Salmon is a tool for quantifying the expression of transcripts using RNA-seq data.
>TRINITY_DN2_c1_g1_i1 len=201 path=[0:0-200]
TGACAGCAAGAAAGACACCTCAGAAAATCAAAATATTACTACCTCTCATACTAAGGGGAGGGTGGGGGCAGGATTTTTAGTTCACGATCTGTGAGGCGTCTTTCAAACTGGAACCATGGGAGTCATTGAGTTGATAAGAATTATGTTCACATGAATGTCTAATTTGTCATCTTTCAGGAAAATTTTGGAATTGGAAGAGGA
>TRINITY_DN2_c0_g1_i1 len=226 path=[0:0-225]
TTAGAGAATATGTAGACTATAAAACATATTTAGATGATCTACACAATTTGTACAGGTTTGCTTATTTTAGACAATTTTATTTTATTAAATGAAGTATTCAGATGATAATTTATCAGCCTTAAAGATGAGATGACAATATTTTAGGTTAGCGGTCTTAAAGATGAGATGAGATGACAGTTCTTTTTTTGGTTGATGATGAATTTGGCATGGTGTGATTCCGTTTTAG
>TRINITY_DN2_c0_g2_i1 len=1045 path=[0:0-471 2:472-606 3:607-710 9:711-794 12:795-867 13:868-868 14:869-935 15:936-1044]
ACTTGCTCTGATAGGCTGCCTGGCACATTCCGTATCAGTCTTCCTTCAAACTATTTGGCAGACGAGCAAATCTGTTTACTTGGTTGCAGCCCTTTCGAGTCGCACGAAGGAGAGAGTTGTTCAGAGGAGTGAGAACTCTCGTCTGCAGTAGAAGTCTTCCGAGCCATTCCCTTCTTCTTTTATATTCCTTTTTATTTTGTAGCCGTAAGGACCACTAAATAAACTTATCATCATGGACGCCATCAAGAAGAAGATGATTGCGATGAAAACGGAGAAAGAGAATGCTCTTGACCGCGCAGAGCAGCTCGAACAAAAATTAAGGGATACAGAAGAAGAGAAGACAAAGGTTGAAGACGAATTAAGTGCTCTTCAAAAGAAACACTCGAACTTAGAAAACGAATTCGATTCCATCAACGAGAAATATCAGGAAGCACAAACTAAGTTAGAAGCGGCAGAGAAGGCAGCATCCGAGGCAGAACAAGAGGTTCAAGGTTTGAACAGGAGGATACAGCTGTTAGAGGAAGACTTAGAAAGATCTGAAGAAAGATTACAGTCTGCCACAGAAAAATTAGAGGAGGCTTCTAAAGCTGCAGATGAGAGTGAAAGAAACCGCAAGGTCTTGGAAAACCTGAACAATGCATCAGAGGAGAGGTCAGACGTGCTGGAGAAACAGTTATCTGAGGCCAAATGGATCGCAGAGGAAGCAGACAAAAAATATGATGAGGCAGCACGTAAACTTGCTATCACAGAGGTTGACCTTGAGCGTGCCGAAGCTCGTTTGGAGGCAGCTGAGGCCAAAATTATTAACCTTGAAGAAGAGCTGACAGTTGTGGGTGCCAATATCAAAACCCTACAGGTCCAAAATGACCAGGCCTCACAGCGGGAGGACAGCTACGAGGAGACCATTCGTGACCTTACACAGCGGCTGAAGGATGCAGATAATCGTGCAGAGTTCGCCGAACGAGAGGTGAATACTCTGCAGAAAATGGTAGAAAAACTAGAAGGTAGGAAGTCCAATCTATCACCTAGCACTCTAACTTTACAG
>TRINITY_DN2_c0_g2_i3 len=2356 path=[0:0-471 2:472-606 3:607-710 9:711-794 12:795-867 13:868-868 14:869-935 16:936-2355]
ACTTGCTCTGATAGGCTGCCTGGCACATTCCGTATCAGTCTTCCTTCAAACTATTTGGCAGACGAGCAAATCTGTTTACTTGGTTGCAGCCCTTTCGAGTCGCACGAAGGAGAGAGTTGTTCAGAGGAGTGAGAACTCTCGTCTGCAGTAGAAGTCTTCCGAGCCATTCCCTTCTTCTTTTATATTCCTTTTTATTTTGTAGCCGTAAGGACCACTAAATAAACTTATCATCATGGACGCCATCAAGAAGAAGATGATTGCGATGAAAACGGAGAAAGAGAATGCTCTTGACCGCGCAGAGCAGCTCGAACAAAAATTAAGGGATACAGAAGAAGAGAAGACAAAGGTTGAAGACGAATTAAGTGCTCTTCAAAAGAAACACTCGAACTTAGAAAACGAATTCGATTCCATCAACGAGAAATATCAGGAAGCACAAACTAAGTTAGAAGCGGCAGAGAAGGCAGCATCCGAGGCAGAACAAGAGGTTCAAGGTTTGAACAGGAGGATACAGCTGTTAGAGGAAGACTTAGAAAGATCTGAAGAAAGATTACAGTCTGCCACAGAAAAATTAGAGGAGGCTTCTAAAGCTGCAGATGAGAGTGAAAGAAACCGCAAGGTCTTGGAAAACCTGAACAATGCATCAGAGGAGAGGTCAGACGTGCTGGAGAAACAGTTATCTGAGGCCAAATGGATCGCAGAGGAAGCAGACAAAAAATATGATGAGGCAGCACGTAAACTTGCTATCACAGAGGTTGACCTTGAGCGTGCCGAAGCTCGTTTGGAGGCAGCTGAGGCCAAAATTATTAACCTTGAAGAAGAGCTGACAGTTGTGGGTGCCAATATCAAAACCCTACAGGTCCAAAATGACCAGGCCTCACAGCGGGAGGACAGCTACGAGGAGACCATTCGTGACCTTACACAGCGGCTGAAGGATGCTGAAAACCGTGCCACTGAAGCTGAAAGGACAGTATCCAAATTGCAGAAAGAAGTCGACAGGTTGGAAGATGAATTGCTTTCGGAGAAGGAGAGATACAAAGCGATTAGTGACGAGTTGGATCAGACCTTTGCCGAGCTTGCAGGATACTAATCACTTCCATTGTCGTGCCCTCACTGTTAATAACTCTCTCGGTCGGCATCAAATTGCCATTATTTCATCAAAATTTAGGACAAAAGGATGTAATGGTTTATCATTTRNA-seq~salmon -c 8 -m 32 -l ON -b ON input_1 input_2/Trinity.fasta
