Reply to An integrated software for virus community sequencing data analysis on Tue, 24 May 2022 13:02:31 GMT

anneng — Tue, 24 May 2022 13:02:31 GMT

修复环状参考基因组
root@1f7293c590d6:/$qap FixCircRef /opt/qap/bin/FixCircRef.pl -1 /data/data/SRR6378032_1.fastq.gz,/data/data/SRR6377924_1.fastq.gz,/data/data/SRR6377925_1.fastq.gz -2 /data/data/SRR6378032_2.fastq.gz,/data/data/SRR6377924_2.fastq.gz,/data/data/SRR6377925_2.fastq.gz -r /data/data/HBV_C_AB033556.fasta

You are now running subprogram: FixCircRef

WARNING @ [2022-05-24 12:32:34 UTC]: The output directory is not provided!
WARNING @ [2022-05-24 12:32:34 UTC]: Will mkdir /qap_Results_for_FixCircRef_20220524_12h32m34s and use it as the output directory.
INFO @ [2022-05-24 12:32:34 UTC]: Building Bowtie2 index for /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/HBV_C_AB033556.2line.fix0.fasta.
INFO @ [2022-05-24 12:32:34 UTC]: /opt/qap/bin/3rdPartyTools/bowtie2/bowtie2-build /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/HBV_C_AB033556.2line.fix0.fasta /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/HBV_C_AB033556.2line.fix0
Settings:
Output files: "/qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/HBV_C_AB033556.2line.fix0..bt2"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 4 (one in 16)
FTable chars: 10
Strings: unpacked
Max bucket size: default
Max bucket size, sqrt multiplier: default
Max bucket size, len divisor: 4
Difference-cover sample period: 1024
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
/qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/HBV_C_AB033556.2line.fix0.fasta
Building a SMALL index
Reading reference sizes
Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:00
bmax according to bmaxDivN setting: 928
Using parameters --bmax 696 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 696 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:00
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:00
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:00
Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
(Using difference cover)
Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
Splitting and merging time: 00:00:00
Split 2, merged 4; iterating...
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 463.5 (target: 695)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
Reserving size (696) for bucket 1
Calculating Z arrays for bucket 1
Entering block accumulator loop for bucket 1:
bucket 1: 10%
bucket 1: 20%
bucket 1: 30%
bucket 1: 40%
bucket 1: 50%
bucket 1: 60%
bucket 1: 70%
bucket 1: 80%
bucket 1: 90%
bucket 1: 100%
Sorting block of length 354 for bucket 1
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 355 for bucket 1
Getting block 2 of 8
Reserving size (696) for bucket 2
Calculating Z arrays for bucket 2
Entering block accumulator loop for bucket 2:
bucket 2: 10%
bucket 2: 20%
bucket 2: 30%
bucket 2: 40%
bucket 2: 50%
bucket 2: 60%
bucket 2: 70%
bucket 2: 80%
bucket 2: 90%
bucket 2: 100%
Sorting block of length 521 for bucket 2
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 522 for bucket 2
Getting block 3 of 8
Reserving size (696) for bucket 3
Calculating Z arrays for bucket 3
Entering block accumulator loop for bucket 3:
bucket 3: 10%
bucket 3: 20%
bucket 3: 30%
bucket 3: 40%
bucket 3: 50%
bucket 3: 60%
bucket 3: 70%
bucket 3: 80%
bucket 3: 90%
bucket 3: 100%
Sorting block of length 409 for bucket 3
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 410 for bucket 3
Getting block 4 of 8
Reserving size (696) for bucket 4
Calculating Z arrays for bucket 4
Entering block accumulator loop for bucket 4:
bucket 4: 10%
bucket 4: 20%
bucket 4: 30%
bucket 4: 40%
bucket 4: 50%
bucket 4: 60%
bucket 4: 70%
bucket 4: 80%
bucket 4: 90%
bucket 4: 100%
Sorting block of length 291 for bucket 4
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 292 for bucket 4
Getting block 5 of 8
Reserving size (696) for bucket 5
Calculating Z arrays for bucket 5
Entering block accumulator loop for bucket 5:
bucket 5: 10%
bucket 5: 20%
bucket 5: 30%
bucket 5: 40%
bucket 5: 50%
bucket 5: 60%
bucket 5: 70%
bucket 5: 80%
bucket 5: 90%
bucket 5: 100%
Sorting block of length 579 for bucket 5
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 580 for bucket 5
Getting block 6 of 8
Reserving size (696) for bucket 6
Calculating Z arrays for bucket 6
Entering block accumulator loop for bucket 6:
bucket 6: 10%
bucket 6: 20%
bucket 6: 30%
bucket 6: 40%
bucket 6: 50%
bucket 6: 60%
bucket 6: 70%
bucket 6: 80%
bucket 6: 90%
bucket 6: 100%
Sorting block of length 670 for bucket 6
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 671 for bucket 6
Getting block 7 of 8
Reserving size (696) for bucket 7
Calculating Z arrays for bucket 7
