'call' phase fails - no inversions?

ggstatgen commented 5 years ago

Hi

The pipeline is failing at 'call' stage. I believe, but I might be wrong, the exception is caused by lack of called inversions.

This is the exception:

[Mon Mar 25 13:00:27 2019]                                                                                                                                                                
rule call_tile_contigs_from_alignments:                                                     
    input: assemble/local_assemblies.bam                                                                                                                                                      output: call/tiling_contigs.tab                     
    jobid: 45                                                                                                            

[Mon Mar 25 13:04:10 2019]               
Finished job 45.                                                    
7 of 46 steps (15%) done          

[Mon Mar 25 13:04:10 2019]                                                        
rule call_merge_inversions:                                                                                      
    input: call/sv_calls/inversions.bed, assemble/local_assemblies.bam
    output: call/sv_calls/merged_inversions.bed                                                                                                       
    jobid: 7                  

localrules directive specifies rules that are not present in the Snakefile:
        call_variants

Job counts:                                                                                          
        count   jobs      
        1       call_merge_inversions           
        1       
[Mon Mar 25 13:04:11 2019]     
Finished job 7.
8 of 46 steps (17%) done

[Mon Mar 25 13:04:11 2019]
rule call_convert_inversion_bed_to_vcf:
    input: call/sv_calls/merged_inversions.bed, reference/ref.fasta
    output: call/inversions.vcf
    jobid: 4

Traceback (most recent call last):
  File "<CODE>/smrtsv2/scripts/call/variants_bed_to_vcf.py", line 133, in <module>
    convert_bed_to_vcf(args.bed, args.reference, args.vcf, args.sample, args.type)
  File "<CODE>/smrtsv2/scripts/call/variants_bed_to_vcf.py", line 35, in convert_bed_to_vcf
    calls["quality"] = calls.apply(calculate_variant_quality, axis=1)
  File "<CODE>/smrtsv2/dep/conda/build/envs/python2/lib/python2.7/site-packages/pandas/core/frame.py", line 3119, in __setitem__
    self._set_item(key, value)
  File "<CODE>/smrtsv2/dep/conda/build/envs/python2/lib/python2.7/site-packages/pandas/core/frame.py", line 3193, in _set_item
    self._ensure_valid_index(value)
  File "<CODE>/smrtsv2/dep/conda/build/envs/python2/lib/python2.7/site-packages/pandas/core/frame.py", line 3175, in _ensure_valid_index
    raise ValueError('Cannot set a frame with no defined index '
ValueError: Cannot set a frame with no defined index and a value that cannot be converted to a Series
[Mon Mar 25 13:04:11 2019]
Error in rule call_convert_inversion_bed_to_vcf:
    jobid: 4
    output: call/inversions.vcf

After the above, in the /call/sv_calls directory I see the following

-rw-rw---- [...] 40177608 Mar 25 12:36 gaps.bed
-rw-rw---- [...]        0 Mar 25 12:53 inversions.bed
-rw-rw---- [...] 10535423 Mar 25 12:57 calls.ins.bed
-rw-rw---- [...] 5694580 Mar 25 13:00 calls.del.bed
-rw-rw---- [...] 0 Mar 25 13:04 merged_inversions.bed

Any suggestions? Thanks!

paudano commented 5 years ago

Pull the latest commit into the repository (git pull). Commit e6e39bb93bc1ee121d604f10e5561761b891f6b1 fixed this or a similar issue. Let me know if it solved the problem.

ggstatgen commented 5 years ago

This solved it - thanks so much.

EichlerLab / smrtsv2

'call' phase fails - no inversions? #25