Name 0h_A_1.fq.gz
TRINITY_DN2_c1_g1_i1 201 49.468711
TRINITY_DN2_c0_g1_i1 226 57.944612
TRINITY_DN2_c0_g2_i1 1045 3621.331135
TRINITY_DN2_c0_g2_i3 2356 1898.440265
TRINITY_DN2_c0_g2_i2 720 8.314388
TRINITY_DN2_c0_g2_i5 2356 676.072270
TRINITY_DN2_c0_g2_i4 829 34.550581
TRINITY_DN2_c0_g3_i1 410 12.699434
TRINITY_DN8_c0_g1_i1 845 4264.950632
Name 0h_A_1.fq.gz
TRINITY_DN2_c1_g1_i1 201 2.000
TRINITY_DN2_c0_g1_i1 226 3.000
TRINITY_DN2_c0_g2_i1 1045 2549.377
TRINITY_DN2_c0_g2_i3 2356 3550.548
TRINITY_DN2_c0_g2_i2 720 3.438
TRINITY_DN2_c0_g2_i5 2356 1264.421
TRINITY_DN2_c0_g2_i4 829 17.638
TRINITY_DN2_c0_g3_i1 410 2.000
TRINITY_DN8_c0_g1_i1 845 2238.243
Checking the realpath of input files.
0 input_1
1 /yoshitake/test/RNA-seq~salmon/input_1/0h_A_1.fq.gz
1 /yoshitake/test/RNA-seq~salmon/input_1/0h_A_2.fq.gz
1 /yoshitake/test/RNA-seq~salmon/input_1/0h_B_1.fq.gz
1 /yoshitake/test/RNA-seq~salmon/input_1/0h_B_2.fq.gz
1 /yoshitake/test/RNA-seq~salmon/input_1/1week_A1_1.fq.gz
1 /yoshitake/test/RNA-seq~salmon/input_1/1week_A1_2.fq.gz
1 /yoshitake/test/RNA-seq~salmon/input_1/1week_A2_1.fq.gz
1 /yoshitake/test/RNA-seq~salmon/input_1/1week_A2_2.fq.gz
0 input_2/Trinity.fasta
centos:centos6 quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 quay.io/biocontainers/salmon:1.8.0--h7e5ed60_1
using docker
+ set -o pipefail
+ exec
++ tee log.txt
+ LANG=C
+ threads=8
+ three=8
++ expr 8 / 2
+ threads2=4
++ expr 8 - 2
+ threads1=6
++ free -g
++ grep Mem
++ sed -e 's/Mem: *\([0-9]*\) .*/\1/'
+ memG=251
++ expr 251 '*' 3 / 4
+ memG3=188
+ echo '
#####SYSTEM ENVIRONMENT#####
threads=8
memory=251G
############################
'
#####SYSTEM ENVIRONMENT#####
threads=8
memory=251G
############################
++ date +%s
+ time0=1653644350
+ echo start at 1653644350
start at 1653644350
++ dirname /yoshitake/PortablePipeline/PortablePipeline/scripts/RNA-seq~salmon
+ cur_prg=/yoshitake/PortablePipeline/PortablePipeline/scripts
+ echo 'extract parameters from parameter files'
extract parameters from parameter files
+ index_param='-k 31'
+ mapping_param='-l A --validateMappings'
+ out_contig_length=ON
+ bam_output=ON
+ cat
++ echo input_2/Trinity.fasta
++ grep '[.]gz$'
++ wc -l
++ true
+ '[' 0 = 1 ']'
+ ref=input_2/Trinity.fasta
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20220527_183910_529_11681
+ echo pp20220527_183910_529_11681
+ docker run --name pp20220527_183910_529_11681 -v /yoshitake/test/RNA-seq~salmon:/yoshitake/test/RNA-seq~salmon -w /yoshitake/test/RNA-seq~salmon -u 2007:600 -i --rm quay.io/biocontainers/salmon:1.8.0--h7e5ed60_1 salmon index -t input_2/Trinity.fasta -i index -k 31
Version Info: This is the most recent version of salmon.
[2022-05-27 09:39:11.266] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.