Entering block accumulator loop for bucket 7:
bucket 7: 10%
bucket 7: 20%
bucket 7: 30%
bucket 7: 40%
bucket 7: 50%
bucket 7: 60%
bucket 7: 70%
bucket 7: 80%
bucket 7: 90%
bucket 7: 100%
Sorting block of length 659 for bucket 7
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 660 for bucket 7
Getting block 8 of 8
Reserving size (696) for bucket 8
Calculating Z arrays for bucket 8
Entering block accumulator loop for bucket 8:
bucket 8: 10%
bucket 8: 20%
bucket 8: 30%
bucket 8: 40%
bucket 8: 50%
bucket 8: 60%
bucket 8: 70%
bucket 8: 80%
bucket 8: 90%
bucket 8: 100%
Sorting block of length 225 for bucket 8
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 226 for bucket 8
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 832
fchr[G]: 1857
fchr[T]: 2662
fchr[$]: 3715
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4195809 bytes to primary EBWT file: /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/HBV_C_AB033556.2line.fix0.1.bt2
Wrote 936 bytes to secondary EBWT file: /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/HBV_C_AB033556.2line.fix0.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 3715
bwtLen: 3716
sz: 929
bwtSz: 929
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 233
offsSz: 932
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 20
numLines: 20
ebwtTotLen: 1280
ebwtTotSz: 1280
color: 0
reverse: 0
Total time for call to driver() for forward index: 00:00:01
Reading reference sizes
Time reading reference sizes: 00:00:00
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:00
Time to reverse reference sequence: 00:00:00
bmax according to bmaxDivN setting: 928
Using parameters --bmax 696 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 696 --dcv 1024
Constructing suffix-array element generator
Building DifferenceCoverSample
Building sPrime
Building sPrimeOrder
V-Sorting samples
V-Sorting samples time: 00:00:00
Allocating rank array
Ranking v-sort output
Ranking v-sort output time: 00:00:00
Invoking Larsson-Sadakane on ranks
Invoking Larsson-Sadakane on ranks time: 00:00:00
Sanity-checking and returning
Building samples
Reserving space for 12 sample suffixes
Generating random suffixes
QSorting 12 sample offsets, eliminating duplicates
QSorting sample offsets, eliminating duplicates time: 00:00:00
Multikey QSorting 12 samples
(Using difference cover)
Multikey QSorting samples time: 00:00:00
Calculating bucket sizes
Splitting and merging
Splitting and merging time: 00:00:00
Split 1, merged 6; iterating...
Splitting and merging
Splitting and merging time: 00:00:00
Avg bucket size: 463.5 (target: 695)
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering Ebwt loop
Getting block 1 of 8
Reserving size (696) for bucket 1
Calculating Z arrays for bucket 1
Entering block accumulator loop for bucket 1:
bucket 1: 10%
bucket 1: 20%
bucket 1: 30%
bucket 1: 40%
bucket 1: 50%
bucket 1: 60%
bucket 1: 70%
bucket 1: 80%
bucket 1: 90%
bucket 1: 100%
Sorting block of length 441 for bucket 1
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 442 for bucket 1
Getting block 2 of 8
Reserving size (696) for bucket 2
Calculating Z arrays for bucket 2
Entering block accumulator loop for bucket 2:
bucket 2: 10%
bucket 2: 20%
bucket 2: 30%
bucket 2: 40%
bucket 2: 50%
bucket 2: 60%
bucket 2: 70%
bucket 2: 80%
bucket 2: 90%
bucket 2: 100%
Sorting block of length 638 for bucket 2
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 639 for bucket 2
Getting block 3 of 8
Reserving size (696) for bucket 3
Calculating Z arrays for bucket 3
Entering block accumulator loop for bucket 3:
bucket 3: 10%
bucket 3: 20%
bucket 3: 30%
bucket 3: 40%
bucket 3: 50%
bucket 3: 60%
bucket 3: 70%
bucket 3: 80%
bucket 3: 90%
bucket 3: 100%
Sorting block of length 332 for bucket 3
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 333 for bucket 3
Getting block 4 of 8
Reserving size (696) for bucket 4
Calculating Z arrays for bucket 4
Entering block accumulator loop for bucket 4:
bucket 4: 10%
bucket 4: 20%
bucket 4: 30%
bucket 4: 40%
bucket 4: 50%
bucket 4: 60%
bucket 4: 70%
bucket 4: 80%
bucket 4: 90%
bucket 4: 100%
Sorting block of length 442 for bucket 4
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 443 for bucket 4
Getting block 5 of 8
Reserving size (696) for bucket 5
Calculating Z arrays for bucket 5
Entering block accumulator loop for bucket 5:
bucket 5: 10%
bucket 5: 20%
bucket 5: 30%
bucket 5: 40%
bucket 5: 50%
bucket 5: 60%
bucket 5: 70%
bucket 5: 80%
bucket 5: 90%
bucket 5: 100%
Sorting block of length 425 for bucket 5
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 426 for bucket 5
Getting block 6 of 8
Reserving size (696) for bucket 6
Calculating Z arrays for bucket 6
