Joinging output blocks...seg fault error

DaveTh

New member
Hi,
I'm using DIAMOND to aligned my fasta file just about 8MB but after a couple of hours, the command is terminated and notified "Joining output blocks... Segmentation fault". I also tried to run twice again but the same problem still happens.
I just used the manual code without adding or adjusting anything.
I have checked previous thread but there is no solution.

Code:
diamond blastx -d nr -q ./mnt/d/sequences.fasta -o sequences_matched.daa --log
Thanks,

Dave
 

DaveTh

New member
Hi Benjamin,
I have tried v0.9.24 and it worked well, there is no segmentation fault anymore.
But is that unusual to get a blank output (m8, daa) file?
Total time = 10887.5s
Low complexity seeds = 0
Hits (filter stage 0) = 0
Hits (filter stage 1) = 0 (-nan %)
Hits (filter stage 2) = 0 (-nan %)
Hits (filter stage x) = 0 (-nan %)
Hits (filter stage 3) = 0 (-nan %)
Hits (filter stage 4) = 0 (-nan %)
Target hits (stage 0) = 0
Target hits (stage 1) = 0
Target hits (stage 2) = 0
Time (greedy extension) = 0s
MSE = -nan
Temporary disk space used: 0 GB
Memory pool maximum allocation size: 0 GB
Outranked hits = 0 (-nan%)
Reported 0 pairwise alignments, 0 HSPs.
0 queries aligned.
 

Benjamin Buchfink

Administrator
Staff member
No, certainly not, unless there's nothing in there that matches the database in any way. Could you upload your data file or a small part of it so I can check it myself?
 

DaveTh

New member
No, certainly not, unless there's nothing in there that matches the database in any way. Could you upload your data file or a small part of it so I can check it myself?
Is it because my data is already aligned? I used mothur to do some QC filtering and aligning. There was some dash in my sequences, but DIAMOND not allow dash in the sequences so I changed it to X.
Can you give me your email? I will send you my data. Don't know why I cannot upload directly here.
 

Benjamin Buchfink

Administrator
Staff member
Code:
>M01235_52_000000000XC65VW_1_2105_13879_16114 
ACXXXAGXAGXGTGXXXXXCCGXAXGXCXGXXTXTXXAGXGXCGGXAAXXXTCXAXXCXTXXGGXGCXXTTXAXXXXAAXGCXGTXGTXXGXTAXGXGXCXGXXGXGXTGXCXCXTXXXXAAXGXTXAXCXXXCXTXTXGXXTGXXAXAAXTCXXCXCXACXGXGXXXCTXCXAAXXXXCXCXGXTXGXGXAXXAXCXTXGXXCXTXTXGXXGXXTAXTXAXXXCXXXXXXXXXXXXTXXGXGXXGTXXAXTXCXXXXXTXTXGXAXGXCXXCXXXXXAXCTXXXXXTAXGXGXGXGXCXTXXXACXCXXXXXXXGGXAXXACAXXXXAXAXTXGXGTXXGGXAXGXCGXGTXXGXXXXAXXAXAXXXXXXXXXXXXXXXTGXCXGTXAGXXATXAXTCXXXXXXXAXTXXTXTXGXGXAXACXGXCCXXXXAAXTXXGXXGTXGAAXAXXAXCXXXXAXXXGXXGXTXAXGXXXCTGXGXXGAXGXTXXXXXXXXXXXXXXXXXXXXXXGXTXGXCXTXXGAXXCGXXCXXTXGXAXGAXXCXAXCGXAXXAAXGXCXCXAGXXGGXGXXAGXCXGXAAXXCGXXGGXATXXTA
This has way too many X's in it to work properly. You can have some masked letters but not that many (btw you need to use N for masking DNA, not X). Try to use the reads before alignment with mothur.
 
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