metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end

Meta-barcoding metagenome analysis pipeline using SILVA SSU+LSU, PR2 database and NCBI 16S, 23S, mito and plastid database

input_1:single-end FASTQ(.gz)

input_1/18-2-100.fq

@Q8-3fde602c-5233-4e88-b1d2-86d1d3671212:28:516:1:MiseqIndex-i5-UDP0002:Index10bp-i7-UDP0002
AGCAGAAGACGGCATAGGAGTCTACAAGATAGTGACTGAGTTCAGACGTGTGCTCTTCGATCCGGGCGATGTGGTGCGCGTGCAGCCCAGAACATCTAAGGGCCATCACAGACCTGTTGGCTGCCTCATACTTCCATTGGCTAGACGCCAACAGTCCCTCTAAGGCGCCCGCGCGACTGCACGGCGCTGCGCTCTAATCAACTGTTTGGCGGGTTCTTGAGGTCTCGTTCAATTTACCGGAATCAACCTGATGACAACCCACCATTCCAGGGGCATTTTTTTTTTTTCCTACACATGAATCAAAGAAAAACCTGCTCAAATGTGATGGTCCTTCCTATGTCTGGACCCTGGTAAGTTTTCCCGTGTTGAGTCAGATGCTGACACACCCAAAGGCTCCACGCCTGGTGGTGCCCTTCAATGAATTCGCTAGTCGGAAGAACGTCGTGTAGGGAAAGAGTGTAGGTCAGATAGTGTAGATCTCGGTGGTCG
+
'''''(),5599866.('''*+++//../0100//011*''((...12223266544+&$$%%&%&&(1266.,,,--/.-(((&&'').175:;=---3/-,+))*++*+**+''))&%%%%%&)++11::=>>999;;<;9:;<;;@??@<;<;;=/1.-+'%%%%(((*++*,,-++'''''%%%%$###$%&&&&&%$%$#$$$&'$$$#$$$$$$&'(('%%&&'('%&+*,./089<=5212)((%$$$$$$%%$'((''&%$$%%%%$%&&*/000///+++)%%$$$%%%$%(&%%%''''&%%%$$$%$$#$$$$$$$#$$$')))**+/13::;<?<,)/211115888@;7377DI;52,+)'&&&&%$%%%%&*++*)&&(+))),,@CC@;65543>FB7686+*(''&&+*'&%%&%%%&--73(''''1///////13.*.5;?BAA;=?)((((((((-B????;:::;.+*+
@Q8-5c18ecf2-456f-4693-a732-b201f358cc29:33:508:-1:MiseqIndex-i5-UDP0002:Index10bp-i7-UDP0002
CAAGCAGGAAGACGGCATACGAGATCTACAAGATAGTGACTGAGTTCAGACGCGTGCTCTTCCGACTTGAGGGTGTGTGAGTGCGCGTGCGGCCCAGAACACCAAGTGTCACAGACCTGTTATTGCCTCATATCACCGGCCGGTTGACGCCACCAGTCCCTCTGTAGCGCAGGACTGCTTGTGCAGACGTCACTATTTAGAGGACAGAGTCTGCTCTGTTATCGCATTAAGCAGACAAATCGAGATCAATCCGTTGACTGGCTTTATGCACCACCACCCACCTGAATGAGGAGAGCTCTTGATCTGTCAATCCTGAGTTGTGTGTCCGGGCCTGCGAGATTTCCCGTGCTGAGTCAAATTGCCGCAGGCTCCACTCCTGGTGGTGCCCTCCCCGCCACCCTCACATAGATCGAAGAGCGTCGTGGTAGGGAAGAGTGTAGGTCAGACAGTGTAGATCTCGGTGGTCGCCAGATCAT
+
6999889;66644667:;<<=43000027740-+++*+))*44430-,)&&&''''())(''&%$$$&*%'((()''&$%&&)(,,--+*)&%$$$''&%$$%&&%&(248::;667<>>?98431.)'&&((%$$$%&%&(()3754''''(59+**1+(('('(((&%%&%%&%$$%%%&-.0.//-'&&&&&&$$%'(.///.0-+*(''&',,,,++++)%%%%%%&((3/*)&'()(((*))'&%%%%%%'''()'$$$%&)+,-,,,,,()*&%%$$$$$%''',+('&&%%%%&''((.-,-+***),---,,,./88864/.++**)3486;7-4643100/00-)(('&'')))---554/.-,*+,,++++65404642(2431,'%&''&%$%%'12---1.)&&&&&%%$$%()-/./6,)'''))))(('')(((&&&&**('&&&))*-+)((&$#$%$$%$
@Q8-a0078df2-60b1-4b62-95a0-1fa59ab3c9c8:19:449:1:MiseqIndex-i5-UDP0002:Index10bp-i7-UDP0002