Entering block accumulator loop for bucket 6:
bucket 6: 10%
bucket 6: 20%
bucket 6: 30%
bucket 6: 40%
bucket 6: 50%
bucket 6: 60%
bucket 6: 70%
bucket 6: 80%
bucket 6: 90%
bucket 6: 100%
Sorting block of length 373 for bucket 6
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 374 for bucket 6
Getting block 7 of 8
Reserving size (696) for bucket 7
Calculating Z arrays for bucket 7
Entering block accumulator loop for bucket 7:
bucket 7: 10%
bucket 7: 20%
bucket 7: 30%
bucket 7: 40%
bucket 7: 50%
bucket 7: 60%
bucket 7: 70%
bucket 7: 80%
bucket 7: 90%
bucket 7: 100%
Sorting block of length 439 for bucket 7
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 440 for bucket 7
Getting block 8 of 8
Reserving size (696) for bucket 8
Calculating Z arrays for bucket 8
Entering block accumulator loop for bucket 8:
bucket 8: 10%
bucket 8: 20%
bucket 8: 30%
bucket 8: 40%
bucket 8: 50%
bucket 8: 60%
bucket 8: 70%
bucket 8: 80%
bucket 8: 90%
bucket 8: 100%
Sorting block of length 618 for bucket 8
(Using difference cover)
Sorting block time: 00:00:00
Returning block of 619 for bucket 8
Exited Ebwt loop
fchr[A]: 0
fchr[C]: 832
fchr[G]: 1857
fchr[T]: 2662
fchr[$]: 3715
Exiting Ebwt::buildToDisk()
Returning from initFromVector
Wrote 4195809 bytes to primary EBWT file: /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/HBV_C_AB033556.2line.fix0.rev.1.bt2
Wrote 936 bytes to secondary EBWT file: /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/HBV_C_AB033556.2line.fix0.rev.2.bt2
Re-opening _in1 and _in2 as input streams
Returning from Ebwt constructor
Headers:
len: 3715
bwtLen: 3716
sz: 929
bwtSz: 929
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 233
offsSz: 932
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 20
numLines: 20
ebwtTotLen: 1280
ebwtTotSz: 1280
color: 0
reverse: 1
Total time for backward call to driver() for mirror index: 00:00:00
INFO @ [2022-05-24 12:32:35 UTC]: Start to map reads to /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/HBV_C_AB033556.2line.fix0.fasta using Bowtie2.
INFO @ [2022-05-24 12:32:35 UTC]: Running Bowtie2 for paired-end read mapping
INFO @ [2022-05-24 12:32:35 UTC]: /opt/qap/bin/3rdPartyTools/bowtie2/bowtie2 --very-sensitive-local --threads 1 -x /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/HBV_C_AB033556.2line.fix0 -1 /data/data/SRR6378032_1.fastq.gz -2 /data/data/SRR6378032_2.fastq.gz -S /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/0.sam
57699 reads; of these:
57699 (100.00%) were paired; of these:
7821 (13.55%) aligned concordantly 0 times
37033 (64.18%) aligned concordantly exactly 1 time
12845 (22.26%) aligned concordantly >1 times
----
7821 pairs aligned concordantly 0 times; of these:
7622 (97.46%) aligned discordantly 1 time
----
199 pairs aligned 0 times concordantly or discordantly; of these:
398 mates make up the pairs; of these:
101 (25.38%) aligned 0 times
55 (13.82%) aligned exactly 1 time
242 (60.80%) aligned >1 times
99.91% overall alignment rate
INFO @ [2022-05-24 12:40:54 UTC]: Converting /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/0.sam to bam file
INFO @ [2022-05-24 12:40:54 UTC]: /opt/qap/bin/3rdPartyTools/samtools/samtools view -h -@ 1 -Sb /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/0.sam > /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/0.bam
INFO @ [2022-05-24 12:40:59 UTC]: Sorting bam file /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/0.bam with coordinates.
INFO @ [2022-05-24 12:40:59 UTC]: /opt/qap/bin/3rdPartyTools/samtools/samtools sort -@ 1 -O bam -T 0.PosSorted.1653396059 -o /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/0.PosSorted.bam /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/0.bam
INFO @ [2022-05-24 12:41:03 UTC]: Indexing sorted bam file.
INFO @ [2022-05-24 12:41:03 UTC]: /opt/qap/bin/3rdPartyTools/samtools/samtools index /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/0.PosSorted.bam
INFO @ [2022-05-24 12:41:03 UTC]: /opt/qap/bin/3rdPartyTools/samtools/samtools depth -aa /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/0.PosSorted.bam > /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/depth/0.depth
INFO @ [2022-05-24 12:41:05 UTC]: Rscript /opt/qap/bin/Rscripts/FindDepthInterval.R -i /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/depth/0.depth -o /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/depth/0.interval
INFO @ [2022-05-24 12:41:05 UTC]: Start to map reads to /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/HBV_C_AB033556.2line.fix0.fasta using Bowtie2.
INFO @ [2022-05-24 12:41:05 UTC]: Running Bowtie2 for paired-end read mapping
