Yves, These are the results: 110901_6_12_random_1 110901_6_12_random_2 Στις Πέμ, 8 Αυγ 2019 στις 2:06 μ.μ., ο/η Yves Wetzels yveswetzels@users.sourceforge.net έγραψε: 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 %0Danastmx@users.sourceforge.net: Mr Yves, I commented all commands exept the "map_vs_consensus.pl". The ./run.sh returned on the VirVarSeq.log...
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...
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 44. 2019-08-07 19:27:12 ./map_vs_consensus.pl 3.1 Get sample names from file [./testdata/samples.txt]... " Thanks!
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...
Mr Yves, Thanks for the quick response, the ls -lrt testdata/results/* command returned me this: results/map_vs_consensus: total 0 results/codon_table: total 0 results/mixture_model: total 0 results/map_vs_ref: total 1104884 -rw-r--r-- 1 ubagen-2 ubagen-2 17515360 Jul 29 16:02 110901_6_12_random_1.1.sai -rw-r--r-- 1 ubagen-2 ubagen-2 17735008 Jul 29 16:05 110901_6_12_random_1.2.sai -rw-r--r-- 1 ubagen-2 ubagen-2 530442673 Jul 29 16:05 110901_6_12_random_1.sam -rw-r--r-- 1 ubagen-2 ubagen-2 17515360...
Mr Yves, Thanks for the quick response, the ls -lrt testdata/results/* is: results/map_vs_consensus: total 0 results/codon_table: total 0 results/mixture_model: total 0 results/map_vs_ref: total 1104884 -rw-r--r-- 1 ubagen-2 ubagen-2 17515360 Jul 29 16:02 110901_6_12_random_1.1.sai -rw-r--r-- 1 ubagen-2 ubagen-2 17735008 Jul 29 16:05 110901_6_12_random_1.2.sai -rw-r--r-- 1 ubagen-2 ubagen-2 530442673 Jul 29 16:05 110901_6_12_random_1.sam -rw-r--r-- 1 ubagen-2 ubagen-2 17515360 Jul 29 16:09 110901_6_12_random_2.1.sai...
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--...
Greetings, I' am trying to run the program but i am facing some issues. I'am getting this error: Undefined subroutine &Files::openFile calles at ./map_vsconsensus.pl line 44 and after some prints Could not open ./testdata/results/map_vs_consensus/110901_6_12_random_1.sam and after some prints again... Error in file(file,"rt") : Cannot open the connection Calls: read.delim -> read.table -> file The program seems to work fine in the beggining but after a bit it fails with the above error messages....
Hi, After running your software on the test dataset you provided, I get the output codon table with the following headers: SAMPLE POSITION REF_CODON CODON REF_AA AA FWD_CNT FWD_DENOM REV_CNT REV_DENOM FWD_MEAN_MIN_QUAL REV_MEAN_MIN_QUAL FWD_FREQ REV_FREQ LOW_FREQ LOW_FREQ_DIRECTION FWD_STDDEV_MIN_QUAL REV_STDDEV_MIN_QUAL CNT DENOM FREQ What do each of these headers mean? Where can I find the explanation of these headers? Thanks Rahil
Hi, I avving some issues when running ./map_vs_ref.pl, which instead of generating the .sam file it sends the content to the log file, which makes other scripts in the pipeline fail. Any ideas, Thanks, Selene
Hi, I used your pieline, but ./map_vs_ref.pl fails to create the.sam file, it prints it out in the log instead, therefore when it tries to generate the consensus it cannot locate the file. Any ideas? Thanks, Selene
I think you have some trouble between the file samples.txt and the name of the folder...
hi im trying to run the virvarseq pipline its starts good but than in the ./map_vs_ref.pl...
Thanks Luca
Hi Luca Yes, I think this is correct. Cheers Yves 2015-04-27 15:22 GMT+02:00 luca...
Hi Yves Thanks you for your answer. I converted .sam to .bam file and then extracted...
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Hi, how can I find the number of mapped reads best regards Luca
Hi, I can comment on this one. This is a bug introduced in bwa aln after version...
Hi Radko Since the pipeline runs on our test HCV data proofs all is in place. If...
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Hi Radko It seems there is something wrong with bwa. In the logfile you should see...
Dear Yves Wetzels Thank you for your answer. I attached log file. I use Linux. I...
Hi Radko Do you have all pre-requisites in place? (BWA, R, ...) What OS are you running?...
Please check if the Perl scripts (and the run.sh) have the execute permission. [sbsuser@pipeline...
I am having some trouble installing VirVarSeq. I should clarify that I am working...
indel stats in seperate subfunction
Added indel table
Deleted folder testdata
Initial commit
