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Anastasios Mx — Wed, 07 Aug 2019 16:31:19 -0000

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!

Discussion for Home page

Anastasios Mx — Thu, 01 Aug 2019 14:19:59 -0000

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
-rw-r--r-- 1 ubagen-2 ubagen-2 17735008 Jul 29 16:12 110901_6_12_random_2.2.sai
-rw-r--r-- 1 ubagen-2 ubagen-2 530442673 Jul 29 16:13 110901_6_12_random_2.sam

results/consensus:
total 24
-rw-r--r-- 1 ubagen-2 ubagen-2 9628 Jul 29 16:31 110901_6_12_random_1_consensus.fa
-rw-r--r-- 1 ubagen-2 ubagen-2 9628 Jul 29 16:32 110901_6_12_random_2_consensus.fa

If i type on my terminal (>bwa), it prints the bwa info, soo bwa seems to be in PATH and work (?)
Thanks in advance!

Discussion for Home page

Anastasios Mx — Mon, 29 Jul 2019 12:55:58 -0000

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.
Any suggestions? Thanks! (I'll attach the .log file too)

Discussion for Home page

Rahil Sethi — Mon, 13 Nov 2017 19:50:07 -0000

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

Discussion for Home page

Selene Zarate — Thu, 12 Oct 2017 20:41:38 -0000

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

Discussion for Home page

Selene Zarate — Thu, 12 Oct 2017 20:35:27 -0000

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

Discussion for Home page

luca carioti — Mon, 13 Feb 2017 16:52:51 -0000

I think you have some trouble between the file samples.txt and the name of the folder where you localize the fastq.gz file

IHTH

Discussion for Home page

Efrat Bucris — Tue, 31 Jan 2017 13:34:14 -0000

hi im trying to run the virvarseq pipline its starts good but than in the ./map_vs_ref.pl script its doenwt recognize my sample name, there is '*' insted of '.'
see here:

-2017-01-31 10:09:24 ./map_vs_ref.pl 1.4.1 Locate reads ...
ls: cannot access /home/efrat/Downloads/VirVarSeq/miseq5/fastq/Sample_/R1gz: No such file or directory
ls: cannot access /home/efrat/Downloads/VirVarSeq/miseq5/fastq/Sample_/R2gz: No such file or directory

this is all the log file:

017-01-31 10:09:12 ./map_vs_ref.pl 1.0 Checking command line arguments ...
2017-01-31 10:09:12 ./map_vs_ref.pl 1.1 Checking input and output locations ...
2017-01-31 10:09:12 ./map_vs_ref.pl |--- Check fastq dir ...
2017-01-31 10:09:12 ./map_vs_ref.pl |--- Check map_vs_ref dir ...
2017-01-31 10:09:12 ./map_vs_ref.pl 1.2 Load in reference ...
2017-01-31 10:09:12 ./map_vs_ref.pl 1.3 Get sample names from file [/home/efrat/Downloads/VirVarSeq/miseq5/samples.txt]...
2017-01-31 10:09:12 ./map_vs_ref.pl 1.4 Do read mapping and save SAM file ...
2017-01-31 10:09:12 ./map_vs_ref.pl 1.4.1 Locate reads ...
2017-01-31 10:09:13 ./map_vs_ref.pl 1.4.2 Map reads for sample [110901_6_12_random_1] ...
2017-01-31 10:09:13 ./map_vs_ref.pl !---- Paired end mapping using /home/efrat/Downloads/VirVarSeq/miseq5/fastq/Sample_110901_6_12_random_1/110901_6_12_random_1_CTTGTA_L006_R1_001.fastq.gz /home/efrat/Downloads/VirVarSeq/miseq5/fastq/Sample_110901_6_12_random_1/110901_6_12_random_1_CTTGTA_L006_R2_001.fastq.gz ...
2017-01-31 10:09:13 ./map_vs_ref.pl Start aligning read
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.70 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 33933 sequences have been processed.
[main] Version: 0.7.5a-r405
[main] CMD: bwa aln -t 8 -q 15 -n 12 -k 6 -f /home/efrat/Downloads/VirVarSeq/miseq5/results/map_vs_ref/110901_6_12_random_1.1.sai /home/efrat/Downloads/VirVarSeq/miseq5/ref/HXB2.fasta /home/efrat/Downloads/VirVarSeq/miseq5/fastq/Sample_110901_6_12_random_1/110901_6_12_random_1_CTTGTA_L006_R1_001.fastq.gz
[main] Real time: 4.898 sec; CPU: 36.804 sec
2017-01-31 10:09:17 ./map_vs_ref.pl End aligning read
2017-01-31 10:09:17 ./map_vs_ref.pl Start aligning read
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 36.01 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 33933 sequences have been processed.
[main] Version: 0.7.5a-r405
[main] CMD: bwa aln -t 8 -q 15 -n 12 -k 6 -f /home/efrat/Downloads/VirVarSeq/miseq5/results/map_vs_ref/110901_6_12_random_1.2.sai /home/efrat/Downloads/VirVarSeq/miseq5/ref/HXB2.fasta /home/efrat/Downloads/VirVarSeq/miseq5/fastq/Sample_110901_6_12_random_1/110901_6_12_random_1_CTTGTA_L006_R2_001.fastq.gz
[main] Real time: 4.804 sec; CPU: 36.116 sec
2017-01-31 10:09:22 ./map_vs_ref.pl End aligning read
2017-01-31 10:09:22 ./map_vs_ref.pl Start generating paired alignment
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (142, 219, 311)
[infer_isize] low and high boundaries: 251 and 649 for estimating avg and std
[infer_isize] inferred external isize from 6751 pairs: 361.615 +/- 89.942
[infer_isize] skewness: 0.950; kurtosis: 0.175; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 793 (4.80 sigma)
[bwa_sai2sam_pe_core] time elapses: 0.09 sec
[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 6614 out of 7236 Q17 singletons are mated.
[bwa_paired_sw] 0 out of 10410 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.01 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.08 sec
[bwa_sai2sam_pe_core] print alignments... 0.10 sec
[bwa_sai2sam_pe_core] 33933 sequences have been processed.
[main] Version: 0.7.5a-r405
[main] CMD: bwa sampe -P -f /home/efrat/Downloads/VirVarSeq/miseq5/results/map_vs_ref/110901_6_12_random_1.sam /home/efrat/Downloads/VirVarSeq/miseq5/ref/HXB2.fasta /home/efrat/Downloads/VirVarSeq/miseq5/results/map_vs_ref/110901_6_12_random_1.1.sai /home/efrat/Downloads/VirVarSeq/miseq5/results/map_vs_ref/110901_6_12_random_1.2.sai /home/efrat/Downloads/VirVarSeq/miseq5/fastq/Sample_110901_6_12_random_1/110901_6_12_random_1_CTTGTA_L006_R1_001.fastq.gz /home/efrat/Downloads/VirVarSeq/miseq5/fastq/Sample_110901_6_12_random_1/110901_6_12_random_1_CTTGTA_L006_R2_001.fastq.gz
[main] Real time: 1.653 sec; CPU: 1.520 sec
2017-01-31 10:09:24 ./map_vs_ref.pl End generating paired alignment
2017-01-31 10:09:24 ./map_vs_ref.pl 1.5 End.
2017-01-31 10:09:24 ./map_vs_ref.pl 1.4.1 Locate reads ...
ls: cannot access /home/efrat/Downloads/VirVarSeq/miseq5/fastq/Sample_/R1gz: No such file or directory
ls: cannot access /home/efrat/Downloads/VirVarSeq/miseq5/fastq/Sample_/R2gz: No such file or directory
2017-01-31 10:09:24 ./map_vs_ref.pl 1.4.2 Map reads for sample [] ...
2017-01-31 10:09:24 ./map_vs_ref.pl !---- Paired end mapping using ...
2017-01-31 10:09:24 ./map_vs_ref.pl Start aligning read

Usage: bwa aln [options] <prefix> <in.fq>

Options: -n NUM max #diff (int) or missing prob under 0.02 err rate (float) [-1.00]
-o INT maximum number or fraction of gap opens [1]
-e INT maximum number of gap extensions, -1 for disabling long gaps [-1]
-i INT do not put an indel within INT bp towards the ends [5]
-d INT maximum occurrences for extending a long deletion [10]
-l INT seed length [32]
-k INT maximum differences in the seed [6]
-m INT maximum entries in the queue [2000000]
-t INT number of threads [8]
-M INT mismatch penalty [3]
-O INT gap open penalty [11]
-E INT gap extension penalty [4]
-R INT stop searching when there are >INT equally best hits [30]
-q INT quality threshold for read trimming down to 35bp [15]
-f FILE file to write output to instead of stdout
-B INT length of barcode
-L log-scaled gap penalty for long deletions
-N non-iterative mode: search for all n-difference hits (slooow)
-I the input is in the Illumina 1.3+ FASTQ-like format
-b the input read file is in the BAM format
-0 use single-end reads only (effective with -b)
-1 use the 1st read in a pair (effective with -b)
-2 use the 2nd read in a pair (effective with -b)
-Y filter Casava-filtered sequences

2017-01-31 10:09:24 ./map_vs_ref.pl End aligning read
2017-01-31 10:09:24 ./map_vs_ref.pl Start aligning read

somone know why?
thanks
efrat

Discussion for Home page

luca carioti — Tue, 28 Apr 2015 08:50:05 -0000

Thanks

Luca

Discussion for Home page

luca carioti — Mon, 27 Apr 2015 13:22:29 -0000

Hi Yves

Thanks you for your answer.
I converted .sam to .bam file and then extracted the numer of mapped reads by samtools

Can this be appropriate?

Best,

Luca