[2022-05-27 09:39:11.266] [jLog] [info] building index
out : index
[2022-05-27 09:39:11.267] [puff::index::jointLog] [info] Running fixFasta
[Step 1 of 4] : counting k-mers
counted k-mers for 10000 transcripts
counted k-mers for 20000 transcripts
counted k-mers for 30000 transcripts
[2022-05-27 09:39:11.726] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
[2022-05-27 09:39:11.726] [puff::index::jointLog] [info] Clipped poly-A tails from 86 transcripts
wrote 34752 cleaned references
[2022-05-27 09:39:11.774] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
[2022-05-27 09:39:11.902] [puff::index::jointLog] [info] ntHll estimated 12023510 distinct k-mers, setting filter size to 2^28
Threads = 2
Vertex length = 31
Hash functions = 5
Filter size = 268435456
Capacity = 2
Files:
index/ref_k31_fixed.fa
--------------------------------------------------------------------------------
Round 0, 0:268435456
Pass Filling Filtering
1 3 4
2 1 0
True junctions count = 20424
False junctions count = 112544
Hash table size = 132968
Candidate marks count = 210289
--------------------------------------------------------------------------------
Reallocating bifurcations time: 0
TwoPaCo::buildGraphMain:: allocated with scalable_malloc; freeing.
TwoPaCo::buildGraphMain:: Calling scalable_allocation_command(TBBMALLOC_CLEAN_ALL_BUFFERS, 0);
True marks count: 130839
Edges construction time: 0
--------------------------------------------------------------------------------
Distinct junctions = 20424
allowedIn: 25
Max Junction ID: 77675
seen.size():621409 kmerInfo.size():77676
approximateContigTotalLength: 11288230
counters for complex kmers:
(prec>1 & succ>1)=348 | (succ>1 & isStart)=36 | (prec>1 & isEnd)=24 | (isStart & isEnd)=2
contig count: 55051 element count: 13735244 complex nodes: 410
# of ones in rank vector: 55050
[2022-05-27 09:39:21.428] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
[2022-05-27 09:39:21.428] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory index
size = 13735244
-----------------------------------------
| Loading contigs | Time = 2.1264 ms
-----------------------------------------
size = 13735244
-----------------------------------------
| Loading contig boundaries | Time = 1.1103 ms
-----------------------------------------
Number of ones: 55050
Number of ones per inventory item: 512
Inventory entries filled: 108
55050
[2022-05-27 09:39:21.451] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
[2022-05-27 09:39:21.452] [puff::index::jointLog] [info] contig count for validation: 55050
[2022-05-27 09:39:21.472] [puff::index::jointLog] [info] Total # of Contigs : 55050
[2022-05-27 09:39:21.472] [puff::index::jointLog] [info] Total # of numerical Contigs : 55050
[2022-05-27 09:39:21.475] [puff::index::jointLog] [info] Total # of contig vec entries: 97748
[2022-05-27 09:39:21.475] [puff::index::jointLog] [info] bits per offset entry 17
[2022-05-27 09:39:21.478] [puff::index::jointLog] [info] Done constructing the contig vector. 55051
[2022-05-27 09:39:21.491] [puff::index::jointLog] [info] # segments = 55050
[2022-05-27 09:39:21.491] [puff::index::jointLog] [info] total length = 13735244
[2022-05-27 09:39:21.499] [puff::index::jointLog] [info] Reading the reference files ...
[2022-05-27 09:39:21.574] [puff::index::jointLog] [info] positional integer width = 24
[2022-05-27 09:39:21.574] [puff::index::jointLog] [info] seqSize = 13735244
[2022-05-27 09:39:21.574] [puff::index::jointLog] [info] rankSize = 13735244
[2022-05-27 09:39:21.574] [puff::index::jointLog] [info] edgeVecSize = 0
[2022-05-27 09:39:21.574] [puff::index::jointLog] [info] num keys = 12083744
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[2022-05-27 09:39:22.357] [puff::index::jointLog] [info] mphf size = 7.54842 MB
[2022-05-27 09:39:22.368] [puff::index::jointLog] [info] chunk size = 6867622
[2022-05-27 09:39:22.368] [puff::index::jointLog] [info] chunk 0 = [0, 6867622)
[2022-05-27 09:39:22.368] [puff::index::jointLog] [info] chunk 1 = [6867622, 13735214)
[2022-05-27 09:39:23.395] [puff::index::jointLog] [info] finished populating pos vector
[2022-05-27 09:39:23.395] [puff::index::jointLog] [info] writing index components
[2022-05-27 09:39:23.445] [puff::index::jointLog] [info] finished writing dense pufferfish index
[2022-05-27 09:39:23.452] [jLog] [info] done building index
for info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000
Bitarray 63320768 bits (100.00 %) (array + ranks )
final hash 0 bits (0.00 %) (nb in final hash 0)
+ pppair1=()
+ pppair2=()
+ ppsingle=()
+ IFS=
+ read i
++ find input_1/
++ egrep '(_R1.*|_1)[.]f(ast|)q(|[.]gz)$'
++ echo input_1/0h_A_1.fq.gz
++ egrep '_1[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1/0h_A_1.fq.gz
++ sed 's/_1[.]\(f\(\(ast\|\)\(q\|a\)\|na\|sa\)\(\|[.]gz\)\)$/_2.\1/'
+ temppair2=input_1/0h_A_2.fq.gz
+ '[' -e input_1/0h_A_2.fq.gz ']'
+ pppair1+=("$i")
+ pppair2+=("$temppair2")
+ IFS=
+ read i
++ echo input_1/0h_B_1.fq.gz
++ egrep '_1[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
++ wc -l
+ '[' 1 = 1 ']'
++ echo input_1/0h_B_1.fq.gz
++ sed 's/_1[.]\(f\(\(ast\|\)\(q\|a\)\|na\|sa\)\(\|[.]gz\)\)$/_2.\1/'
+ temppair2=input_1/0h_B_2.fq.gz
+ '[' -e input_1/0h_B_2.fq.gz ']'
+ pppair1+=("$i")
+ pppair2+=("$temppair2")
+ IFS=
+ read i
++ echo input_1/1week_A1_1.fq.gz
++ wc -l
++ egrep '_1[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
+ '[' 1 = 1 ']'
++ echo input_1/1week_A1_1.fq.gz
++ sed 's/_1[.]\(f\(\(ast\|\)\(q\|a\)\|na\|sa\)\(\|[.]gz\)\)$/_2.\1/'
+ temppair2=input_1/1week_A1_2.fq.gz
+ '[' -e input_1/1week_A1_2.fq.gz ']'
+ pppair1+=("$i")
+ pppair2+=("$temppair2")
+ IFS=
+ read i
++ echo input_1/1week_A2_1.fq.gz
++ wc -l
++ egrep '_1[.]f((ast|)(q|a)|na|sa)(|[.]gz)$'
+ '[' 1 = 1 ']'
++ echo input_1/1week_A2_1.fq.gz
++ sed 's/_1[.]\(f\(\(ast\|\)\(q\|a\)\|na\|sa\)\(\|[.]gz\)\)$/_2.\1/'
+ temppair2=input_1/1week_A2_2.fq.gz
+ '[' -e input_1/1week_A2_2.fq.gz ']'
+ pppair1+=("$i")
+ pppair2+=("$temppair2")
+ IFS=
