How do I see my log.progress.out file

Question

[maria.faleeva]

Hi there, I am mapping my FASTQ files using STAR, but it is taking a rather long time. In order to check if everything is ok I want to look at my log.progress.out files, but the file that I currently have in the directory doesnt have a format/does not let me open it. Does anybody know how to check the progress/current status of the running job in terminal? Using a macOS if that helps? many thanks!

Answer 1

[Ram]

What command are you trying to use right now? STAR's logs are plain text, so any plain text viewer should work.

[maria.faleeva]

I am currently trying to run

STAR --runThreadN 4 --genomeDir genome_index --readFilesCommand gunzip -c --readFilesIn /Users/mfaleeva/Desktop/Day30/Day-30-R1_S1_L008_R1_001.fastq.gz /Users/mfaleeva/Desktop/Day30/Day-30-R1_S1_L008_R2_001.fastq.gz --outSAMattrRGline ID:Day30_R1

For some reason, my log.progress.out file is not text, its not annotated as anything, thats why I am wondering whether I did something wrong?

[GenoMax]

tail -f log.progress.out should work. That must be a text file.

[maria.faleeva]

and I can run this line of code whilst the initial code is running?

[Ram]

Yes. Please read tool documentation to understand what each tool does. man <toolname> should give you the manual. Example: man tail.

[merfer0206]

unfortunately when I do that nothing changes and the log.progress.out file remains the same?

[Ram]

When you do what exactly? man tail or tail -f log.progress.out? If it's the former, that has nothing to do with the log file, and if it's the latter, tail can only show you what's there. What's the size of the log file?

[merfer0206]

The log.progress.out file has 6KB, and my aligned.out.sam file has 10.07GB?

[GenoMax]

Looks like the job is working then.

[merfer0206]

any clue on how big a typical SAM file for a human genome supposed to be?

[GenoMax]

It will depend on the number of input reads in your data, their length and number of secondary alignments etc. SAM files could be tens to hundreds of GB, especially since they are plain text/uncompressed.

[Ram]

Hi, you seem to be using 2 accounts, which is not recommended. Do you have a reason for using multiple accounts? If you'd like them merged, please let us know. If not, please stick to a single account.