CAAGCAGAAGACGGCATACGAGATCTACAAGATAGTGGCTGGAGTTCAGACGTGTGCTCTTCCAAATGTGCGTGCTGTATGACATCAAGAGCATCTAAAAGGGCATCACCAATTGTTATTGCCCCCCACCACTGGTTGGTCACCAGAATAAAATGATGCAAAAGCTAAAGCCACACTAACCTTATCGAGCAGGGTCTCGTTTGCCAGAACAGACAAATCACTCCTGTGAAGGCGACGCACACACAAGATCAAGAAAAGCTCTAAATCTGTCAATCCTTATTGTGTGGATATCTAGGTAGGTTCCCGTGTTAGGTCAAGTATGCAGATACACCTGGTGGTGCCCTTCCGTCAATTCTAGATCGGAAAGGCGTCGATTGTAGGAAAGAGTGTAGGTCAGATAGTGCATAGATCTCGGTGGTCGCCGTATCATT

input_1/18-1-100.fq

@Q8-45e07f95-345a-4963-9602-a5f9038f68fd:26:485:1:MiseqIndex-i5-UDP0001:Index10bp-i7-UDP0001
CAAGCAGAAGACGGCATACTGCAATTCGTGGAGCAGTGACTGGAGTTCAGACGTGTGCTCTTCCGGTGACCAATGTAGTACGGGCAGGCCAGGACATTGGGGCATTGCTGAGTTACAACCTCAACTTTATGGCCTAAACATTACTTAGTCCCTCTAGGAGAGGGTAGCACACAAGTCACCAGACGAAACATCTGAACTAGTAAGCGGAGGTCTCATTCTCGTTATCGAATTAAGCAGACAAATCACTCCACCAACTAAGAACATTACATGCACCACCATAGAATCAAGAAGAAGACCTTTCGTCTGTCAATCCTCACCATGTCTGGACCAGTTTCCCGTGTTGAGTCAAATTAAGCCCAGGCTCACACTCCTGTTGCTTCGTCAATTCCACATCAAGATCGGAAAATAAGGGAAAAGTGGCGAACTGAGCGGTGTGATCTCGGTGAGTCGCCGTATCATT
+
+-..010/./-0(&&&&&&&%&'((7<98880-+)(('*-7997677;3221''&(())12791(''&&''%$$$$%'('('%$$%%%$$&&&'**'$$#$$$'((%$$$$%%&%$$$$%$%&%&(()-(&%%'')121((((''))*,/20-0.,,''&'&&''*''''&&%%$$&&'(&&(*((((,377:11111+***),+++4733334+++,*'&'())9*)).016)))()../-,0.../+**+,,156555780-,,,,,-.../33/,&(-01594/..*((((),0013+&&&'*67323;*(((683,,0000154,('**,.3-'*,483----/12148;877,*&%&')((&&&((*+()&'+,.(((669<84333465.*''(%%&((''&%$$%'*)'((()(''(,-('('('''&&''(-.1001,++**,-,)**((''
@Q8-b12a3dbe-44fc-429f-8f64-59dd3f7fa319:25:500:-1:MiseqIndex-i5-UDP0001:Index10bp-i7-UDP0001
CAAGCAGAAGACGGCGACGAGATTCGTGGAGCGGTGACTGGAGTTCAGACGTGCGCTCTTCCGATTTGGATGTAGTGCGCGTGCGGCCCAGGACATCTAAGGGCATCACAGACCTGTTATTGCCTCCAACTCCGTACTTAAACGACCATAGTCCCTCTAGGAAGACGCTACTGTCCGCAGACGAAACATCTAGACTAGTAGGCGAGGTTCTGTTCGTTATCGGAATTAACCGCTAGACAGACTACCCACCCGAACTAAGAACGGCCATGCACTCACTCACCCATAGAATCAAGACCTTTCAATTCCGTCGTCTCACCATGTCTGGACCTGGTAAGTTTCCAAAAGGAGAGTCAAATTTAAGCCGCAGGTCTTTTACCTCAGGTGCCCTTCCTAATTTCTTGGTTCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGGCAACTGGAGCGGTGTAGATCTCGGTGGTCGCCGTATCATT
+
/++++<=96)''''''6810///22==RF@?>@:;53//.1//0145;6+*))*444486,**'*--0,++,,-3100736675788712<<655556;78644444:;;54446AA?3++**))++*('))*.-''0)'&'+22239::10-+)**(()9993333++++,6+***,55566=><<===<,,,++1113(((6/...,,,--22?>;;:7772111+'''''')&$$$$%%(*),(&%%&&'')*>74.,+,,,,121-**)'(()10/00114>1/,&'''('&&''&'&%%'())('(*30./,++,)(((/.,+*+,,,**(%$%%%%%&(**-(5422/('''&%%%&((()*+)'*,))()*-.,(''),,&$%%&*)),+(&&((((0:9600;<<554330+***0/26<==:7/.('())))-44///..//05766335.,,+***+,----++)(
