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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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Error, fewer reads in file specified with -1 than in file specified with -2 #786

Closed franccalabrese closed 2 months ago

franccalabrese commented 5 months ago

I used your pipe in the past three years and I thank you for the great effort. While running the pipe on huge-size metatranscriptomics files (more than 230M reads), in merged mode, I met an error that prevented the pipe from ongoing and made it stop at step 10. The error says

"Error, fewer reads in file specified with -1 than in file specified with -2" terminate called recursively terminate called after throwing an instance of 'int' Aborted (core dumped) (ERR): bowtie2-align exited with value 134

May you please indicate if in your opinion this is dependent on $accumrpk/=1000000 in 10.mapsamples.pl script? As a second question, I asked if by installing the new conda version of the SqueezeMeta pipeline this error could be avoided. Many thanks for your time and work.

jtamames commented 5 months ago

Hello Could you please share your syslog and your samples file? This should not be dependent of the calculation of abundances, but rather of the input sequences. Then I don´t think a new installation will solve this issue. Letś take a look at your data first. Best, J

franccalabrese commented 5 months ago

syslog.txt

jtamames commented 5 months ago

Could you please check the number of entries in /media/francesco/DATA/SqueezeMeta/try_2sample_OUTPUT/temp/try_2sample_OUTPUT.BS_2A.current_1.gz and /media/francesco/DATA/SqueezeMeta/try_2sample_OUTPUT/temp/try_2sample_OUTPUT.BS_2A.current_2.gz? Just type: zcat /media/francesco/DATA/SqueezeMeta/try_2sample_OUTPUT/temp/try_2sample_OUTPUT.BS_2A.current_1.gz | wc; zcat /media/francesco/DATA/SqueezeMeta/try_2sample_OUTPUT/temp/try_2sample_OUTPUT.BS_2A.current_2.gz | wc

franccalabrese commented 5 months ago

many thanks. The outputs indicate different count sizes. Moreover, for the first sample an invalid compressed data--crc error has been detected.

~/Documenti$ zcat try_2sample_OUTPUT.BS_2A.current_2.gz | wc 448441572 560551965 41757347723 ~/Documenti$ zcat try_2sample_OUTPUT.BS_2A.current_1.gz | wc gzip: try_2sample_OUTPUT.BS_2A.current_1.gz: invalid compressed data--crc error 266529844 333162305 24818329625

jtamames commented 5 months ago

It looks like the first file is corrupted. Could you fix it and run the analysis again?

fpusan commented 2 months ago

Closing due to lack of activity, feel free to reopen