Question: How do I see my log.progress.out file
0
gravatar for maria.faleeva
14 days ago by
maria.faleeva0 wrote:

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!

rna-seq terminal star fastq • 99 views
ADD COMMENTlink written 14 days ago by maria.faleeva0
1
gravatar for _r_am
14 days ago by
_r_am32k
Baylor College of Medicine, Houston, TX
_r_am32k wrote:

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

ADD COMMENTlink written 14 days ago by _r_am32k

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?

ADD REPLYlink written 14 days ago by maria.faleeva0
1

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

ADD REPLYlink written 14 days ago by GenoMax95k

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

ADD REPLYlink written 14 days ago by maria.faleeva0
1

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

ADD REPLYlink written 14 days ago by _r_am32k

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

ADD REPLYlink written 14 days ago by merfer02060

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?

ADD REPLYlink written 14 days ago by _r_am32k

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

ADD REPLYlink written 14 days ago by merfer02060
2

Looks like the job is working then.

ADD REPLYlink written 14 days ago by GenoMax95k

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

ADD REPLYlink written 13 days ago by merfer02060

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.

ADD REPLYlink modified 13 days ago • written 13 days ago by GenoMax95k

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.

ADD REPLYlink written 13 days ago by _r_am32k
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