@Q8-9f320dfe-8e55-49aa-b675-c87477ab8e33:21:503:-1:MiseqIndex-i5-UDP0001:Index10bp-i7-UDP0001
CAAGCAGAAGACAGCACAATGAGATTCGTGGAGCGGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTGCTAGTGTAGCGCGCGCGCAGCCCAGGGCGTATCTAAGGGCATCACAGACCTGTTATTGCCTCCAATCCTTACGTCACAACGACCATATCCCTTCTAGGAAAAGACGACACCGTCCGTGGTCGGGCTGCTCCAATTGCTATGGCGTCTCAGCCTGTTATCGGAATTAAATCCGTGACAAATCATCTTGAATTAACTAAGAACGGCCATGCACCACCACCATAGAATCAAGAAAGACCTTTCAATTCCACACCACTAGTGTCTGACCCTCTGTAAGTTTCTGCATGAGTCAAATTGTTTAGTGCTCCATCTCTGAGGTGCCCTTCCGTCAATTCTGTAGCACAGATCGGAAGAGCGTCGTAGGGAAAGAGTGTGAACTGAGTTGTGTAGATCTCGGTGGTCCGCCGTATCATT

Command

metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -c 8 -m 32 input_1/

Output

all.html

view all outputs

Log

pp metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -c 8 -m 32 input_1/
Checking the realpath of input files.
0 input_1/
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end/input_1/18-2.fq
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end/input_1/18-1.fq
/home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work
/home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end
/data/yoshitake.kazutoshi/work
/data/yoshitake.kazutoshi/work/pp-dev
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end
c2997108/centos7:2-blast-taxid-2-KronaTools-2.7-pr2-mito-silva-2 c2997108/centos7:3-java centos:centos6
using docker
++ docker pull c2997108/centos7:2-blast-taxid-2-KronaTools-2.7-pr2-mito-silva-2
2-blast-taxid-2-KronaTools-2.7-pr2-mito-silva-2: Pulling from c2997108/centos7
8395db55f28d: Pulling fs layer
07a5b0e61101: Pulling fs layer
ecc7efef2bb7: Pulling fs layer
dd38eafa9837: Pulling fs layer
c4c31ded563a: Pulling fs layer
851cab83bf22: Pulling fs layer
71c662b21b88: Pulling fs layer
a5c36ef11142: Pulling fs layer
ae113d1ed560: Pulling fs layer
8b535496c48e: Pulling fs layer
11ec9429c7b2: Pulling fs layer
dd38eafa9837: Waiting
c4c31ded563a: Waiting
ae113d1ed560: Waiting
11ec9429c7b2: Waiting
8b535496c48e: Waiting
851cab83bf22: Waiting
a5c36ef11142: Waiting
ecc7efef2bb7: Download complete
8395db55f28d: Download complete
8395db55f28d: Pull complete
07a5b0e61101: Download complete
851cab83bf22: Download complete
07a5b0e61101: Pull complete
ecc7efef2bb7: Pull complete
71c662b21b88: Verifying Checksum
71c662b21b88: Download complete
a5c36ef11142: Verifying Checksum
a5c36ef11142: Download complete
c4c31ded563a: Verifying Checksum