+ read i
+ IFS=
+ read i
++ find input_1/
++ egrep '[.]f(ast|)q(|[.]gz)$'
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_A_1.fq.gz = input_1/0h_A_1.fq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_A_1.fq.gz = input_1/0h_A_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_B_1.fq.gz = input_1/0h_A_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/1week_A1_1.fq.gz = input_1/0h_A_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/1week_A2_1.fq.gz = input_1/0h_A_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_A_2.fq.gz = input_1/0h_A_2.fq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_A_1.fq.gz = input_1/0h_B_1.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_B_1.fq.gz = input_1/0h_B_1.fq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_A_1.fq.gz = input_1/0h_B_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_B_1.fq.gz = input_1/0h_B_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/1week_A1_1.fq.gz = input_1/0h_B_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/1week_A2_1.fq.gz = input_1/0h_B_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_A_2.fq.gz = input_1/0h_B_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_B_2.fq.gz = input_1/0h_B_2.fq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_A_1.fq.gz = input_1/1week_A1_1.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_B_1.fq.gz = input_1/1week_A1_1.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/1week_A1_1.fq.gz = input_1/1week_A1_1.fq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_A_1.fq.gz = input_1/1week_A1_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_B_1.fq.gz = input_1/1week_A1_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/1week_A1_1.fq.gz = input_1/1week_A1_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/1week_A2_1.fq.gz = input_1/1week_A1_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_A_2.fq.gz = input_1/1week_A1_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_B_2.fq.gz = input_1/1week_A1_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/1week_A1_2.fq.gz = input_1/1week_A1_2.fq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_A_1.fq.gz = input_1/1week_A2_1.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_B_1.fq.gz = input_1/1week_A2_1.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/1week_A1_1.fq.gz = input_1/1week_A2_1.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/1week_A2_1.fq.gz = input_1/1week_A2_1.fq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ ppinputcheck=0
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_A_1.fq.gz = input_1/1week_A2_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_B_1.fq.gz = input_1/1week_A2_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/1week_A1_1.fq.gz = input_1/1week_A2_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/1week_A2_1.fq.gz = input_1/1week_A2_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_A_2.fq.gz = input_1/1week_A2_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/0h_B_2.fq.gz = input_1/1week_A2_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/1week_A1_2.fq.gz = input_1/1week_A2_2.fq.gz ']'
+ for j in '${pppair1[@]:-}' '${pppair2[@]:-}' '${ppsingle[@]:-}'
+ '[' input_1/1week_A2_2.fq.gz = input_1/1week_A2_2.fq.gz ']'
+ ppinputcheck=1
+ break
+ '[' 1 = 0 ']'
+ IFS=
+ read i
+ mkdir -p output
+ (( i = 0 ))
+ (( i < 4 ))
+ xargs -I '{}' -P 1 bash -c '{}'
++ basename input_1/0h_A_1.fq.gz
+ id=0h_A_1.fq.gz
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~salmon/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/salmon:1.8.0--h7e5ed60_1 salmon quant -i index -p 6 -l A --validateMappings -1 "input_1/0h_A_1.fq.gz" -2 "input_1/0h_A_2.fq.gz" -o output/"0h_A_1.fq.gz" --writeMappings=output/"0h_A_1.fq.gz"/"0h_A_1.fq.gz".sam; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~salmon/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bash run-make_output.sh "0h_A_1.fq.gz" "6" "ON" "ON" "input_2/Trinity.fasta"'
+ (( i++ ))
+ (( i < 4 ))
++ basename input_1/0h_B_1.fq.gz
+ id=0h_B_1.fq.gz
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~salmon/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/salmon:1.8.0--h7e5ed60_1 salmon quant -i index -p 6 -l A --validateMappings -1 "input_1/0h_B_1.fq.gz" -2 "input_1/0h_B_2.fq.gz" -o output/"0h_B_1.fq.gz" --writeMappings=output/"0h_B_1.fq.gz"/"0h_B_1.fq.gz".sam; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~salmon/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bash run-make_output.sh "0h_B_1.fq.gz" "6" "ON" "ON" "input_2/Trinity.fasta"'
+ (( i++ ))
+ (( i < 4 ))
++ basename input_1/1week_A1_1.fq.gz
+ id=1week_A1_1.fq.gz
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~salmon/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/salmon:1.8.0--h7e5ed60_1 salmon quant -i index -p 6 -l A --validateMappings -1 "input_1/1week_A1_1.fq.gz" -2 "input_1/1week_A1_2.fq.gz" -o output/"1week_A1_1.fq.gz" --writeMappings=output/"1week_A1_1.fq.gz"/"1week_A1_1.fq.gz".sam; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~salmon/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bash run-make_output.sh "1week_A1_1.fq.gz" "6" "ON" "ON" "input_2/Trinity.fasta"'
+ (( i++ ))
+ (( i < 4 ))
++ basename input_1/1week_A2_1.fq.gz
+ id=1week_A2_1.fq.gz
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~salmon/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/salmon:1.8.0--h7e5ed60_1 salmon quant -i index -p 6 -l A --validateMappings -1 "input_1/1week_A2_1.fq.gz" -2 "input_1/1week_A2_2.fq.gz" -o output/"1week_A2_1.fq.gz" --writeMappings=output/"1week_A2_1.fq.gz"/"1week_A2_1.fq.gz".sam; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/RNA-seq~salmon/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD -u 2007:600 -i --rm quay.io/biocontainers/bbmap:38.96--h5c4e2a8_1 bash run-make_output.sh "1week_A2_1.fq.gz" "6" "ON" "ON" "input_2/Trinity.fasta"'
+ (( i++ ))
+ (( i < 4 ))
Version Info: This is the most recent version of salmon.
