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KeyError in unknownMods(), mmquant.py #9
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If I set the option is there another way to solve this issue, without changing '--misinc-thresh '? can anybody explain why this error is thrown and what it exactly means? Thanks! |
Hi Uwe, First of all, could you tell me which version of mimseq you are using by typing The problem seems to be coming from new mods detection where a non-existent entry for a tRNA (Homo_sapiens_tRNA-Ala-AGC-2-1) is being looked up but does not exist. We've had similar issues in the past, and I've worked to solve them. Unfortunately, with new data such as yours, some new specific cases can arise. I would be happy to try fix this bug but I would need to be able to recreate the error. This means having access to the sequencing data you are using as input (or at least a subset of this which would hopefully be enough to recreate the issue). |
Hi Drew, thanks for the response. I was running version: mimseq 0.3.4.1 |
Hi @uschwartz, |
Hi Drew, Sounds great! I will upgrade mimseq and test it. As soon as I have the results I will let you know |
Hi,
I am trying to run mim-tRNAseq and I am ending in an "KeyError:'Homo_sapiens_tRNA-Ala-AGC-2-1'"
This is my code:
mimseq -t $AnnoDir'/'hg19-tRNAs.fa \ -o $AnnoDir'/'hg19-tRNAs.out.nohap \ -m $AnnoDir'/'hg19-mitotRNAs.fa \ --cluster --cluster-id 0.95 \ --threads 15 --min-cov 2000 \ --max-mismatches 0.1 \ --control-condition Input \ -n TD1_IP \ --out-dir $outDir'/02_default_hg19' \ --max-multi 4 --remap --remap-mismatches 0.075 \ $AnalysisDir'/script/mim-trnaseq/normal_Samples.tsv'
I tried to use the provided tRNA annotation of hg19 and GRCh38, but both end up in the same error :
`
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/Users/admin/anaconda3/envs/mimseq/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/Users/admin/anaconda3/envs/mimseq/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/Users/admin/anaconda3/envs/mimseq/lib/python3.7/site-packages/mimseq/mmQuant.py", line 274, in bamMods_mp
new_mods, new_Inosines = unknownMods(inputs, knownTable, cluster_dict, modTable_prop, misinc_thresh, cov_table_newMods, min_cov, tRNA_dict, remap)
File "/Users/admin/anaconda3/envs/mimseq/lib/python3.7/site-packages/mimseq/mmQuant.py", line 73, in unknownMods
if (sum(modTable[isodecoder][pos].values()) >= misinc_thresh and any(cov >= min_cov) and pos-1 not in knownTable[isodecoder]): # misinc above threshold, cov above threshold and not previously known
KeyError: 'Homo_sapiens_tRNA-Ala-AGC-2-1'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/admin/anaconda3/envs/mimseq/bin/mimseq", line 10, in
sys.exit(main())
File "/Users/admin/anaconda3/envs/mimseq/lib/python3.7/site-packages/mimseq/mimseq.py", line 361, in main
args.misinc_thresh, args.mito, args.pretrnas, args.local_mod, args.sampledata)
File "/Users/admin/anaconda3/envs/mimseq/lib/python3.7/site-packages/mimseq/mimseq.py", line 135, in mimseq
new_mods, new_Inosines, filtered_cov, filter_warning = generateModsTable(coverageData, out, name, threads, min_cov, mismatch_dict, insert_dict, del_dict, cluster_dict, cca, remap, misinc_thresh, new_mod_lists, Inosine_lists, newtRNA_dict, Inosine_clusters, unique_isodecoderMMs, newSplitBool, isodecoder_sizes, cluster)
File "/Users/admin/anaconda3/envs/mimseq/lib/python3.7/site-packages/mimseq/mmQuant.py", line 598, in generateModsTable
new_mods, new_Inosines = zip(*pool.map(func, bamlist))
File "/Users/admin/anaconda3/envs/mimseq/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/Users/admin/anaconda3/envs/mimseq/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
KeyError: 'Homo_sapiens_tRNA-Ala-AGC-2-1'
`
Thanks for helping
Uwe
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