INFO @ [2022-05-24 12:41:05 UTC]: /opt/qap/bin/3rdPartyTools/bowtie2/bowtie2 --very-sensitive-local --threads 1 -x /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/HBV_C_AB033556.2line.fix0 -1 /data/data/SRR6377924_1.fastq.gz -2 /data/data/SRR6377924_2.fastq.gz -S /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/1.sam
58549 reads; of these:
58549 (100.00%) were paired; of these:
13245 (22.62%) aligned concordantly 0 times
33871 (57.85%) aligned concordantly exactly 1 time
11433 (19.53%) aligned concordantly >1 times
----
13245 pairs aligned concordantly 0 times; of these:
7533 (56.87%) aligned discordantly 1 time
----
5712 pairs aligned 0 times concordantly or discordantly; of these:
11424 mates make up the pairs; of these:
11181 (97.87%) aligned 0 times
74 (0.65%) aligned exactly 1 time
169 (1.48%) aligned >1 times
90.45% overall alignment rate
INFO @ [2022-05-24 12:48:48 UTC]: Converting /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/1.sam to bam file
INFO @ [2022-05-24 12:48:48 UTC]: /opt/qap/bin/3rdPartyTools/samtools/samtools view -h -@ 1 -Sb /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/1.sam > /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/1.bam
INFO @ [2022-05-24 12:48:53 UTC]: Sorting bam file /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/1.bam with coordinates.
INFO @ [2022-05-24 12:48:53 UTC]: /opt/qap/bin/3rdPartyTools/samtools/samtools sort -@ 1 -O bam -T 1.PosSorted.1653396533 -o /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/1.PosSorted.bam /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/1.bam
INFO @ [2022-05-24 12:48:57 UTC]: Indexing sorted bam file.
INFO @ [2022-05-24 12:48:57 UTC]: /opt/qap/bin/3rdPartyTools/samtools/samtools index /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/1.PosSorted.bam
INFO @ [2022-05-24 12:48:57 UTC]: /opt/qap/bin/3rdPartyTools/samtools/samtools depth -aa /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/1.PosSorted.bam > /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/depth/1.depth
INFO @ [2022-05-24 12:48:58 UTC]: Rscript /opt/qap/bin/Rscripts/FindDepthInterval.R -i /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/depth/1.depth -o /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/depth/1.interval
INFO @ [2022-05-24 12:48:59 UTC]: Start to map reads to /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/HBV_C_AB033556.2line.fix0.fasta using Bowtie2.
INFO @ [2022-05-24 12:48:59 UTC]: Running Bowtie2 for paired-end read mapping
INFO @ [2022-05-24 12:48:59 UTC]: /opt/qap/bin/3rdPartyTools/bowtie2/bowtie2 --very-sensitive-local --threads 1 -x /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/HBV_C_AB033556.2line.fix0 -1 /data/data/SRR6377925_1.fastq.gz -2 /data/data/SRR6377925_2.fastq.gz -S /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/2.sam
55473 reads; of these:
55473 (100.00%) were paired; of these:
8817 (15.89%) aligned concordantly 0 times
32750 (59.04%) aligned concordantly exactly 1 time
13906 (25.07%) aligned concordantly >1 times
----
8817 pairs aligned concordantly 0 times; of these:
6382 (72.38%) aligned discordantly 1 time
----
2435 pairs aligned 0 times concordantly or discordantly; of these:
4870 mates make up the pairs; of these:
3810 (78.23%) aligned 0 times
935 (19.20%) aligned exactly 1 time
125 (2.57%) aligned >1 times
96.57% overall alignment rate
INFO @ [2022-05-24 12:55:21 UTC]: Converting /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/2.sam to bam file
INFO @ [2022-05-24 12:55:21 UTC]: /opt/qap/bin/3rdPartyTools/samtools/samtools view -h -@ 1 -Sb /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/2.sam > /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/2.bam
INFO @ [2022-05-24 12:55:26 UTC]: Sorting bam file /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/2.bam with coordinates.
INFO @ [2022-05-24 12:55:26 UTC]: /opt/qap/bin/3rdPartyTools/samtools/samtools sort -@ 1 -O bam -T 2.PosSorted.1653396926 -o /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/2.PosSorted.bam /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/2.bam
INFO @ [2022-05-24 12:55:30 UTC]: Indexing sorted bam file.
INFO @ [2022-05-24 12:55:30 UTC]: /opt/qap/bin/3rdPartyTools/samtools/samtools index /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/2.PosSorted.bam
INFO @ [2022-05-24 12:55:30 UTC]: /opt/qap/bin/3rdPartyTools/samtools/samtools depth -aa /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/bwa/2.PosSorted.bam > /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/depth/2.depth
INFO @ [2022-05-24 12:55:31 UTC]: Rscript /opt/qap/bin/Rscripts/FindDepthInterval.R -i /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/depth/2.depth -o /qap_Results_for_FixCircRef_20220524_12h32m34s/tmp/depth/2.interval
INFO @ [2022-05-24 12:55:32 UTC]: Program completed!

