Question: VIROMESCAN; Srprism : inconsistent columns error
1
gravatar for nludowyke
10 months ago by
nludowyke10
nludowyke10 wrote:

Dear All,

I tried to analyse paired end fastq data of Illumina using Viromescan after successfully following the instructions given in sourceforge.net (files section) and ended up getting the following error.

" ./options_parser_priv.hpp:246 [3] argument missing (missing required option paired) ERROR: ./options_parser_priv.hpp:246 [3] argument missing (missing required option paired) <srprism.cpp:850> real 0m0.008s user 0m0.002s sys 0m0.000s FAILED: srprism for viromescan_sample_D/tmp//bmtagger.1564403652.pr615-Lenovo-Legion-Y530-15ICH.27953.short "

Then, I changed line 34 of bmtagger.sh from, srprismopts="-b 100000000 -n 5 -R 0 -r 1 -M 7168" to srprismopts="-b 100000000 -n 5 -R 0 -r 1 -M 7168 -p true" because I came across the following sentence in the bmtagger,.sh script.

"notes: "You may find it necessary to create a bmtagger.conf file to specify paired or single-end searching. The file should contain the line 'srprismopts=\"-b 100000000 -n 5 -R 0 -r 1 -M 7168\"' along with '-p true' or '-p false' for paired, and single, respectively. This config file can be passed to bmtagger.sh via the '-C' option." "

After the above correction, I am getting the below error.

paired_stream.hpp:154 [1] inconsistent columns (ids do not match: M05773:20:000000000-C8WP2:1:1101:16364:6851 , M05773:20:000000000-C8WP2:1:1101:13627:8301) ERROR: paired_stream.hpp:154 [1] inconsistent columns (ids do not match: M05773:20:000000000-C8WP2:1:1101:16364:6851 , M05773:20:000000000-C8WP2:1:1101:13627:8301) <srprism.cpp:850>

Appreciate if anyone could give me a suggestion to solve this problem. Thank you!

ADD COMMENTlink modified 6 months ago by Bioinfochen0 • written 10 months ago by nludowyke10
0
gravatar for Bioinfochen
6 months ago by
Bioinfochen0 wrote:

I had the same error when I used the Viromescan, Did you have solve the problem?

Appreciate if you could give me a suggestion for the problem. Thank you!

ADD COMMENTlink written 6 months ago by Bioinfochen0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1433 users visited in the last hour