Key error and custom database error

[jagos01]

Hello,
I am having a couple of problems when trying to classify nanopore reads with PanGIA.

1. When trying to classify a mix of 15 isolates PanGIA exits with the following error:
   (pangia.py -i /home/Analyzed_data/ATCC_gDNAs_plasmid_mix/mix.ghac.fastq -db /home/data0/pangia_db/PanGIA/NCBI_genomes_refseq89_*.fa -t 70 --keepTemp -sb -se -np )

Parsing SAM files with 70 subprocesses...
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/mnt/data0/miniconda3/envs/pangia/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/home/pangia/pangia.py", line 714, in worker
lcr_lvl, lcr_name, lcr_info = lineageLCR(taxids)
File "/home/pangia/pangia.py", line 378, in lineageLCR
lng = t.taxid2lineageDICT(tid, 1, 1)
File "/home/pangia/taxonomy.py", line 265, in taxid2lineageDICT
return _taxid2lineage( tid, print_all_rank, print_strain, replace_space2underscore, output_type )
File "/home/pangia/taxonomy.py", line 305, in _taxid2lineage
rank = _getTaxRank(taxID)
File "/home/pangia/taxonomy.py", line 372, in _getTaxRank
return taxRanks[taxID]
KeyError: '134962'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/pangia/pangia.py", line 2316, in
(res, mapped_r_cnt) = processSAMfile( os.path.abspath(samfile), argvs.threads, lines_per_process)
File "/home/pangia/pangia.py", line 921, in processSAMfile
results.append( job.get() )
File "/mnt/data0/miniconda3/envs/pangia/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
KeyError: '134962'

2. When trying to classify a single isolate with a custom built database, PanGIA exits with the following error:
   [00:05:49] Saving bitmasks in JSON format...
   [00:05:49] Done.
   Traceback (most recent call last):
   File "/home/DRDC/pangia/pangia.py", line 2357, in
   outputResultsAsReport( res_rollup, out_fp, argvs.relAbu, argvs.taxonomy, argvs.reportFields, argvs.scoreMethod, argvs.minScore, argvs.minCov, argvs.minRsnb, argvs.minReads, argvs.minLen, argvs.minDc, argvs.minRsdcnr, argvs.displayAll )
   File "/home/DRDC/pangia/pangia.py", line 1677, in outputResultsAsReport
   s = "%.6f"%res_rollup[tid]["S_SA_CL"] if res_rollup[tid]["S_SA_CL"] != "none" else "none"
   TypeError: must be real number, not str

Any help would be appreciated.
Thanks,
Scott

[poeli-lanl]

Hi Scott,

I'm on this. I have identified the errors and will push a patch real soon.

Thanks,
Paul

[jagos01]

Thanks Paul.

…

On Wed., Jan. 13, 2021, 1:39 p.m. Po-E Li, ***@***.***> wrote: Hi Scott, I'm on this. I have identified the errors and will push a patch real soon. Thanks, Paul — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALWFTRG5UUH7JYC3FRPGHQLSZYAJJANCNFSM4V6VARJA> .