c4c31ded563a: Download complete
dd38eafa9837: Verifying Checksum
dd38eafa9837: Download complete
dd38eafa9837: Pull complete
c4c31ded563a: Pull complete
851cab83bf22: Pull complete
71c662b21b88: Pull complete
a5c36ef11142: Pull complete
ae113d1ed560: Download complete
ae113d1ed560: Pull complete
11ec9429c7b2: Verifying Checksum
11ec9429c7b2: Download complete
8b535496c48e: Download complete
8b535496c48e: Pull complete
11ec9429c7b2: Pull complete
Digest: sha256:712810b86c93ee5884219373950c8bdf40240eac20876dd96f3e043de543aa3c
Status: Downloaded newer image for c2997108/centos7:2-blast-taxid-2-KronaTools-2.7-pr2-mito-silva-2
docker.io/c2997108/centos7:2-blast-taxid-2-KronaTools-2.7-pr2-mito-silva-2
++ set +ex
++ docker pull c2997108/centos7:3-java
3-java: Pulling from c2997108/centos7
8395db55f28d: Already exists
07a5b0e61101: Already exists
ecc7efef2bb7: Already exists
a38a030c98cc: Pulling fs layer
f076acacc97b: Pulling fs layer
a38a030c98cc: Verifying Checksum
a38a030c98cc: Download complete
a38a030c98cc: Pull complete
f076acacc97b: Verifying Checksum
f076acacc97b: Download complete
f076acacc97b: Pull complete
Digest: sha256:f99843e71acffde81296e63970b1c57d90b3a7376e5b0d699e2bdeffd9b9e96a
Status: Downloaded newer image for c2997108/centos7:3-java
docker.io/c2997108/centos7:3-java
++ set +ex
+ set -o pipefail
+ cat
+ sed s/zcat/cat/g run-gz.sh
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
++ find input_1//
++ egrep '[.]f(ast|)q$'
+ for i in `find $input_1/|egrep "[.]f(ast|)q$"||true`
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -u 2007:600 -i --rm c2997108/centos7:2-blast-taxid-2-KronaTools-2.7-pr2-mito-silva-2 bash run.sh input_1//18-2.fq 100 0.95 8 ''
+ for i in `find $input_1/|egrep "[.]f(ast|)q$"||true`
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -u 2007:600 -i --rm c2997108/centos7:2-blast-taxid-2-KronaTools-2.7-pr2-mito-silva-2 bash run.sh input_1//18-1.fq 100 0.95 8 ''
++ find input_1//
++ egrep '[.]f(ast|)q[.]gz$'
++ true
+ echo '##count reads'
##count reads
+++ cat input_1//18-2.fq
+++ wc -l
++ expr 14968 / 4
+ n0=3742
+ echo '##convert fastq to fasta'
##convert fastq to fasta
+ j=input_1//18-2.fasta
+ cat input_1//18-2.fq
+ awk 'NR%4==1{print ">"substr($0,2)} NR%4==2{print $0}'
+ echo '##blast'
##blast
+ blastn -db /usr/local/blastdb/database.fasta -query input_1//18-2.fasta -outfmt 6 -out input_1//18-2.fasta.ssu.all.blast -num_threads 8
Checking the realpath of input files.
