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poeli / PanGIA

PanGIA (Pan-Genomics for Infectious Agents)
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Error: no module named 'mappy' #1

Open jagos01 opened 4 years ago

jagos01 commented 4 years ago

Hello, I get the following error while running PanGIA.

Traceback (most recent call last): File "./pangia.py", line 2278, in genome_size, host_genome = getStrainSize( argvs.database ) File "./pangia.py", line 2055, in getStrainSize import mappy ModuleNotFoundError: No module named 'mappy'

The command used was as follows: pangia.py -i /home/Desktop/guppy_basecalled/basecall_combined.fastq -d /home/data0/pangia_db/PanGIA/NCBI_genomesrefseq89*.fa.mmi -t 70 --keepTemp -rm minimap2

Does pangia currently work with minimap2 or only bwa? Are bwa index files available or do they have to be generated from the 20180915_NCBI_genomes_refseq89*.fa.tar files? I have attached the log file if need. basecall_combined.pangia.log

Thanks, Scott

jagos01 commented 4 years ago

So I installed the mappy module, pangia now returns the following error: Traceback (most recent call last): File "/home/DRDC/pangia/pangia.py", line 2320, in res_rollup = taxonomyRollUp(res, patho_meta, mapped_r_cnt, argvs.minRsnb, argvs.minReads, argvs.minLen, argvs.minCov, argvs.minDc) File "/home/pangia/pangia.py", line 1199, in taxonomyRollUp genome_size[taxid] KeyError: '546272'

I also noticed lines 2052 & 2053 in pangia.py are WARNING: This is not working!!! The mappy library seems to have issue not reporting all seq_names. Should bwa be used instead of minimap2? Thanks, Scott

poeli commented 4 years ago

Hey Scott,

I don't think I use mappy anymore (as comment). Will get back to you shortly.

Thanks, Paul

jagos01 commented 4 years ago

Hello Paul, Depending on the dataset used, the error reported earlier generates a KeyError for different taxid. Thanks for your help. Scott

On Wed., Aug. 19, 2020, 9:39 a.m. poeli, notifications@github.com wrote:

Hey Scott,

I don't think I use mappy anymore (as comment). Will get back to you shortly.

Thanks, Paul

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/poeli/PanGIA/issues/1#issuecomment-676502400, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALWFTRETDHQR5WC2DL2VE5LSBPW2LANCNFSM4QCLLWPA .

jagos01 commented 4 years ago

I could not get this to work with the .mmi files alone. I needed to include the bwa index files for PanGIA to work. Thanks, Scott