search

egaffo / circompara2

Improved bioinformatic pipeline to identify and quantify circRNA expression from RNA-seq data by combining multiple circRNA detection methods
Other
7 stars 0 forks source link

Error in strsplit(grep("Sequence length", x = fastqc_data.txt, value = T), : subscript out of bounds #22

Open wer7894562 opened 10 months ago

wer7894562 commented 10 months ago

Hi egaffo, I'm trying to run circompara on my samples, but I got the following error:

echo "No reads in /home/aaa/Desktop/circompara2/test_circompara/reads/SRR12383421_2.fastq.gz" > samples/SRR12383421/read_statistics/fastqc_stats/SRR12383421_2_fastqc.html && echo "No reads in /home/aaa/Desktop/circompara2/test_circompara/reads/SRR12383421_2.fastq.gz" > samples/SRR12383421/read_statistics/fastqc_stats/SRR12383421_2_fastqc/fastqc_data.txt && fastqc /home/aaa/Desktop/circompara2/test_circompara/reads/SRR12383421_2.fastq.gz -o samples/SRR12383421/read_statistics/fastqc_stats --extract > samples/SRR12383421/read_statistics/fastqc_stats/SRR12383421_2.fastq_fastqc.log 2> samples/SRR12383421/read_statistics/fastqc_stats/SRR12383421_2.fastq_fastqc.err get_stringtie_rawcounts.R -g samples/SRR12383421/processings/stringtie/SRR12383421_transcripts.gtf -f /home/aaa/Desktop/circompara2/test_circompara/analysis/samples/SRR12383421/read_statistics/fastqc_stats/SRR12383421_1_fastqc/fastqc_data.txt,/home/aaa/Desktop/circompara2/test_circompara/analysis/samples/SRR12383421/read_statistics/fastqc_stats/SRR12383421_2_fastqc/fastqcdata.txt -o samples/SRR12383421/processings/stringtie/SRR12383421 Error in strsplit(grep("Sequence length", x = fastqc_data.txt, value = T), : subscript out of bounds Calls: mean -> sapply -> lapply -> FUN -> mean -> strsplit Execution halted scons: *** [samples/SRR12383421/processings/stringtie/SRR12383421_gene_expression_rawcounts.csv] Error 1 scons: building terminated because of errors.

What could I do to solve it?

Best Yaming

egaffo commented 8 months ago

What's inside the /home/aaa/Desktop/circompara2/test_circompara/analysis/samples/SRR12383421/read_statistics/fastqc_stats/SRR12383421_2_fastqc/fastqc_data.txt file? Its first lines should look like this:

##FastQC    0.11.9
>>Basic Statistics  pass
#Measure    Value
Filename    SRR6674618_1.fastq.gz
File type   Conventional base calls
Encoding    Sanger / Illumina 1.9
Total Sequences 59292516
Sequences flagged as poor quality   0
Sequence length 100-125
%GC 49
>>END_MODULE
>>Per base sequence quality pass
...

Also check the same file for the SRR12383421_1 file.