20,000 records lead to segmentation fault

[ElDeveloper]

I was trying to process a pair of files (attached) with the command below, and inevitably I will get a segmentation fault. When I shorten the size of the files, the program executes correctly.

Command:

SeqPrep -f r1.fastq -s seqprep_assembled.fastq.gz -r r2.fastq -y J -1 seqprep_unassembled_R1.fastq.gz -2 seqprep_unassembled_R2.fastq.gz 
Processing reads... |Segmentation fault: 11

Not sure what might be going on, the same command executes just fine in a colleague's computer, and in my linux system. I believe it may be a problem with some of the libraries installed in my machine, but I have no idea what the problem would be.

[LordGenome]

I’m also seeing this on a recent iMac whereas an old MacBook Air works fine. Both running El Capitain. Graham

On 28 Sep 2016, at 5:27 PM, Yoshiki Vázquez Baeza [email protected] wrote:

I was trying to process a pair of files (attached) with the command below, and inevitably I will get a segmentation fault. When I shorten the size of the files, the program executes correctly.

Command:

SeqPrep -f r1.fastq -s seqprep_assembled.fastq.gz -r r2.fastq -y J -1 seqprep_unassembled_R1.fastq.gz -2 seqprep_unassembled_R2.fastq.gz Processing reads... |Segmentation fault: 11 Not sure what might be going on, the same command executes just fine in a colleague's computer, and in my linux system. I believe it may be a problem with some of the libraries installed in my machine, but I have no idea what the problem would be.

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[ElDeveloper]

Oddly enough in our situation, the machine that works is a newer MacBook Pro (mid 2014), the machine that doesn't is an old MacBook Pro (mid 2012).

On (Sep-28-16| 9:31), LordGenome wrote:

I’m also seeing this on a recent iMac whereas an old MacBook Air works fine. Both running El Capitain. Graham

On 28 Sep 2016, at 5:27 PM, Yoshiki Vázquez Baeza [email protected] wrote:

I was trying to process a pair of files (attached) with the command below, and inevitably I will get a segmentation fault. When I shorten the size of the files, the program executes correctly.

Command:

SeqPrep -f r1.fastq -s seqprep_assembled.fastq.gz -r r2.fastq -y J -1 seqprep_unassembled_R1.fastq.gz -2 seqprep_unassembled_R2.fastq.gz Processing reads... |Segmentation fault: 11 Not sure what might be going on, the same command executes just fine in a colleague's computer, and in my linux system. I believe it may be a problem with some of the libraries installed in my machine, but I have no idea what the problem would be.

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[jstjohn]

I wonder if has to do with differences in how compilers treated the inline keyword. I removed all of that in the most recent commit, maybe try again? Also if you still want the spinner, add -S to the arg list.

[ElDeveloper]

Thanks for pushing in those changes, however I'm still seeing the same problem.

yoshikivazquezbaeza:SeqPrep@master$ git rev-parse HEAD 575507b0b9c94701bdf67bb592da8ba91ba9639c yoshikivazquezbaeza:SeqPrep@master$ ./SeqPrep -f small/rMK0LS1080_L001_R1_prime_001.fastq -s seqprep_assembled.fastq.gz -r small/rMK0LS1080_L001_R2_prime_001.fastq -y J -1 seqprep_unassembled_R1.fastq.gz -2 seqprep_unassembled_R2.fastq.gz -S Processing reads... |Segmentation fault: 11

PS - I like the false sense of hope, so I added -S, however removing that flag did not change the outcome.

On (Oct-04-16|13:20), John St. John wrote:

I wonder if has to do with differences in how compilers treated the inline keyword. I removed all of that in the most recent commit, maybe try again? Also if you still want the spinner, add -S to the arg list.

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