idba_ud : Segmentation fault

[chenziwu5]

Dear Yu Peng Thanks for your great tool for assembly the metagenome reads. But when i assembled a bigger data than before(about 46Gb,150bp paired-end reads),i met some troubles as blow:

number of threads 50 reads 166504600 long reads 0 extra reads 0 read_length 150 kmer 95 kmers 4043406679 3973976227 merge bubble 74 contigs: 1643 n50: 144 max: 7843 mean: 167 total length: 274971 n80: 107 aligned 14418 reads confirmed bases: 27136 correct reads: 7834 bases: 3762 kmer 40 kmers 7586101528 7531112438 merge bubble 1564262 contigs: 3213050 n50: 150 max: 20467 mean: 138 total length: 446525742 n80: 110 aligned 226248 reads confirmed bases: 2332670 correct reads: 27184 bases: 6318 distance mean -nan sd -nan invalid insert distance more kmers ... ... /opt/pbs/dispatcher/mom_priv/jobs/20145.mgmt.SC: line 14: 151550 Segmentation fault (core dumped) /share/home/yuanqingc/idba-master/bin/idba_ud -r /share/home/yuanqingc/test_data/F7.fa --mink 40 --maxk 150 --step 5 --num_threads 50 --min_contig 1000 --pre_correction -o idba_F7out/

All the local-contig-*.fa file were ampty. and my server have 96x32 Gb RAM can use.my hard disk capacity is about 1.5T Can you give some suggestions for these troubles

Best regards chenziwu

[chichizhao]

hi,friend. here i got the same question, did you solve this problem? how did you solve it? i would appriceate it very much, thank you!

here is some information about my problem number of threads 50 reads 442187424 long reads 0 extra reads 0 read_length 150 kmer 20 kmers 1358728697 1383007787 merge bubble 2862253 contigs: 22892761 n50: 134 max: 1973 mean: 65 total length: 1501473097 n80: 36 aligned 67981939 reads confirmed bases: 312563523 correct reads: 21543289 bases: 1821430 distance mean -nan sd -nan invalid insert distance kmer 30 kmers 1363087010 1369777557 merge bubble 1360552 contigs: 2132901 n50: 7465 max: 75290 mean: 571 total length: 1219679752 n80: 2688 aligned 286675061 reads confirmed bases: 1094780096 correct reads: 234338621 bases: 18801863 distance mean 61.0069 sd 7216.47 invalid insert distance kmer 40 kmers 1295973262 1298190021 merge bubble 120003 contigs: 1093115 n50: 14370 max: 169564 mean: 1108 total length: 1211212759 n80: 5377 aligned 294905334 reads confirmed bases: 1125047372 correct reads: 241708491 bases: 1138255 distance mean -50.4066 sd 14260.5 invalid insert distance kmer 50 kmers 1261816094 1263728865 merge bubble 64350 contigs: 664113 n50: 19555 max: 182166 mean: 1815 total length: 1205436269 n80: 7678 aligned 300243405 reads confirmed bases: 1141160357 correct reads: 245522060 bases: 531728 distance mean 1113.02 sd 18788.7 invalid insert distance kmer 60 kmers 1246167785 1247514085 merge bubble 43268 contigs: 473865 n50: 25100 max: 219342 mean: 2539 total length: 1203596827 n80: 10097 aligned 303759463 reads confirmed bases: 1149990612 correct reads: 247685048 bases: 351378 distance mean -32.2509 sd 23611.9 invalid insert distance kmer 70 kmers 1233058292 1233987085 merge bubble 32916 contigs: 369915 n50: 29354 max: 217552 mean: 3252 total length: 1203108621 n80: 11912 aligned 306223562 reads confirmed bases: 1155007616 correct reads: 248695259 bases: 232844 distance mean 563.184 sd 26822.6 invalid insert distance kmer 80 kmers 1221379483 1221996248 merge bubble 15869 contigs: 609958 n50: 22776 max: 216695 mean: 2024 total length: 1234996652 n80: 8688 reads 442187424 aligned 305494955 reads distance mean 568.651 sd 22063.1 invalid insert distance

when the program run into this step, it appear that “ Segmentation fault (core dumped)” and a core.19779 file was created in the file folder when i use the command " gdb core-file core.19779" some information displayed like the below, and the main information is "Core was generated by `idba_ud -r SRR13376033in1.fa --maxk 80 --step 10 -o ./idba/ --num_threads 50'. Program terminated with signal 11, Segmentation fault.

0 0x000000000040e6c9 in ?? () "

And i wonder that it is really some segmentation fault, most probably segments is maxk what i think ( doesn`t important)

[New LWP 19779] [New LWP 25481] [New LWP 25466] [New LWP 25482] [New LWP 25476] [New LWP 25491] [New LWP 25492] [New LWP 25488] [New LWP 19780] [New LWP 25509] [New LWP 25471] [New LWP 25484] [New LWP 25508] [New LWP 25499] [New LWP 25504] [New LWP 25486] [New LWP 25494] [New LWP 25470] [New LWP 25514] [New LWP 25472] [New LWP 25480] [New LWP 25501] [New LWP 25489] [New LWP 25485] [New LWP 25478] [New LWP 25474] [New LWP 25469] [New LWP 25467] [New LWP 25475] [New LWP 25477] [New LWP 25483] [New LWP 25513] [New LWP 25510] [New LWP 25479] [New LWP 25496] [New LWP 25498] [New LWP 25503] [New LWP 25505] [New LWP 25506] [New LWP 25493] [New LWP 25511] [New LWP 25502] [New LWP 25490] [New LWP 25468] [New LWP 25473] [New LWP 25507] [New LWP 25487] [New LWP 25495] [New LWP 25500] [New LWP 25497] [New LWP 25512] Core was generated by `idba_ud -r SRR13376033in1.fa --maxk 80 --step 10 -o ./idba/ --num_threads 50'. Program terminated with signal 11, Segmentation fault.

0 0x000000000040e6c9 in ?? ()

[jvollme]

It looks a bit like you only gave it forward reads. Could that be? Idba can only work if it has at least one set of paired reads.

[chichizhao]

yes，you are right，but i use the command “fq2fa --merge file1.fq file2.fq filein1.fa” to form the paired reads in one file in fasta form. did I do something wrong？thank you for your respons, I really appreciate it!