Yves Wetzels

Hi Anastasios not sure what is going wrong. Can you cat the output of file './testdata/samples.txt'? Kind Regards Yves Op wo 7 aug. 2019 om 18:31 schreef Anastasios Mx anastmx@users.sourceforge.net: Mr Yves, I commented all commands exept the "map_vs_consensus.pl". The ./run.sh returned on the VirVarSeq.log (I didnt redirect the output) this: " 2019-08-07 19:27:12 ./map_vs_consensus.pl 3.0 Checking command line arguments ... Undefined subroutine &Files::openFile called at ./map_vs_consensus.pl line...

Hi Anastasios Since I don't see any files in the 'map_vs_consensus' it is likely that something went wrong with the 3 step 'map_vs_consensus.pl'. Can you please modify the run.sh script and put all commands in comment and only execute the 'mapping versus consensus' step? You could remove the redirection to the logfile to see what the script is doing. for example: [ywetzel@awsabiirl1105 VirVarSeq]$ more run.sh indir=./testdata/fastq outdir=./testdata/results samples=./testdata/samples.txt ref=./testdata/ref/1b_con1_AJ238799.NCBI.fa...

Hi Anastasios Could you to a listing of the files in the 'results' directory like [ywetzel@awsabiirl1105 VirVarSeq]$ ls -lrt testdata/results/* testdata/results/map_vs_ref: total 1104880 -rw-r--r-- 1 ywetzel zusers 17515360 Jul 29 16:32 110901_6_12_random_1.1.sai -rw-r--r-- 1 ywetzel zusers 17735008 Jul 29 16:33 110901_6_12_random_1.2.sai -rw-r--r-- 1 ywetzel zusers 530443090 Jul 29 16:34 110901_6_12_random_1.sam -rw-r--r-- 1 ywetzel zusers 17515360 Jul 29 16:35 110901_6_12_random_2.1.sai -rw-r--r--...

Hi Luca Yes, I think this is correct. Cheers Yves 2015-04-27 15:22 GMT+02:00 luca...

Hi Luca The number of mapped reads is not available as output. The only thing I think...

Hi Radko Since the pipeline runs on our test HCV data proofs all is in place. If...

Hi Radko Avi I can see an error in your VirVarSeq.txt logfile in the refine gapped...

Hi Radko It seems there is something wrong with bwa. In the logfile you should see...