0 input_1/
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end/input_1/18-2-100.fq
1 /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end/input_1/18-1-100.fq
/home/yoshitake.kazutoshi/work -> /data/yoshitake.kazutoshi/work
/home/yoshitake.kazutoshi/work/pp-dev -> /data/yoshitake.kazutoshi/work/pp-dev
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -> /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end
/data/yoshitake.kazutoshi/work
/data/yoshitake.kazutoshi/work/pp-dev
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test
/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end
c2997108/centos7:2-blast-taxid-2-KronaTools-2.7-pr2-mito-silva-2 c2997108/centos7:3-java centos:centos6
using docker
+ set -o pipefail
+ cat
+ sed s/zcat/cat/g run-gz.sh
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
++ find input_1//
++ egrep '[.]f(ast|)q$'
+ for i in `find $input_1/|egrep "[.]f(ast|)q$"||true`
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -u 2007:600 -i --rm c2997108/centos7:2-blast-taxid-2-KronaTools-2.7-pr2-mito-silva-2 bash run.sh input_1//18-2-100.fq 100 0.95 8 ''
+ for i in `find $input_1/|egrep "[.]f(ast|)q$"||true`
+ echo 'PPDOCNAME=pp`date' '+%Y%m%d_%H%M%S_%3N`_$RANDOM;' echo '$PPDOCNAME' '>>' '/home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end/pp-docker-list;' docker run --name '${PPDOCNAME}' -v '$PWD:$PWD' -w '$PWD' -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -u 2007:600 -i --rm c2997108/centos7:2-blast-taxid-2-KronaTools-2.7-pr2-mito-silva-2 bash run.sh input_1//18-1-100.fq 100 0.95 8 ''
++ find input_1//
++ egrep '[.]f(ast|)q[.]gz$'
++ true
##count reads
+ echo '##count reads'
+++ cat input_1//18-2-100.fq
+++ wc -l
++ expr 400 / 4
+ n0=100
+ echo '##convert fastq to fasta'
##convert fastq to fasta
+ j=input_1//18-2-100.fasta
+ cat input_1//18-2-100.fq
+ awk 'NR%4==1{print ">"substr($0,2)} NR%4==2{print $0}'
+ echo '##blast'
##blast
+ blastn -db /usr/local/blastdb/database.fasta -query input_1//18-2-100.fasta -outfmt 6 -out input_1//18-2-100.fasta.ssu.all.blast -num_threads 8
+ echo 'blast status: ' 0
+ rm input_1//18-2-100.fasta
blast status:  0
+ echo '##filtering'
##filtering
+ cat input_1//18-2-100.fasta.ssu.all.blast
+ awk '-F\t' '$12>100{if(a[$1]==1){if($12>=topbit*0.95){print $0}}else{a[$1]=1; topbit=$12; print $0}}'
+ echo '##determine LCA'
##determine LCA
+ awk '-F\t' 'FILENAME==ARGV[1]{split($1,arr,"[.]"); name[arr[1]]=$2} FILENAME==ARGV[2]{split($2,arr,"[.]"); print name[arr[1]]"\t"$0}' /usr/local/blastdb/database.fasta.path input_1//18-2-100.fasta.ssu.blast.filtered
+ awk '-F\t' '
function searchLCA(data,  i, j, res, res2, str, n, stopflag){
 for(i in data){
  if(n==0){n=split(i,res,";")}
  else{split(i,res2,";"); for(j in res){if(res[j]!=res2[j]){res[j]=""}}}
 }
 if(res[1]!=""){str=res[1]}else{str="unknown"; stopflag=1};
 for(i=2;i<=n;i++){if(stopflag==0 && res[i]!=""){str=str";"res[i]}else{stopflag=1}}
 return str;
}
{
 if($2!=old){if(old!=""){print searchLCA(data)"\t"oldstr}; delete data; data[$1]=1; old=$2; oldstr=$0}
 else{data[$1]=1}
}
END{if(length(data)>0){print searchLCA(data)"\t"oldstr}}
' input_1//18-2-100.fasta.ssu.blast.filtered.name
+ awk '-F\t' '{cnt[$1]++} END{PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print i"\t"cnt[i]}}' input_1//18-2-100.fasta.ssu.blast.filtered.name.lca
+ awk '-F\t' '{print "root;"$0}' input_1//18-2-100.fasta.ssu.blast.filtered.name.lca.cnt
