Dear all, I obtained an empty text file which I designated for the output of the command seqkit stats upon running on multiple fastq trimmed files. I have run the same command on some individual files, each at once, and it generated the expected results, and I have also run it on 6 files together using also similar code (to the one I mentioned below), i.e. using *.fastq). I have 24 paired end fastq files (so 48 in total) and is running this on my laptop, which is ok, and worked previously during the trimming. I checked the available size of the VM, there still > 50 gb. When following the progression of the file processing, it moves a bit slowly, but I can see it moving from file 1 to 2 and so on till the end. I checked the actual fastqc report and could see that there is reads in the file as expected. See below my code and how the output on the screen looks like
My code was for 42 files together:
seqkit stats *.fastq > trimed_count.txt
When it finished the 48 files, the screen showed this
processed files: 39 / 42 [==================================>---] ETA: 2m9s
processed files: 42 / 42 [======================================] ETA: 0s. done
Here I sought it might be a hang in the system, which prevent it from delivering the results in the text file ? but not sure.
Could you advise please
Not sure. May be some files are corrupted.
How about try