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course-fish546-2023 / assistance-public

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problem with code #12

Open sggarcia6 opened 1 year ago

sggarcia6 commented 1 year ago

/home/shared/hisat2-2.2.1/hisat2 \ -x ../output/cgigas_uk_roslin_v1_genomic-mito.index \ -p 4 \ -1 ../data/F143n08_R1_001.fastq.gz \ -2 ../data/F143n08_R2_001.fastq.gz \ -S ../output/F143_cgigas.sam

from this code i am having issue with reading the fasta files it is not working? with a broken pipe

sr320 commented 1 year ago

Can you paste the exact error message you get?

sggarcia6 commented 1 year ago

gzip: ../data/F143n08_R2_001.fastq.gz: unexpected end of file Error: Read NGSNJ-086:949:GW2303262992nd:2:1108:23050:31391 2:N:0:CGGCTATG+TCAGAGCC has more read characters than quality values. terminate called after throwing an instance of 'int' Aborted (core dumped) (ERR): hisat2-align exited with value 134

gzip: stdout: Broken pipe

sr320 commented 1 year ago

why run gzip?

sr320 commented 1 year ago

and can you post url to Rmd and line #?