++ awk '-F\t' '{a+=$2} END{if(a==""){a=0}; print a}' input_1//18-2-100.fasta.ssu.blast.filtered.name.lca.cnt
+ cnt=84
++ expr 100 - 84
+ echo -e 'No Hit\t16'
+ awk '-F\t' '
{n=split($1,arr,";"); ORS="\t"; print $2; for(i=1;i"substr($0,2)} NR%4==2{print $0}'
+ echo '##blast'
##blast
+ blastn -db /usr/local/blastdb/database.fasta -query input_1//18-1-100.fasta -outfmt 6 -out input_1//18-1-100.fasta.ssu.all.blast -num_threads 8
blast status:  0
+ echo 'blast status: ' 0
+ rm input_1//18-1-100.fasta
##filtering
+ echo '##filtering'
+ cat input_1//18-1-100.fasta.ssu.all.blast
+ awk '-F\t' '$12>100{if(a[$1]==1){if($12>=topbit*0.95){print $0}}else{a[$1]=1; topbit=$12; print $0}}'
+ echo '##determine LCA'
+ awk '-F\t' 'FILENAME==ARGV[1]{split($1,arr,"[.]"); name[arr[1]]=$2} FILENAME==ARGV[2]{split($2,arr,"[.]"); print name[arr[1]]"\t"$0}' /usr/local/blastdb/database.fasta.path input_1//18-1-100.fasta.ssu.blast.filtered
##determine LCA
+ awk '-F\t' '
function searchLCA(data,  i, j, res, res2, str, n, stopflag){
 for(i in data){
  if(n==0){n=split(i,res,";")}
  else{split(i,res2,";"); for(j in res){if(res[j]!=res2[j]){res[j]=""}}}
 }
 if(res[1]!=""){str=res[1]}else{str="unknown"; stopflag=1};
 for(i=2;i<=n;i++){if(stopflag==0 && res[i]!=""){str=str";"res[i]}else{stopflag=1}}
 return str;
}
{
 if($2!=old){if(old!=""){print searchLCA(data)"\t"oldstr}; delete data; data[$1]=1; old=$2; oldstr=$0}
 else{data[$1]=1}
}
END{if(length(data)>0){print searchLCA(data)"\t"oldstr}}
' input_1//18-1-100.fasta.ssu.blast.filtered.name
+ awk '-F\t' '{cnt[$1]++} END{PROCINFO["sorted_in"]="@val_num_desc"; for(i in cnt){print i"\t"cnt[i]}}' input_1//18-1-100.fasta.ssu.blast.filtered.name.lca
+ awk '-F\t' '{print "root;"$0}' input_1//18-1-100.fasta.ssu.blast.filtered.name.lca.cnt
++ awk '-F\t' '{a+=$2} END{if(a==""){a=0}; print a}' input_1//18-1-100.fasta.ssu.blast.filtered.name.lca.cnt
+ cnt=93
++ expr 100 - 93
+ echo -e 'No Hit\t7'
+ awk '-F\t' '
{n=split($1,arr,";"); ORS="\t"; print $2; for(i=1;i1){for(i=2;i<=NF;i++){a[i]+=$i}}}
 FILENAME==ARGV[2]{if(FNR==1){OFS="\t"; for(i=2;i<=NF;i++){$i=$i" (counts per 10000)"; if(a[i]==0){a[i]=1}}; print $0}
                   else{ORS=""; print $1;for(i=2;i<=NF;i++){print "\t"$i/a[i]*10000}; print "\n"}}
' all.counts.txt ./all.counts.txt
+ PP_RUN_IMAGE=c2997108/centos7:3-java
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20231109_011228_653_30680
+ echo pp20231109_011228_653_30680
++ id -u
++ id -g
+ docker run --name pp20231109_011228_653_30680 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -u 2007:600 -i --rm c2997108/centos7:3-java awk '-F\t' '
 FILENAME==ARGV[1]{if(FNR>1){for(i=2;i<=NF;i++){a[i]+=$i}}}
 FILENAME==ARGV[2]{if(FNR==1){OFS="\t"; for(i=2;i<=NF;i++){$i=$i" (counts per 10000)"; if(a[i]==0){a[i]=1}}; print $0}
                   else{ORS=""; print $1;for(i=2;i<=NF;i++){print "\t"$i/a[i]*10000}; print "\n"}}
' all.counts.txt ./all.counts.txt
+ FUNC_RUN_DOCKER c2997108/centos7:3-java java -Xmx1G -jar /usr/local/bin/excel2.jar all.counts.txt all.counts.xlsx
+ PP_RUN_IMAGE=c2997108/centos7:3-java
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20231109_011229_423_1941
+ echo pp20231109_011229_423_1941
++ id -u
++ id -g
+ docker run --name pp20231109_011229_423_1941 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -u 2007:600 -i --rm c2997108/centos7:3-java java -Xmx1G -jar /usr/local/bin/excel2.jar all.counts.txt all.counts.xlsx
Start converting
+ FUNC_RUN_DOCKER c2997108/centos7:3-java java -Xmx1G -jar /usr/local/bin/excel2.jar all.counts.per.10000.txt all.counts.per.10000.xlsx
