kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
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getfastq is broken in single-end samples #75

Closed kfuku52 closed 2 years ago

kfuku52 commented 2 years ago
Running fastp.
Command: fastp --thread 8 --length_required 25 -j /dev/null -h /dev/null --in1 /lustre7/home/lustre4/kfuku/my_project/nepenthes_gracilis/20211013_RNAseq/amalgkit_out/getfastq/SRR3581686/SRR3581686_1.fastq.gz --out1 /lustre7/home/lustre4/kfuku/my_project/nepenthes_gracilis/20211013_RNAseq/amalgkit_out/getfastq/SRR3581686/SRR3581686_1.fastp.fastq.gz
fastp stdout:

fastp stderr:
Error to read gzip file
Detecting adapter sequence for read1...
Error to read gzip file
No adapter detected for read1

ERROR: file '/lustre7/home/lustre4/kfuku/my_project/nepenthes_gracilis/20211013_RNAseq/amalgkit_out/getfastq/SRR3581686/SRR3581686_1.fastq.gz' doesn't exist, quit now

--- getfastq final report ---
Target size (--max_bp): 999,999,999,999,999 bp
Sum of fastq_dump dumped reads: 1,159,831,050 bp
Sum of fastq_dump rejected reads: 62,420,250 bp
Sum of fastq_dump written reads: 1,097,410,800 bp
Sum of fastp input reads: 0 bp
Sum of fastp output reads: 0 bp
Individual SRA IDs: SRR3581686
Individual fastq_dump dumped reads (bp): 1,159,831,050
Individual fastq_dump rejected reads (bp): 62,420,250
Individual fastq_dump written reads (bp): 1,097,410,800
Individual fastp input reads (bp): 0
Individual fastp output reads (bp): 0