Just checked recent weekly CI errors. Seems that
samtools sort output may depend on the number of used CPUs (sorting is correct, just the order of alignments with the same mapping position may differ). Wondering how to deal with this ..
Just check for the number of lines and maybe some regex (does this work for bam?)?
mapper | samtools sort -@2 ... | samtools -@\$GALAXY_SLOTS.. which also solves the problem the parallel sorting and mapping may use to many CPUs
I was trying to figure out why most of the tool tests of all versions of Pangolin 3.x fail on usegalaxy.org with:
AttributeError in line 112 of /usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/pangolin/scripts/pangolearn.smk: 'DecisionTreeClassifier' object has no attribute 'n_features_' File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/pangolin/scripts/pangolearn.smk", line 112, in __rule_pangolearn File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/pangolin/pangolearn/pangolearn.py", line 170, in assign_lineage File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/sklearn/tree/_classes.py", line 922, in predict_proba File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/site-packages/sklearn/tree/_classes.py", line 395, in _validate_X_predict File "/usr/local/tools/_conda/envs/mulled-v1-72f7a2d4de377591b330113007411515001882bdf41ef6a774876b7e70240654/lib/python3.8/concurrent/futures/thread.py", line 57, in run Exiting because a job execution failed. Look above for error message
Both conda and singularity, and so wanted to see how usegalaxy.eu had fixed it - turns out, it's broken on EU too.
Error: the input query fasta could not be parsed. Double check your query fasta and that compressed stdin was not passed. Please enter your fasta sequence file and refer to pangolin usage at: https://cov-lineages.org/pangolin.html for detailed instructions. Error: the input query fasta could not be parsed. Double check your query fasta and that compressed stdin was not passed. Please enter your fasta sequence file and refer to pangolin usage at: https://cov-lineages.org/pangolin.html for detailed instructions. rm: cannot remove '/data/jwd/main/046/882/46882007/tmp/out.3651279': No such file or directory rm: cannot remove '/data/jwd/main/046/882/46882007/tmp/err.3651279': No such file or directory
4.0.5+galaxy2in the toolshed already (not sure why it didn't get installed on .eu over the weekend), which addresses a few issues. Your error message really looks like something's wrong with your FASTA input though. If not, then what were the exact parameters you've been using?
> library('dissUtils') 2022-05-17T07:43:35.5948057Z Error in library("dissUtils") : there is no package called 'dissUtils'