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How do I see my log.progress.out file

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!

fastq terminal star rna-seq
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written by maria.faleeva • maria.faleeva

1 answer

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

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written by Ram Ram

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?

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written by maria.faleeva • maria.faleeva

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

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written by GenoMax GenoMax

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

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written by maria.faleeva • maria.faleeva

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

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written by Ram Ram

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

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written by merfer0206 • merfer0206

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?

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written by Ram Ram

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

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written by merfer0206 • merfer0206

Looks like the job is working then.

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written by GenoMax GenoMax

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

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written by merfer0206 • merfer0206

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.

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written by GenoMax GenoMax

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.

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written by Ram Ram

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