### salmon (selective-alignment-based) v1.8.0
### [ program ] => salmon
### [ command ] => quant
### [ index ] => { index }
### [ threads ] => { 6 }
### [ libType ] => { A }
### [ validateMappings ] => { }
### [ mates1 ] => { input_1/0h_A_1.fq.gz }
### [ mates2 ] => { input_1/0h_A_2.fq.gz }
### [ output ] => { output/0h_A_1.fq.gz }
### [ writeMappings ] => { output/0h_A_1.fq.gz/0h_A_1.fq.gz.sam }
Logs will be written to output/0h_A_1.fq.gz/logs
-----------------------------------------
| Loading contig table | Time = 10.392 ms
-----------------------------------------
size = 55051
-----------------------------------------
| Loading contig offsets | Time = 166.03 us
-----------------------------------------
-----------------------------------------
| Loading reference lengths | Time = 53.281 us
-----------------------------------------
-----------------------------------------
| Loading mphf table | Time = 3.8227 ms
-----------------------------------------
size = 13735244
Number of ones: 55050
Number of ones per inventory item: 512
[2022-05-27 09:39:24.482] [jointLog] [info] setting maxHashResizeThreads to 6
[2022-05-27 09:39:24.482] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
[2022-05-27 09:39:24.482] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-05-27 09:39:24.482] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-05-27 09:39:24.482] [jointLog] [info] parsing read library format
[2022-05-27 09:39:24.482] [jointLog] [info] There is 1 library.
[2022-05-27 09:39:24.482] [jointLog] [info] Loading pufferfish index
[2022-05-27 09:39:24.482] [jointLog] [info] Loading dense pufferfish index.
Inventory entries filled: 108
-----------------------------------------
| Loading contig boundaries | Time = 22.383 ms
-----------------------------------------
size = 13735244
-----------------------------------------
| Loading sequence | Time = 2.0487 ms
-----------------------------------------
size = 12083744
-----------------------------------------
| Loading positions | Time = 20.606 ms
-----------------------------------------
size = 17192700
-----------------------------------------
| Loading reference sequence | Time = 2.7591 ms
-----------------------------------------
-----------------------------------------
| Loading reference accumulative lengths | Time = 94.895 us
-----------------------------------------
[2022-05-27 09:39:24.545] [jointLog] [info] done
[2022-05-27 09:39:24.566] [jointLog] [info] Index contained 34752 targets
[2022-05-27 09:39:24.574] [jointLog] [info] Number of decoys : 0
[2022-05-27 09:39:24.918] [jointLog] [info] Automatically detected most likely library type as ISR
[A
[32mprocessed[31m 500000 [32mfragments[0m
hits: 973845, hits per frag: 2.01252
[2022-05-27 09:39:27.264] [jointLog] [info] Thread saw mini-batch with a maximum of 1.30% zero probability fragments
[2022-05-27 09:39:27.281] [jointLog] [info] Thread saw mini-batch with a maximum of 1.20% zero probability fragments
[2022-05-27 09:39:27.286] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments
[2022-05-27 09:39:27.323] [jointLog] [info] Thread saw mini-batch with a maximum of 1.32% zero probability fragments
[2022-05-27 09:39:27.370] [jointLog] [info] Thread saw mini-batch with a maximum of 1.16% zero probability fragments
[2022-05-27 09:39:27.389] [jointLog] [info] Thread saw mini-batch with a maximum of 1.14% zero probability fragments
[2022-05-27 09:39:27.469] [jointLog] [info] Computed 27479 rich equivalence classes for further processing
[2022-05-27 09:39:27.469] [jointLog] [info] Counted 446837 total reads in the equivalence classes
[2022-05-27 09:39:27.473] [jointLog] [info] Number of mappings discarded because of alignment score : 70855
[2022-05-27 09:39:27.473] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 11346
[2022-05-27 09:39:27.473] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2022-05-27 09:39:27.473] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 14621
[2022-05-27 09:39:27.476] [jointLog] [warning] Only 446837 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.
[2022-05-27 09:39:27.476] [jointLog] [info] Mapping rate = 89.3674%
[2022-05-27 09:39:27.476] [jointLog] [info] finished quantifyLibrary()
[2022-05-27 09:39:27.476] [jointLog] [info] Starting optimizer
[2022-05-27 09:39:27.489] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-05-27 09:39:27.492] [jointLog] [info] iteration = 0 | max rel diff. = 1163.97
[2022-05-27 09:39:27.655] [jointLog] [info] iteration = 100 | max rel diff. = 0.232063
[2022-05-27 09:39:27.806] [jointLog] [info] iteration = 200 | max rel diff. = 0.297536
[2022-05-27 09:39:27.922] [jointLog] [info] iteration = 277 | max rel diff. = 0.00595793
[2022-05-27 09:39:27.923] [jointLog] [info] Finished optimizer
[2022-05-27 09:39:27.923] [jointLog] [info] writing output
calulating flagstat...