Reply to An integrated software for virus community sequencing data analysis on Tue, 17 May 2022 02:50:13 GMT

anneng — Tue, 17 May 2022 02:50:13 GMT

There are totally 40 dependencies need to be installed: [1] cutadapt; [2] Bio::Perl(Perl module); [3] Perl4::CoreLibs(Perl module); [4] Clone(Perl module); [5] Config::General(Perl module); [6] Font::TTF::Font(Perl module); [7] GD(Perl module); [8] GD::Polyline(Perl module); [9] List::MoreUtils(Perl module); [10] Math::Bezier(Perl module); [11] Math::Round(Perl module); [12] Math::VecStat(Perl module); [13] Params::Validate(Perl module); [14] Readonly(Perl module); [15] Regexp::Common(Perl module); [16] SVG(Perl module); [17] Set::IntSpan(Perl module); [18] Statistics::Basic(Perl module); [19] Text::Format(Perl module); [20] gplots (R package); [21] RColorBrewer (R package); [22] ggplot2 (R package); [23] seqinr (R package); [24] optparse (R package); [25] plyr (R package); [26] rJava (R package); [27] xlsx (R package); [28] stringr (R package); [29] scatterplot3d (R package); [30] devtools (R package); [31] ggpubr (R package); [32] ape (R package); [33] Biostrings (R package); [34] ggbiplot (R package); [35] Biopython; [36] ShoRAH; [37] ViQuaS; [38] Circos; [39] GSL; [40] system PATH;

conda install -c bioconda perl-appconfig
conda install -c bioconda perl-bioperl
conda install -c r r-gplots

Reply to An integrated software for virus community sequencing data analysis on Sat, 14 May 2022 09:33:28 GMT

anneng — Sat, 14 May 2022 09:33:28 GMT

12864_2020_6744_MOESM1_ESM.docx
这个文献里面提到了41个工具
FastQC:check the quality of input fastq files
Cutadapt：reads filtration with two main parameters regarding base quality and read length.
BarcodeSplitter、BarcodeTrimmer：barcode identification and trimming by using regular expression in Perl
ExtractReadID and ExtractSeq
BWA mem [2] and Bowtie2 --very-sensitive-local：mapping short reads to a reference genome
Picard tools and SAMtools