fatal signal: SIGSEGV(11) while creating index

[SanderClaus]

Hi,

I'm getting fatal signal: SIGSEGV(11) while trying to create a Sailfish index. I already posted a thread in the forum, but nobody is answering.

Sailfish output:

$ sailfish index -t Alcanivorax_dieselolei293.fasta -k 20 -o /store/home/sclaus/sailfish_custom_indexes/2014_040/Alcanivorax_dieselolei/
Version Info: This is the most recent version

writing logs to /store/home/sclaus/sailfish_custom_indexes/2014_040/Alcanivorax_dieselolei/logs
readFile: Alcanivorax_dieselolei293.fasta,
file Alcanivorax_dieselolei293.fasta:
reading from 1 streams
reading from Alcanivorax_dieselolei293.fasta
hit eof!

Running Jellyfish on transcripts
file: Alcanivorax_dieselolei293.fasta has size 4750477 bytes
running jellyfish with --timing=/store/home/sclaus/sailfish_custom_indexes/2014_040/Alcanivorax_dieselolei/jf.time -m 20 -t 2 -o /store/home/sclaus/sailfish_custom_indexes/2014_040/Alcanivorax_dieselolei/jf.counts -s 5700572 Alcanivorax_dieselolei293.fasta
In Jellyfish process. Counting transcript kmers
Jellyfish terminated with return code 0
Jellyfish finished
transcriptHash size is 4644187
Building a perfect hash from the Jellyfish hash.
 4.234908s wall, 4.040000s user + 0.190000s system = 4.230000s CPU (99.9%)
saving keys in perfect hash . . . 1.090936s wall, 2.150000s user + 0.000000s system = 2.150000s CPU (197.1%)
done
took: 0.234922 us / key
writing index to file "/store/home/sclaus/sailfish_custom_indexes/2014_040/Alcanivorax_dieselolei/transcriptome.sfi"
writing transcript counts to file "/store/home/sclaus/sailfish_custom_indexes/2014_040/Alcanivorax_dieselolei/transcriptome.sfc"
done writing index
done writing transcript counts
building transcript to gene map using transcript fasta file [Alcanivorax_dieselolei293.fasta] . . .
reading from 1 streams
reading from Alcanivorax_dieselolei293.fasta
hit eof!
there are 211 transcripts . . . done
Saving transcritpt to gene map to ["/store/home/sclaus/sailfish_custom_indexes/2014_040/Alcanivorax_dieselolei/transcriptome.tgm"]
Reading transcript index from ["/store/home/sclaus/sailfish_custom_indexes/2014_040/Alcanivorax_dieselolei/transcriptome.sfi"] . . .done
Reading transcript counts from [/store/home/sclaus/sailfish_custom_indexes/2014_040/Alcanivorax_dieselolei/transcriptome.sfc] . . .read length = 0, numLengths = 0
done
reading from 1 streams
Number of kmers : 4644187
Parsing transcripts and building k-mer equivalence classes
reading from Alcanivorax_dieselolei293.fasta               ] ETA > 1 week
hit eof!
100% [=====================================================] in 2s

after relabling, there are 1687 eq classes
Building the k-mer equiv. class <=> transcript mappings
  0% [>                                                    ] ETA > 1 week

***** FATAL TRIGGER RECEIVED *******
Received fatal signal: SIGSEGV(11)
        PID: 477
        stack dump [1]  /lib/x86_64-linux-gnu/libpthread.so.0+0xfcb0 [0x7ff563266cb0]
        stack dump [2]  /store/opt/sailfish-0.6.3/lib/libsailfish_core.so+0xfbf8e [0x7ff564926f8e]
        stack dump [3]  /store/opt/sailfish-0.6.3/lib/libsailfish_core.so+0xfc6cd [0x7ff5649276cd]
        stack dump [4]  /store/opt/sailfish-0.6.3/lib/libtbb.so.2+0x2203a [0x7ff562e3003a]
        stack dump [5]  /store/opt/sailfish-0.6.3/lib/libtbb.so.2+0x1dd96 [0x7ff562e2bd96]
        stack dump [6]  /store/opt/sailfish-0.6.3/lib/libtbb.so.2+0x1d45b [0x7ff562e2b45b]
        stack dump [7]  /store/opt/sailfish-0.6.3/lib/libtbb.so.2+0x1ae5f [0x7ff562e28e5f]
        stack dump [8]  /store/opt/sailfish-0.6.3/lib/libtbb.so.2+0x1b059 [0x7ff562e29059]
        stack dump [9]  /lib/x86_64-linux-gnu/libpthread.so.0+0x7e9a [0x7ff56325ee9a]
        stack dump [10]  /lib/x86_64-linux-gnu/libc.so.6clone+0x6d [0x7ff5620e131d]

***** RETHROWING SIGNAL SIGSEGV(11)

g2log exiting after receiving fatal event
Log file at: [/store/home/sclaus/sailfish_custom_indexes/2014_040/Alcanivorax_dieselolei/logs/storeoptsailfish-063binsailfish.g2log.20141121-113703.log]

Exiting - FATAL SIGNAL: 11   /store/bin/sailfish: line 25:   477 Segmentation fault      (core dumped) $sailfishcmd

Directory content after running Sailfish:

$ ls -l /store/home/sclaus/sailfish_custom_indexes/2014_040/Alcanivorax_dieselolei/
total 135748
-rw-r--r-- 1 sclaus sclaus    17937 Nov 21 11:37 bias_feats.txt
-rw-r--r-- 1 sclaus sclaus 41798403 Nov 21 11:37 jf.counts_0
-rw-r--r-- 1 sclaus sclaus 37153504 Nov 21 11:37 kmerEquivClasses.bin
drwxr-xr-x 2 sclaus sclaus     4096 Nov 21 11:37 logs
-rw-r--r-- 1 sclaus sclaus 18576764 Nov 21 11:37 transcriptome.sfc
-rw-r--r-- 1 sclaus sclaus 41437818 Nov 21 11:37 transcriptome.sfi
-rw-r--r-- 1 sclaus sclaus     4754 Nov 21 11:37 transcriptome.tgm

As far as I can see only transcriptome.klut is missing.

[rob-p]

Hi @SanderClaus, It looks like the transcript set on which you're trying to build the index is fairly small. Would you be able to share it to see if we can reproduce the issue (and figure out what's going on)?

--Rob

[SanderClaus]

Sorry, forgot to include. You can find the file here: https://www.dropbox.com/s/o7ky8pzyiyner7e/Alcanivorax_dieselolei293.fasta?dl=0

Sander

[rob-p]

Now that the indexing scheme has completely changed (i.e. indexing happens via RapMap), this particular issue should go away. Please let us know if you have any further indexing problems.