Sorting and indexing bam
[bam_sort_core] merging from 0 files and 6 in-memory blocks...
Proceccing a contig lenght output option
Version Info: This is the most recent version of salmon.
### salmon (selective-alignment-based) v1.8.0
### [ program ] => salmon
### [ command ] => quant
### [ index ] => { index }
### [ threads ] => { 6 }
### [ libType ] => { A }
### [ validateMappings ] => { }
### [ mates1 ] => { input_1/0h_B_1.fq.gz }
### [ mates2 ] => { input_1/0h_B_2.fq.gz }
### [ output ] => { output/0h_B_1.fq.gz }
### [ writeMappings ] => { output/0h_B_1.fq.gz/0h_B_1.fq.gz.sam }
Logs will be written to output/0h_B_1.fq.gz/logs
-----------------------------------------
| Loading contig table | Time = 10.043 ms
-----------------------------------------
size = 55051
-----------------------------------------
| Loading contig offsets | Time = 141.42 us
-----------------------------------------
-----------------------------------------
| Loading reference lengths | Time = 65.179 us
-----------------------------------------
-----------------------------------------
| Loading mphf table | Time = 3.6582 ms
-----------------------------------------
size = 13735244
Number of ones: 55050
Number of ones per inventory item: 512
[2022-05-27 09:39:35.337] [jointLog] [info] setting maxHashResizeThreads to 6
[2022-05-27 09:39:35.337] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
[2022-05-27 09:39:35.337] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-05-27 09:39:35.337] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-05-27 09:39:35.337] [jointLog] [info] parsing read library format
[2022-05-27 09:39:35.337] [jointLog] [info] There is 1 library.
[2022-05-27 09:39:35.337] [jointLog] [info] Loading pufferfish index
[2022-05-27 09:39:35.337] [jointLog] [info] Loading dense pufferfish index.
Inventory entries filled: 108
-----------------------------------------
| Loading contig boundaries | Time = 22.403 ms
-----------------------------------------
size = 13735244
-----------------------------------------
| Loading sequence | Time = 2.1002 ms
-----------------------------------------
size = 12083744
-----------------------------------------
| Loading positions | Time = 19.181 ms
-----------------------------------------
size = 17192700
-----------------------------------------
| Loading reference sequence | Time = 2.5517 ms
-----------------------------------------
-----------------------------------------
| Loading reference accumulative lengths | Time = 99.561 us
-----------------------------------------
[2022-05-27 09:39:35.398] [jointLog] [info] done
[2022-05-27 09:39:35.419] [jointLog] [info] Index contained 34752 targets
[2022-05-27 09:39:35.427] [jointLog] [info] Number of decoys : 0
[2022-05-27 09:39:35.791] [jointLog] [info] Automatically detected most likely library type as ISR
[A
[32mprocessed[31m 500000 [32mfragments[0m
hits: 983502, hits per frag: 2.04113[2022-05-27 09:39:38.200] [jointLog] [info] Thread saw mini-batch with a maximum of 0.90% zero probability fragments
[2022-05-27 09:39:38.212] [jointLog] [info] Thread saw mini-batch with a maximum of 0.92% zero probability fragments
[2022-05-27 09:39:38.226] [jointLog] [info] Thread saw mini-batch with a maximum of 1.12% zero probability fragments
[2022-05-27 09:39:38.275] [jointLog] [info] Thread saw mini-batch with a maximum of 0.86% zero probability fragments
[2022-05-27 09:39:38.289] [jointLog] [info] Thread saw mini-batch with a maximum of 0.90% zero probability fragments
[2022-05-27 09:39:38.306] [jointLog] [info] Thread saw mini-batch with a maximum of 0.76% zero probability fragments
[2022-05-27 09:39:38.386] [jointLog] [info] Computed 26222 rich equivalence classes for further processing
[2022-05-27 09:39:38.386] [jointLog] [info] Counted 451182 total reads in the equivalence classes
[2022-05-27 09:39:38.390] [jointLog] [info] Number of mappings discarded because of alignment score : 56158
[2022-05-27 09:39:38.390] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 10836
[2022-05-27 09:39:38.390] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2022-05-27 09:39:38.390] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 11963
[2022-05-27 09:39:38.393] [jointLog] [warning] Only 451182 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.
[2022-05-27 09:39:38.393] [jointLog] [info] Mapping rate = 90.2364%
[2022-05-27 09:39:38.393] [jointLog] [info] finished quantifyLibrary()
[2022-05-27 09:39:38.393] [jointLog] [info] Starting optimizer
[2022-05-27 09:39:38.407] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-05-27 09:39:38.409] [jointLog] [info] iteration = 0 | max rel diff. = 1276.79
[2022-05-27 09:39:38.571] [jointLog] [info] iteration = 100 | max rel diff. = 1.24167
[2022-05-27 09:39:38.720] [jointLog] [info] iteration = 200 | max rel diff. = 0.20455
[2022-05-27 09:39:38.870] [jointLog] [info] iteration = 300 | max rel diff. = 0.528338
[2022-05-27 09:39:38.966] [jointLog] [info] iteration = 365 | max rel diff. = 0.00778503
[2022-05-27 09:39:38.967] [jointLog] [info] Finished optimizer
[2022-05-27 09:39:38.967] [jointLog] [info] writing output
calulating flagstat...
