Hi,

I’m using fastq-mcf to remove adapter sequences from RNAseq data.

fastq-mcf -o ctrl_clean_1.fastq -o ctrl_clean_2.fastq -l 50 -q 15 -t 0.1 -C 1000000 adaptor.fasta ctrl_1.fastq ctrl_2.fastq

After 4-5 hours running, it came with this error message:

Error during file close, possible partial write, failing

And the resulting trimmed reads are much fewer than expected.

Can anybody please tell me what causes this error?

here is the full log message:

Scale used: 2.2
Phred: 33
Threshold used: 1001 out of 1000000
): counted 6658 at the 'end' of 'ctrl_1.fastq', clip set to 6
): counted 6658 at the 'end' of 'ctrl_1.fastq', clip set to 6
): counted 6658 at the 'end' of 'ctrl_1.fastq', clip set to 6
): counted 6658 at the 'end' of 'ctrl_1.fastq', clip set to 6
): counted 6658 at the 'end' of 'ctrl_1.fastq', clip set to 6
): counted 6658 at the 'end' of 'ctrl_1.fastq', clip set to 6
): counted 6658 at the 'end' of 'ctrl_1.fastq', clip set to 6
): counted 6658 at the 'end' of 'ctrl_1.fastq', clip set to 6
): counted 6658 at the 'end' of 'ctrl_1.fastq', clip set to 6
): counted 6658 at the 'end' of 'ctrl_1.fastq', clip set to 6
): counted 6658 at the 'end' of 'ctrl_1.fastq', clip set to 6
): counted 6658 at the 'end' of 'ctrl_1.fastq', clip set to 6
): counted 6658 at the 'end' of 'ctrl_1.fastq', clip set to 6
): counted 6658 at the 'end' of 'ctrl_1.fastq', clip set to 6
): counted 6658 at the 'end' of 'ctrl_1.fastq', clip set to 6
): counted 6658 at the 'end' of 'ctrl_1.fastq', clip set to 6
Files: 2
Error during file close, possible partial write, failing
Total reads: 63127418
Too short after clip: 148714
Clipped 'end' reads (ctrl_1.fastq): Count 854897, Mean: 17.01, Sd: 10.28
Trimmed 22687152 reads (ctrl_1.fastq) by an average of 2.56 bases on quality < 15
Trimmed 27687235 reads (ctrl_2.fastq) by an average of 2.61 bases on quality < 15

Many thanks,

Ting