+ PP_RUN_IMAGE=c2997108/centos7:3-java
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20231109_011230_869_3164
+ echo pp20231109_011230_869_3164
++ id -u
++ id -g
+ docker run --name pp20231109_011230_869_3164 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -u 2007:600 -i --rm c2997108/centos7:3-java java -Xmx1G -jar /usr/local/bin/excel2.jar all.counts.per.10000.txt all.counts.per.10000.xlsx
Start converting
++ find input_1//
++ egrep '([.]blast[.]filtered(|[.]name[.]lca(|[.]cnt|[.]cnt2|[.]cnt3)))$'
+ for i in `find $input_1/|egrep "([.]blast[.]filtered(|[.]name[.]lca(|[.]cnt|[.]cnt2|[.]cnt3)))$"`
+ FUNC_RUN_DOCKER c2997108/centos7:3-java rm -f input_1//18-1-100.fasta.ssu.blast.filtered.name.lca.cnt3
+ PP_RUN_IMAGE=c2997108/centos7:3-java
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20231109_011232_319_23032
+ echo pp20231109_011232_319_23032
++ id -u
++ id -g
+ docker run --name pp20231109_011232_319_23032 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -u 2007:600 -i --rm c2997108/centos7:3-java rm -f input_1//18-1-100.fasta.ssu.blast.filtered.name.lca.cnt3
+ for i in `find $input_1/|egrep "([.]blast[.]filtered(|[.]name[.]lca(|[.]cnt|[.]cnt2|[.]cnt3)))$"`
+ FUNC_RUN_DOCKER c2997108/centos7:3-java rm -f input_1//18-2-100.fasta.ssu.blast.filtered.name.lca
+ PP_RUN_IMAGE=c2997108/centos7:3-java
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20231109_011233_132_31556
+ echo pp20231109_011233_132_31556
++ id -u
++ id -g
+ docker run --name pp20231109_011233_132_31556 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -u 2007:600 -i --rm c2997108/centos7:3-java rm -f input_1//18-2-100.fasta.ssu.blast.filtered.name.lca
+ for i in `find $input_1/|egrep "([.]blast[.]filtered(|[.]name[.]lca(|[.]cnt|[.]cnt2|[.]cnt3)))$"`
+ FUNC_RUN_DOCKER c2997108/centos7:3-java rm -f input_1//18-1-100.fasta.ssu.blast.filtered
+ PP_RUN_IMAGE=c2997108/centos7:3-java
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20231109_011233_638_1572
+ echo pp20231109_011233_638_1572
++ id -u
++ id -g
+ docker run --name pp20231109_011233_638_1572 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -u 2007:600 -i --rm c2997108/centos7:3-java rm -f input_1//18-1-100.fasta.ssu.blast.filtered
+ for i in `find $input_1/|egrep "([.]blast[.]filtered(|[.]name[.]lca(|[.]cnt|[.]cnt2|[.]cnt3)))$"`
+ FUNC_RUN_DOCKER c2997108/centos7:3-java rm -f input_1//18-2-100.fasta.ssu.blast.filtered
+ PP_RUN_IMAGE=c2997108/centos7:3-java
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20231109_011234_565_13462
+ echo pp20231109_011234_565_13462
++ id -u
++ id -g
+ docker run --name pp20231109_011234_565_13462 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -u 2007:600 -i --rm c2997108/centos7:3-java rm -f input_1//18-2-100.fasta.ssu.blast.filtered
+ for i in `find $input_1/|egrep "([.]blast[.]filtered(|[.]name[.]lca(|[.]cnt|[.]cnt2|[.]cnt3)))$"`
+ FUNC_RUN_DOCKER c2997108/centos7:3-java rm -f input_1//18-1-100.fasta.ssu.blast.filtered.name.lca
+ PP_RUN_IMAGE=c2997108/centos7:3-java
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20231109_011235_297_18684
+ echo pp20231109_011235_297_18684
++ id -u
++ id -g
+ docker run --name pp20231109_011235_297_18684 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -u 2007:600 -i --rm c2997108/centos7:3-java rm -f input_1//18-1-100.fasta.ssu.blast.filtered.name.lca
+ for i in `find $input_1/|egrep "([.]blast[.]filtered(|[.]name[.]lca(|[.]cnt|[.]cnt2|[.]cnt3)))$"`
