Salmon never completes, stuck on processing fragments

Question

[jjrin]

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.

[andrew.j.skelton73]

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

[jjrin]

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

[h.mon]

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.