Sorting and indexing bam
[bam_sort_core] merging from 0 files and 6 in-memory blocks...
Proceccing a contig lenght output option
Version Info: This is the most recent version of salmon.
### salmon (selective-alignment-based) v1.8.0
### [ program ] => salmon
### [ command ] => quant
### [ index ] => { index }
### [ threads ] => { 6 }
### [ libType ] => { A }
### [ validateMappings ] => { }
### [ mates1 ] => { input_1/1week_A1_1.fq.gz }
### [ mates2 ] => { input_1/1week_A1_2.fq.gz }
### [ output ] => { output/1week_A1_1.fq.gz }
### [ writeMappings ] => { output/1week_A1_1.fq.gz/1week_A1_1.fq.gz.sam }
Logs will be written to output/1week_A1_1.fq.gz/logs
[2022-05-27 09:39:46.128] [jointLog] [info] setting maxHashResizeThreads to 6
[2022-05-27 09:39:46.129] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
[2022-05-27 09:39:46.129] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-05-27 09:39:46.129] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-05-27 09:39:46.129] [jointLog] [info] parsing read library format
[2022-05-27 09:39:46.129] [jointLog] [info] There is 1 library.
[2022-05-27 09:39:46.129] [jointLog] [info] Loading pufferfish index
[2022-05-27 09:39:46.129] [jointLog] [info] Loading dense pufferfish index.
-----------------------------------------
| Loading contig table | Time = 10.476 ms
-----------------------------------------
size = 55051
-----------------------------------------
| Loading contig offsets | Time = 148.3 us
-----------------------------------------
-----------------------------------------
| Loading reference lengths | Time = 44.24 us
-----------------------------------------
-----------------------------------------
| Loading mphf table | Time = 3.3958 ms
-----------------------------------------
size = 13735244
Number of ones: 55050
Number of ones per inventory item: 512
Inventory entries filled: 108
-----------------------------------------
| Loading contig boundaries | Time = 25.811 ms
-----------------------------------------
size = 13735244
-----------------------------------------
| Loading sequence | Time = 2.092 ms
-----------------------------------------
size = 12083744
-----------------------------------------
| Loading positions | Time = 18.366 ms
-----------------------------------------
size = 17192700
-----------------------------------------
| Loading reference sequence | Time = 2.4663 ms
-----------------------------------------
-----------------------------------------
| Loading reference accumulative lengths | Time = 100.69 us
-----------------------------------------
[2022-05-27 09:39:46.192] [jointLog] [info] done
[2022-05-27 09:39:46.214] [jointLog] [info] Index contained 34752 targets
[2022-05-27 09:39:46.221] [jointLog] [info] Number of decoys : 0
[2022-05-27 09:39:46.661] [jointLog] [info] Automatically detected most likely library type as ISR
[A
[32mprocessed[31m 500000 [32mfragments[0m
hits: 742328, hits per frag: 1.52738
[2022-05-27 09:39:49.211] [jointLog] [info] Thread saw mini-batch with a maximum of 1.36% zero probability fragments
[2022-05-27 09:39:49.218] [jointLog] [info] Thread saw mini-batch with a maximum of 1.38% zero probability fragments
[2022-05-27 09:39:49.234] [jointLog] [info] Thread saw mini-batch with a maximum of 1.24% zero probability fragments
[2022-05-27 09:39:49.241] [jointLog] [info] Thread saw mini-batch with a maximum of 1.12% zero probability fragments
[2022-05-27 09:39:49.241] [jointLog] [info] Thread saw mini-batch with a maximum of 1.26% zero probability fragments
[2022-05-27 09:39:49.260] [jointLog] [info] Thread saw mini-batch with a maximum of 1.34% zero probability fragments
[2022-05-27 09:39:49.350] [jointLog] [info] Computed 40088 rich equivalence classes for further processing
[2022-05-27 09:39:49.350] [jointLog] [info] Counted 423258 total reads in the equivalence classes
[2022-05-27 09:39:49.354] [jointLog] [info] Number of mappings discarded because of alignment score : 94556
[2022-05-27 09:39:49.354] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 16941
[2022-05-27 09:39:49.354] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2022-05-27 09:39:49.354] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 11202
[2022-05-27 09:39:49.356] [jointLog] [warning] Only 423258 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.
[2022-05-27 09:39:49.356] [jointLog] [info] Mapping rate = 77.5378%
[2022-05-27 09:39:49.357] [jointLog] [info] finished quantifyLibrary()
[2022-05-27 09:39:49.357] [jointLog] [info] Starting optimizer
[2022-05-27 09:39:49.372] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-05-27 09:39:49.375] [jointLog] [info] iteration = 0 | max rel diff. = 1161.32
[2022-05-27 09:39:49.554] [jointLog] [info] iteration = 100 | max rel diff. = 0.940865
[2022-05-27 09:39:49.723] [jointLog] [info] iteration = 200 | max rel diff. = 0.266643
[2022-05-27 09:39:49.834] [jointLog] [info] iteration = 267 | max rel diff. = 0.00102094
[2022-05-27 09:39:49.835] [jointLog] [info] Finished optimizer
[2022-05-27 09:39:49.835] [jointLog] [info] writing output
calulating flagstat...
Sorting and indexing bam
[bam_sort_core] merging from 0 files and 6 in-memory blocks...
Proceccing a contig lenght output option
Version Info: This is the most recent version of salmon.
