f032d35e00 basecall_model=2021-05-17_dna_r9.4.1_minion_384_d37a2ab9  LB:REH-697_1-1000   PL:ONT  PM:MN43522  PU:FAW66019 al:REH-697_1-1000
@PG ID:samtools PN:samtools PP:aligner  VN:1.7  CL:samtools reheader header.sam bam_runid_2eed4e4350523f2b62a858234c2335f032d35e00_0_0_sorted.bam
@PG ID:samtools.1   PN:samtools PP:basecaller   VN:1.7  CL:samtools reheader header.sam bam_runid_2eed4e4350523f2b62a858234c2335f032d35e00_0_0_sorted.bam
SdeBlank commented 1 year ago

Hey,

I am unsure if this the best fix possible, as the error occurs in the nanosv package, which I did not write. However, I forked it and changed something that for me seems to get through the "header" error.

Download the following github and change the path in the paths.ini file and see if it works: https://github.com/SdeBlank/nanosv