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arshajii / ema

Fast & accurate alignment of barcoded short-reads
http://ema.csail.mit.edu
MIT License
32 stars 7 forks source link

Core dump in ema count #27

Closed DRL closed 5 years ago

DRL commented 5 years ago

Hi,

installed ema via conda on an ubuntu server ...

$ cat test.ilv.fq | \ 
    ema count - \
    -w ../3_whitelist_barcodes/4M-with-alts-february-2016.txt \
    -o counts_file
Illegal instruction (core dumped)

Is this because of the fastq file? Or am running it the wrong way?

$ head -8 test.ilv.fq
@D00562:316:HKTGFBCX2:1:1105:1064:2069 1:N:0:AAGCGCTG
AGATGGGTCTGGGACCGCATGAGCTGTGGTAAACTAAGCGCGGCGTTGAGTTTCGTCACTGAACTTGCATGCTTGCGTGTATCATTGCGTGCTTCGAAACTTAACGTCGCGNTTAGTTTACCACAGCTAATAAGTGAAAATAAGTTAANT
+
DADDDHGIIIIIIFHIHIIIIGHHIIIIHIIICHHHCHIIIIHIIHHHGHHHIHHIDHHIHGIHGHHGIGIIIIIGDEHHIIIIIIIIGIHGHHHIIIIIIHEHIIIIIII#<<EHHHIHIIHHIIIIIIIIIIIIHIIHHHHIHEHH#<
@D00562:316:HKTGFBCX2:1:1105:1064:2069 2:N:0:AAGCGCTG
AAAGTATTCACAGTGTGAATACTTTATTGGGTTTAGGTGGAAAGTTACCCTCGGCCCCCCAGGGACCTGCCCTGACCAATTTCCTTGTTGGAAGTTAATTTTAATTGTAAACTAATTATATCGGCATTAGATATTCTTATTGCTTTTACA
+
@@D@DHIIHIIIIIGHHHHIIIIIIHHHIIIHIIIIIIIIIIIIHHIHHHHIIHHIIIIHIIIIIIHIHHIHIHHIIIIIIIIHHIIHHHIHHHHHIIIII<FHIIIIIIIIHHIIIIIIIIIHIIIIIIIIIIIIIHIIIHIIIIIIII

cheers,

dom

arshajii commented 5 years ago

Hi, Can you try building from source? This might be an issue with the pre-built conda version. Also, are you on a 32-bit system by chance?