Question: Salmon never completes, stuck on processing fragments
gravatar for jjrin
2.4 years ago by
jjrin10 wrote:

Hello I have been running salmon on some single-ended data. It runs fine initially and does process fragments, however it never actually completes.

Here is my command history

/usr/local/bin/Salmon-0.8.2_macOX_10.12/bin/salmon quant -p 24 -i /Volumes/RNA_SEQ/Reference_Genomes/Index/XENLA_JGIv18pV4_cdna_index_salmon -l U -r /Volumes/Ding_SRA_data/Ding_stage9_3/SRR5146676_1.fastq.gz -o /Volumes/Ding_SRA_data/salmon_output/stage9_3

My libtype is unstranded and I am sure that all of my options are correct. I have run this exact code with different reads with the 4th replicate of this data (the code above is for replicate 3) and it works fine. I am unsure if it is a problem with salmon or my reads. I downloaded the fastq files from SRA and they were successful, so I am unsure if it has to do with the reads as well.

This is the Salmon output:

Version Info: This is the most recent version of Salmon.
### salmon (mapping-based) v0.8.2
### [ program ] => salmon 
### [ command ] => quant 
### [ threads ] => { 24 }
### [ index ] => { /Volumes/CaChannel/RNA_SEQ/Reference_Genomes/Indexes/XENLA_JGIv18pV4_cdna_index_salmon }
### [ libType ] => { U }
### [ unmatedReads ] => { /Volumes/Saha_Lab_RNA-Seq/Ding_SRA_data/Ding_stage9_3/SRR5146676_1.fastq.gz }
### [ output ] => { /Volumes/Saha_Lab_RNA-Seq/Ding_SRA_data/salmon_output/stage9_3 }
Logs will be written to /Volumes/Saha_Lab_RNA-Seq/Ding_SRA_data/salmon_output/stage9_3/logs
[2017-09-09 14:13:27.759] [jointLog] [info] parsing read library format
[2017-09-09 14:13:27.759] [jointLog] [info] There is 1 library.
[2017-09-09 14:13:27.835] [stderrLog] [info] Loading Suffix Array 
[2017-09-09 14:13:27.832] [jointLog] [info] Loading Quasi index
[2017-09-09 14:13:27.833] [jointLog] [info] Loading 32-bit quasi index
[2017-09-09 14:13:29.200] [stderrLog] [info] Loading Transcript Info 
[2017-09-09 14:13:29.576] [stderrLog] [info] Loading Rank-Select Bit Array
[2017-09-09 14:13:29.607] [stderrLog] [info] There were 45107 set bits in the bit array
[2017-09-09 14:13:29.615] [stderrLog] [info] Computing transcript lengths
[2017-09-09 14:13:29.615] [stderrLog] [info] Waiting to finish loading hash

[2017-09-09 14:13:35.446] [stderrLog] [info] Done loading index
[2017-09-09 14:13:35.446] [jointLog] [info] done
processed 29000000 fragmentsointLog] [info] Index contained 45107 targets
hits: 25232188; hits per frag:  0.871225

Once it gets to the last line, it stops and never completes or outputs the quant.sf file. There are no other error messages as well.

rna-seq salmon fastq • 779 views
ADD COMMENTlink written 2.4 years ago by jjrin10

Looks like you're running this on your Mac, are you sure you want that many threads?

ADD REPLYlink written 2.4 years ago by andrew.j.skelton735.9k

Yes, it's fine for now, I have been running all of my programs with this many threads and i am currently not multithreading.

ADD REPLYlink written 2.4 years ago by jjrin10

I would advise you to contact the authors / open a issue on the project GitHub page. It would be very helpful to them if you could craft a small dataset to reproduce the issue, or share the original problematic dataset.

ADD REPLYlink written 2.4 years ago by h.mon29k
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