I am using mothur v.1.33.3 on a linux box,
I am following the MiSeq SOP,
I do screen.seqs, and just after that I wanna look into the summary, but I get the following error
It took 347 secs to screen 65096 sequences.
mothur > summary.seqs(fasta=current, count=current)
Using /eva/users/djf482/Projects/MS96/output2/stability.trim.contigs.good.good.count_table as input file for the count parameter.
Using /eva/users/djf482/Projects/MS96/output2/stability.trim.contigs.good.unique.good.align as input file for the fasta parameter.
[ERROR]: /eva/users/djf482/Projects/MS96/output2/stability.trim.contigs.good.unique.good.align is blank, aborting.
Using /eva/users/djf482/Projects/MS96/output2/stability.trim.contigs.good.unique.good.align as input file for the fasta parameter.
Using 1 processors.
[porus01:05689] *** Process received signal ***
[porus01:05689] Signal: Segmentation fault (11)
[porus01:05689] Signal code: Address not mapped (1)
[porus01:05689] Failing at address: (nil)
[porus01:05689] [ 0] /lib64/libpthread.so.0(+0xf140) [0x7f9199a5f140]
[porus01:05689] [ 1] ./mothur(_ZN17SeqSummaryCommand7executeEv+0x1344) [0xe2f3a4]
[porus01:05689] [ 2] ./mothur(_ZN14InteractEngine8getInputEv+0x837) [0x974f97]
[porus01:05689] [ 3] ./mothur(main+0xcca) [0x4e98ca]
[porus01:05689] [ 4] /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f91996c9455]
[porus01:05689] [ 5] ./mothur() [0x4ea811]
[porus01:05689] *** End of error message ***
Segmentation fault
my alignment summary is as the following
summary.seqs Start End NBases Ambigs Polymer NumSeqs Minimum: 0 0 0 0 1 1 2.5%-tile: 1 13422 290 0 4 3283 25%-tile: 1 13422 290 0 4 32821 Median: 1 13422 291 0 4 65641 75%-tile: 1 13422 291 0 5 98461 97.5%-tile: 1 13422 292 0 6 127999 Maximum: 13425 13425 297 0 12 131280 Mean: 11.199 13419.6 290.365 0 4.48103 # of unique seqs: 65096 total # of seqs: 131280
and when I go ahead and do filter.seqs, I get:
Unable to open /eva/users/djf482/Projects/MS96/raw_data/stability.trim.contigs.good.unique.good.align. Trying output directory /eva/users/djf482/Projects/MS96/output2/stability.trim.contigs.good.unique.good.align
Using 1 processors.
[ERROR]: /eva/users/djf482/Projects/MS96/output2/stability.trim.contigs.good.unique.good.align is blank. Please correct.
Error in reading your fastafile, at position -1. Blank name.
Creating Filter…
[ERROR]: basic_string::_S_construct null not valid has occurred in the FilterSeqsCommand class function createFilter. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.
I appreciate to hear what is wrong and why it goes segmentation fault !