segmentation fault 11 on salmon tutorial

Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?

salmon

Describe the bug I am getting a consistent segmentation fault 11 when running on the salmon tutorial on the provided arabidopsis data set.

To Reproduce

Which version of salmon was used?

salmon v0.11.3 on MacBook Pro (15-inch, 2016) macOS Sierra 10.12.6.

How was salmon installed (compiled, downloaded executable, through bioconda)?

bioconda

Which reference (e.g. transcriptome) was used?

To the best of my knowledge I followed the instructions in the tutorial at: https://combine-lab.github.io/salmon/getting_started/

This describes where the data come from and how I invoked salmon.

Which read files were used?

See above.

Which which program options were used?

I used the bash script from https://combine-lab.github.io/salmon/getting_started/

Expected behavior

I expected an output indicating successful quantification.

Screenshots

I couldn't figure out how to insert a picture, but here is the text from "terminal" window. `(salmon) MacBook-Pro-2:salmon-tutorial brent$ bash quant_tut_samples.sh Processing sample DRR016125 Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon

salmon (mapping-based) v0.11.3

[ program ] => salmon

[ command ] => quant

[ index ] => { athal_index }

[ libType ] => { A }

[ mates1 ] => { data/DRR016125/DRR016125_1.fastq.gz }

[ mates2 ] => { data/DRR016125/DRR016125_2.fastq.gz }

[ threads ] => { 8 }

[ output ] => { quants/DRR016125_quant }

Logs will be written to quants/DRR016125_quant/logs [2018-11-24 15:08:09.785] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2018-11-24 15:08:09.785] [jointLog] [info] parsing read library format [2018-11-24 15:08:09.785] [jointLog] [info] There is 1 library. [2018-11-24 15:08:09.877] [jointLog] [info] Loading Quasi index [2018-11-24 15:08:09.877] [jointLog] [info] Loading 32-bit quasi index [2018-11-24 15:08:09.877] [stderrLog] [info] Loading Suffix Array [2018-11-24 15:08:10.319] [stderrLog] [info] Loading Transcript Info [2018-11-24 15:08:10.423] [stderrLog] [info] Loading Rank-Select Bit Array [2018-11-24 15:08:10.432] [stderrLog] [info] There were 40,812 set bits in the bit array [2018-11-24 15:08:10.435] [stderrLog] [info] Computing transcript lengths [2018-11-24 15:08:10.435] [stderrLog] [info] Waiting to finish loading hash

quant_tut_samples.sh: line 2: 914 Segmentation fault: 11 salmon quant -i athal_index -l A -1 ${fn}/${samp}_1.fastq.gz -2 ${fn}/${samp}_2.fastq.gz -p 8 -o quants/${samp}_quant (salmon) MacBook-Pro-2:salmon-tutorial brent$ `

Desktop (please complete the following information):

MacBook Pro (15-inch, 2016) macOS Sierra 10.12.6.

Additional context I appreciate any help you can offer and I apologize in advance if there's something obvious I should have read or known about. (it seems like the lines below that are preceded by ### are coming out in fold face. They are not meant to.)

I am getting a consistent segmentation fault 11 when running on the salmon tutorial on the provided arabidopsis data set. Details below:

salmon v0.11.3 on MacBook Pro (15-inch, 2016) macOS Sierra 10.12.6.

The output is below. If I run the bash shell on all the A. thaliana samples it produces the same seg fault on each one. However the number that appears immediately before "Segmentation fault" (914 below) varies from one invocation to the next, even on the same data file.

I appreciate any help you can offer and I apologize in advance if there's something obvious I should have read or known about. (it seems like the lines below that are preceded by ### are coming out in fold face. They are not meant to.)

(salmon) MacBook-Pro-2:salmon-tutorial brent$ bash quant_tut_samples.sh Processing sample DRR016125 Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon

COMBINE-lab / salmon