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Old 03-09-2015, 01:54 AM   #44
Elsie
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Location: Australia

Join Date: Mar 2011
Posts: 85
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No error, just Nas which is why I think I am missing something:
reformat.sh in1=R1.fastq in2=R2.fastq out=interleaved
gzip interleaved
bbmap.sh ref=hg19.fa
bbduk.sh in=interleaved.gz out=trimmed.fq.gz ktrim=r k=23 hdist=1 mink=11 tpe tbo minlen=90 ref=truseq.fa.gz,nextera.fa.gz
bbmap.sh maxindex=200 in=trimmed.fq.fq mhist=mhist.txt bhist=bhist.txt qhist=qhist.txt qahist=qahist.txt

BBMap version 34.56
Set match histogram output to mhist.txt
Set base content histogram output to bhist.txt
Set quality histogram output to qhist.txt
Set quality accuracy histogram output to qahist.txt
Retaining first best site only for ambiguous mappings.
No output file.
Set genome to 1

Loaded Reference: 5.025 seconds.
Loading index for chunk 1-7, build 1
Generated Index: 6.192 seconds.
Analyzed Index: 7.512 seconds.
Cleared Memory: 0.461 seconds.
Processing reads in single-ended mode.
Started read stream.
Started 16 mapping threads.
Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15

------------------ Results ------------------

Genome: 1
Key Length: 13
Max Indel: 200
Minimum Score Ratio: 0.56
Mapping Mode: normal
Reads Used: 0 (0 bases)

Mapping: 0.447 seconds.
Reads/sec: 0.00
kBases/sec: 0.00


Read 1 data: pct reads num reads pct bases num bases

mapped: NaN% 0 NaN% 0
unambiguous: NaN% 0 NaN% 0
ambiguous: NaN% 0 NaN% 0
low-Q discards: NaN% 0 NaN% 0

perfect best site: NaN% 0 NaN% 0
semiperfect site: NaN% 0 NaN% 0

Match Rate: NA NA NaN% 0
Error Rate: NaN% 0 NaN% 0
Sub Rate: NaN% 0 NaN% 0
Del Rate: NaN% 0 NaN% 0
Ins Rate: NaN% 0 NaN% 0
N Rate: NaN% 0 NaN% 0

Total time: 19.975 seconds.

Any advice greatly appreciated. thanks.
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