+ FUNC_RUN_DOCKER c2997108/centos7:3-java rm -f input_1//18-2-100.fasta.ssu.blast.filtered.name.lca.cnt
+ PP_RUN_IMAGE=c2997108/centos7:3-java
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20231109_011236_055_8314
+ echo pp20231109_011236_055_8314
++ id -u
++ id -g
+ docker run --name pp20231109_011236_055_8314 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -u 2007:600 -i --rm c2997108/centos7:3-java rm -f input_1//18-2-100.fasta.ssu.blast.filtered.name.lca.cnt
+ for i in `find $input_1/|egrep "([.]blast[.]filtered(|[.]name[.]lca(|[.]cnt|[.]cnt2|[.]cnt3)))$"`
+ FUNC_RUN_DOCKER c2997108/centos7:3-java rm -f input_1//18-2-100.fasta.ssu.blast.filtered.name.lca.cnt2
+ PP_RUN_IMAGE=c2997108/centos7:3-java
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20231109_011236_485_18723
+ echo pp20231109_011236_485_18723
++ id -u
++ id -g
+ docker run --name pp20231109_011236_485_18723 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -u 2007:600 -i --rm c2997108/centos7:3-java rm -f input_1//18-2-100.fasta.ssu.blast.filtered.name.lca.cnt2
+ for i in `find $input_1/|egrep "([.]blast[.]filtered(|[.]name[.]lca(|[.]cnt|[.]cnt2|[.]cnt3)))$"`
+ FUNC_RUN_DOCKER c2997108/centos7:3-java rm -f input_1//18-1-100.fasta.ssu.blast.filtered.name.lca.cnt
+ PP_RUN_IMAGE=c2997108/centos7:3-java
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20231109_011237_253_28061
+ echo pp20231109_011237_253_28061
++ id -u
++ id -g
+ docker run --name pp20231109_011237_253_28061 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -u 2007:600 -i --rm c2997108/centos7:3-java rm -f input_1//18-1-100.fasta.ssu.blast.filtered.name.lca.cnt
+ for i in `find $input_1/|egrep "([.]blast[.]filtered(|[.]name[.]lca(|[.]cnt|[.]cnt2|[.]cnt3)))$"`
+ FUNC_RUN_DOCKER c2997108/centos7:3-java rm -f input_1//18-2-100.fasta.ssu.blast.filtered.name.lca.cnt3
+ PP_RUN_IMAGE=c2997108/centos7:3-java
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20231109_011237_897_24660
+ echo pp20231109_011237_897_24660
++ id -u
++ id -g
+ docker run --name pp20231109_011237_897_24660 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -u 2007:600 -i --rm c2997108/centos7:3-java rm -f input_1//18-2-100.fasta.ssu.blast.filtered.name.lca.cnt3
+ for i in `find $input_1/|egrep "([.]blast[.]filtered(|[.]name[.]lca(|[.]cnt|[.]cnt2|[.]cnt3)))$"`
+ FUNC_RUN_DOCKER c2997108/centos7:3-java rm -f input_1//18-1-100.fasta.ssu.blast.filtered.name.lca.cnt2
+ PP_RUN_IMAGE=c2997108/centos7:3-java
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20231109_011238_416_25808
+ echo pp20231109_011238_416_25808
++ id -u
++ id -g
+ docker run --name pp20231109_011238_416_25808 -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -w /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -v /data/yoshitake.kazutoshi/work:/data/yoshitake.kazutoshi/work -v /data/yoshitake.kazutoshi/work/pp-dev:/data/yoshitake.kazutoshi/work/pp-dev -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test -v /data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end:/data/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end -u 2007:600 -i --rm c2997108/centos7:3-java rm -f input_1//18-1-100.fasta.ssu.blast.filtered.name.lca.cnt2
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /home/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/metagenome~silva-SSU-LSU_PR2_NCBI-16S-mito-plastid_single-end/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit
PID: 3930147