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rajewsky-lab / mirdeep2

Discovering known and novel miRNAs from small RNA sequencing data
GNU General Public License v3.0
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quantifier.pl not generating pdf files #85

Closed hzuzu closed 2 years ago

hzuzu commented 2 years ago

I am trying to quantify the miRNA's using the quantifier.pl and ran into an error where pdf's are not generated however, all the other files are generated ( html, expressed csv file etc).

Here is the error from the log:

creating PDF files Can't use string ("38") as a HASH ref while "strict refs" in use at mirdeep2/bin/make_html2.pl line 658.

First I ran the mapper.pl module to collapse the reads

mapper.pl read.fastq -e -m -h -s reads.collapsed.fasta

and then ran the quantifier.pl module to quantifiy the miRNA's quantifier.pl -p precursor.fa -m mature.fa -r reads.collapsed.fasta -s star.fa

The mapper.pl worked fine but the end of the quantifier.pl threw an error and did not generate pdf files. Below is a complete log of quantifier.pl:

getting samples and corresponding read numbers

Converting input files building bowtie index mapping mature sequences against index mapping read sequences against index Mapping statistics

desc total mapped unmapped %mapped %unmapped

total: 21678093 8113468 13564625 37.427 62.573 seq: 21678093 8113468 13564625 37.427 62.573 mapping star sequences against index analyzing data

655 mature mappings to precursors

656 star mappings to precursors

Expressed miRNAs are written to expression_analyses/expression_analyses_1632496498/miRNA_expressed.csv not expressed miRNAs are written to expression_analyses/expression_analyses_1632496498/miRNA_not_expressed.csv

Creating miRBase.mrd file

Mapped READS readin - DONE

make_html2.pl -q expression_analyses/expression_analyses_1632496498/miRBase.mrd -k novel_mature.fa -y 1632496498 -o -i expression_analyses/expression_analyses_1632496498/mature.fa_mapped.arf -j expression_analyses/expression_analyses_1632496498/star.fa_mapped.arf -l -M miRNAs_expressed_all_samples_1632496498.csv miRNAs_expressed_all_samples_1632496498.csv file with miRNA expression values parsing miRBase.mrd file finished creating PDF files Can't use string ("38") as a HASH ref while "strict refs" in use at mirdeep2/bin/make_html2.pl line 658.

hzuzu commented 2 years ago

Closing this issue, as Am not getting it anymore, not sure what resolved it!