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Old 04-02-2019, 07:50 AM   #670
seqmore
Junior Member
 
Location: china

Join Date: Apr 2019
Posts: 4
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Thank you for your kindly replay @GenoMax. I didnot specify ref= since I have copied the ref fold genereted by index building with bbmap to the current working directory. As I learned from your post, bbmap will automatically find the ref fold in the current directory. I also succeeded in this way for many times previously. Now, as you indicate, I rerun the command again with ref= specified, but I failed as above. I should mention that the screen output looks like normal, as shown below.
So I'm confused. I would be really appreciate if you could clarify this issue. Thanks a lot in advance.

The screen output during bbmap:
Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=/mnt/e/database/ensembl_grch38_gtf/Homo_sapiens.GRCh38.dna.primary_assembly.fa, maxindel=100k, intronlen=10, in=a.fq, out=a.bb.sam, outu=a.unbbmap.fq, bs=script.sh]
Version 38.22

Retaining first best site only for ambiguous mappings.
Found samtools 0.1.9
Writing reference.
Executing dna.FastaToChromArrays2 [/mnt/e/database/ensembl_grch38_gtf/Homo_sapiens.GRCh38.dna.primary_assembly.fa, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=true, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=false]

Set genScaffoldInfo=true
Writing chunk 1
Writing chunk 2
Writing chunk 3
Writing chunk 4
Writing chunk 5
Writing chunk 6
Writing chunk 7
Set genome to 1

Loaded Reference: 0.010 seconds.
Loading index for chunk 1-7, build 1
No index available; generating from reference genome: /mnt/e/Raw_seq/ref/index/1/chr1-3_index_k13_c2_b1.block
No index available; generating from reference genome: /mnt/e/Raw_seq/ref/index/1/chr4-7_index_k13_c2_b1.block
Indexing threads started for block 4-7
Indexing threads started for block 0-3
Indexing threads finished for block 0-3
Indexing threads finished for block 4-7
Generated Index: 213.256 seconds.
Finished Writing: 19.955 seconds.
Analyzed Index: 7.710 seconds.
Started output stream: 0.045 seconds.
Started output stream: 0.001 seconds.
Cleared Memory: 0.241 seconds.
Processing reads in single-ended mode.
Started read stream.
Started 56 mapping threads.
Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55

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

Genome: 1
Key Length: 13
Max Indel: 100000
Minimum Score Ratio: 0.56
Mapping Mode: normal
Reads Used: 1236379 (56305606 bases)

Mapping: 163.878 seconds.
Reads/sec: 7544.53
kBases/sec: 343.58


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

mapped: 42.1017% 520537 41.2560% 23229413
unambiguous: 28.9375% 357777 29.3317% 16515379
ambiguous: 13.1642% 162760 11.9243% 6714034
low-Q discards: 0.0000% 0 0.0000% 0

perfect best site: 34.4476% 425903 34.5461% 19451376
semiperfect site: 34.4530% 425970 34.5520% 19454715

Match Rate: NA NA 45.7553% 22917698
Error Rate: 7.7666% 94588 54.2440% 27169499
Sub Rate: 7.4116% 90264 0.6028% 301949
Del Rate: 0.7988% 9728 53.6224% 26858156
Ins Rate: 0.3819% 4651 0.0188% 9394
N Rate: 0.0053% 64 0.0007% 372
Splice Rate: 0.4858% 5917 (splices at least 10 bp)

Total time: 438.182 seconds.
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