### salmon (selective-alignment-based) v1.8.0
### [ program ] => salmon
### [ command ] => quant
### [ index ] => { index }
### [ threads ] => { 6 }
### [ libType ] => { A }
### [ validateMappings ] => { }
### [ mates1 ] => { input_1/1week_A2_1.fq.gz }
### [ mates2 ] => { input_1/1week_A2_2.fq.gz }
### [ output ] => { output/1week_A2_1.fq.gz }
### [ writeMappings ] => { output/1week_A2_1.fq.gz/1week_A2_1.fq.gz.sam }
Logs will be written to output/1week_A2_1.fq.gz/logs
[2022-05-27 09:39:56.448] [jointLog] [info] setting maxHashResizeThreads to 6
[2022-05-27 09:39:56.448] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
[2022-05-27 09:39:56.448] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-05-27 09:39:56.448] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-05-27 09:39:56.448] [jointLog] [info] parsing read library format
[2022-05-27 09:39:56.448] [jointLog] [info] There is 1 library.
[2022-05-27 09:39:56.449] [jointLog] [info] Loading pufferfish index
[2022-05-27 09:39:56.449] [jointLog] [info] Loading dense pufferfish index.
-----------------------------------------
| Loading contig table | Time = 11.247 ms
-----------------------------------------
size = 55051
-----------------------------------------
| Loading contig offsets | Time = 146.37 us
-----------------------------------------
-----------------------------------------
| Loading reference lengths | Time = 49.382 us
-----------------------------------------
-----------------------------------------
| Loading mphf table | Time = 3.5654 ms
-----------------------------------------
size = 13735244
Number of ones: 55050
Number of ones per inventory item: 512
Inventory entries filled: 108
-----------------------------------------
| Loading contig boundaries | Time = 21.282 ms
-----------------------------------------
size = 13735244
-----------------------------------------
| Loading sequence | Time = 2.1416 ms
-----------------------------------------
size = 12083744
-----------------------------------------
| Loading positions | Time = 19.155 ms
-----------------------------------------
size = 17192700
-----------------------------------------
| Loading reference sequence | Time = 2.5586 ms
-----------------------------------------
-----------------------------------------
| Loading reference accumulative lengths | Time = 97.14 us
-----------------------------------------
[2022-05-27 09:39:56.509] [jointLog] [info] done
[2022-05-27 09:39:56.531] [jointLog] [info] Index contained 34752 targets
[2022-05-27 09:39:56.538] [jointLog] [info] Number of decoys : 0
[2022-05-27 09:39:56.973] [jointLog] [info] Automatically detected most likely library type as ISR
[2022-05-27 09:39:58.626] [jointLog] [info] Thread saw mini-batch with a maximum of 0.96% zero probability fragments
[2022-05-27 09:39:58.631] [jointLog] [info] Thread saw mini-batch with a maximum of 0.92% zero probability fragments
[2022-05-27 09:39:58.730] [jointLog] [info] Thread saw mini-batch with a maximum of 1.02% zero probability fragments
[2022-05-27 09:39:58.740] [jointLog] [info] Thread saw mini-batch with a maximum of 1.04% zero probability fragments
[2022-05-27 09:39:58.786] [jointLog] [info] Thread saw mini-batch with a maximum of 0.74% zero probability fragments
[2022-05-27 09:39:58.808] [jointLog] [info] Thread saw mini-batch with a maximum of 0.80% zero probability fragments
[2022-05-27 09:39:58.890] [jointLog] [info] Computed 31983 rich equivalence classes for further processing
[2022-05-27 09:39:58.890] [jointLog] [info] Counted 282677 total reads in the equivalence classes
[2022-05-27 09:39:58.894] [jointLog] [info] Number of mappings discarded because of alignment score : 75080
[2022-05-27 09:39:58.894] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 9918
[2022-05-27 09:39:58.894] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2022-05-27 09:39:58.894] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 7564
[2022-05-27 09:39:58.898] [jointLog] [warning] Only 282677 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.
[2022-05-27 09:39:58.898] [jointLog] [info] Mapping rate = 78.6006%
[2022-05-27 09:39:58.898] [jointLog] [info] finished quantifyLibrary()
[2022-05-27 09:39:58.898] [jointLog] [info] Starting optimizer
[2022-05-27 09:39:58.912] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-05-27 09:39:58.915] [jointLog] [info] iteration = 0 | max rel diff. = 780.457
[2022-05-27 09:39:59.082] [jointLog] [info] iteration = 100 | max rel diff. = 0.145292
[2022-05-27 09:39:59.238] [jointLog] [info] iteration = 200 | max rel diff. = 0.936821
[2022-05-27 09:39:59.395] [jointLog] [info] iteration = 300 | max rel diff. = 0.0190692
[2022-05-27 09:39:59.551] [jointLog] [info] iteration = 400 | max rel diff. = 0.0112251
[2022-05-27 09:39:59.717] [jointLog] [info] iteration = 500 | max rel diff. = 0.112742
[2022-05-27 09:39:59.735] [jointLog] [info] iteration = 511 | max rel diff. = 0.00882499
[2022-05-27 09:39:59.736] [jointLog] [info] Finished optimizer
[2022-05-27 09:39:59.736] [jointLog] [info] writing output
calulating flagstat...
Sorting and indexing bam
[bam_sort_core] merging from 0 files and 6 in-memory blocks...
Proceccing a contig lenght output option
++ date
+ echo completion at Fri May 27 18:40:04 JST 2022
completion at Fri May 27 18:40:04 JST 2022
++ date +%s
+ time_fin=1653644404
++ echo 'scale=2; (1653644404 - 1653644350)/60'
++ bc
+ echo -e 'Total running time is .90 min'
Total running time is .90 min
+ echo '/yoshitake/PortablePipeline/PortablePipeline/scripts completed!'
/yoshitake/PortablePipeline/PortablePipeline/scripts completed!
+ post_processing
+ '[' 1 = 1 ']'
+ echo 0
+ exit
PID: 267966