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sanger-pathogens / seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads
https://sanger-pathogens.github.io/seroba/
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seroba stopping signal recieved 28 #45

Closed varunshamanna closed 5 years ago

varunshamanna commented 5 years ago

cluster detected 1 threads available to it cluster reported completion The following command failed with exit code 1 rm -rf /media/crlkims/Data_Vol_1/ROSE/Wghole_genome_sequencing_pneumoniae/RawData_385/ERR1638455/fastq_files/seroba_out/ref/ariba.tmp.1_w_k7u0/cluster

The output was:

rm: cannot remove '/media/crlkims/Data_Vol_1/ROSE/Wghole_genome_sequencing_pneumoniae/RawData_385/ERR1638455/fastq_files/seroba_out/ref/ariba.tmp.1_w_k7u0/cluster': Directory not empty

Stopping! Signal received: 28 Traceback (most recent call last): File "/home/crlkims/anaconda2/bin/seroba", line 4, in import('pkg_resources').run_script('seroba==1.0.1', 'seroba') File "/home/crlkims/.local/lib/python3.6/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/crlkims/.local/lib/python3.6/site-packages/pkg_resources/init.py", line 1460, in run_script exec(script_code, namespace, namespace) File "/home/crlkims/anaconda2/lib/python3.6/site-packages/seroba-1.0.1-py3.6.egg/EGG-INFO/scripts/seroba", line 86, in File "/home/crlkims/anaconda2/lib/python3.6/site-packages/seroba-1.0.1-py3.6.egg/seroba/tasks/sero_run.py", line 19, in run File "/home/crlkims/anaconda2/lib/python3.6/site-packages/seroba-1.0.1-py3.6.egg/seroba/serotyping.py", line 480, in run File "/home/crlkims/anaconda2/lib/python3.6/site-packages/seroba-1.0.1-py3.6.egg/seroba/serotyping.py", line 94, in _run_ariba_on_cluster File "/home/crlkims/anaconda2/lib/python3.6/shutil.py", line 120, in copyfile with open(src, 'rb') as fsrc: FileNotFoundError: [Errno 2] No such file or directory: 'seroba_out/genes/assembled_genes.fa.gz'

I am gettig report.tsv but its not complete

eppinglen commented 5 years ago

looks like a problem with ARIBA. Which version of python are you using?

tseemann commented 5 years ago

@eppinglen the error messages have python3.6 in them. but they are using Ananconda2 ... i would move to miniconda3

varunshamanna commented 5 years ago

Yes i was using anaconda2, i moved to conda3 now working fine