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SamahElmahdi / Glaucoma-variant-calling

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Error Hisat2 - Aligning #18

Open daliamousa opened 4 years ago

daliamousa commented 4 years ago

After indexing chromosome 20, Some of us keep receiving this error on attempting aligning:

Warning: Could not open read file "/ngs/glucoma/SRR5858161_1.fastq" for reading; skipping... Error: No input read files were valid (ERR): hisat2-align exited with value 1

The error keeps repeating despite checking pathways of the read files

daliamousa commented 4 years ago

The command was corrected to be as follows:

R1="$HOME/glucoma/SRR5858161_1.fastq" R2="$HOME/glucoma/SRR5858161_2.fastq" hisat2 -p 1 --rg ID:SRR5858161_F7_II.2 --rg SM:SRR5858161_F7_II.2 --rg PL:ILLUMINA --rg LB:SRR5858161_F7_II.2 --rg PU:SRR5858161_F7_II.2 -x ~/glucoma/Homo_sapiens.GRCh38.dna.chromosome.20 -1 $R1 -2 $R2 -S SRR5858161.sam

It worked fine for sometime, then it gave a "core dumped" error, which is a space limitation error. The first problem was probably a space problem as well. Solved by emptying the trash using the command: rm -rf ~/.local/share/Trash/*