Hello,
I’m using kneaddatav0.7.10 (installed via pip) and I’m having issue with bmtagger. The bmtagger utilities were downloaded from here.
Here is my error message:
10/30/2020 01:28:33 PM - kneaddata.utilities - CRITICAL: Error executing: /home/hfan/build/bmtagger/bmtagger.sh -q 1 -1 sample.R1_kneaddata.repeats.removed.1.fastq -T sample.R1_kneaddata_paired_temp_u8312fsj --extract -b Homo_sapiens_BMT
agger_v0.1/Homo_sapiens_assembly19.fasta.bitmask -x Homo_sapiens_BMTagger_v0.1/Homo_sapiens_a
ssembly19.fasta.srprism -o sample.R1_kneaddata_paired_Homo_sapiens_assem
bly19.fasta_bmtagger -2 sample.R1_kneaddata.repeats.removed.2.fastq
Error message returned from bmtagger :
Info: no ./bmtagger.conf found
Using following programs:
/home/hfan/build/bmtagger/bmfilter
/home/hfan/build/bmtagger/srprism
/home/hfan/miniconda3/bin/blastn
/home/hfan/build/bmtagger/extract_fullseq
MAIN SCRIPT IS /home/hfan/build/bmtagger/bmtagger.sh (PID=4390)
RUNNING bmfilter
* Attaching Homo_sapiens_BMTagger_v0.1/Homo_sapiens_assembly19.fasta.bitmask (pattern = 0b111
111111111111111 of len 18 using 36 bits)
* Notice: creating CFastqFileReader( 1, 0, sample.R1_kneaddata.repeats.r
emoved.1.fastq, sample.R1_kneaddata.repeats.removed.2.fastq)
* Info: Created sample.R1_kneaddata_paired_temp_u8312fsj/bmtagger.160403
5684.Cosette.4390.tag
terminate called after throwing an instance of 'std::runtime_error'
what():
runtime_error ???:0 [0x45913a] offset=0x0
runtime_error ???:0 [0x4591fe] offset=0x0
runtime_error ???:0 [0x4316d2] offset=0x0
runtime_error ???:0 [0x433a79] offset=0x0
runtime_error ???:0 [0x40368b] offset=0x0
runtime_error ???:0 [0x5a1450] offset=0x0
runtime_error ???:0 [0x4001b9] offset=0x0
In file cshortreader.cpp line 189 runtime_error: Error: bad read id in file
sample.R1_kneaddata.repeats.removed.2.fastq: expected A00204:533:HC5CLDSXY:1:1101:16043:1000:N:0:CTAGTTCG+GAAGCCTA#0/1, got
A00204:533:HC5CLDSXY:1:1101:10203:1000:N:0:CTAGTTCG+GAAGCCTA#0/2
/home/hfan/build/bmtagger/bmtagger.sh: line 179: 4398 Aborted (core dumped) $BMFILTER $accession $input1 $input
2 -q $quality $bmfiles $spotId_only -o "$TMPDIR"/bmtagger.$tmpstr $bmoptions
real 0m29.054s
user 0m0.013s
sys 0m3.514s
FAILED: bmfilter with rc=134
As you can see it seems like the problem it’s complaining is:
In file cshortreader.cpp line 189 runtime_error: Error: bad read id in file
sample.R1_kneaddata.repeats.removed.2.fastq: expected A00204:533:HC5CLDSXY:1:1101:16043:1000:N:0:CTAGTTCG+GAAGCCTA#0/1, got
A00204:533:HC5CLDSXY:1:1101:10203:1000:N:0:CTAGTTCG+GAAGCCTA#0/2
However I don’t think we shall expect an id ends with #0/1, which is a R1, in a *.2.fastq (R2). I have another linux machine with bmtagger downloaded from the same place but with kneaddata v0.7.2 and it processes the exact files fine. I was wondering what could have gone wrong.
Any help would be appreciated.
Best,
Huan