annotation~blast-diamond_for_cDNA

Add annotation of reference cDNAs/Proteins with blastn/blastx/diamond

input_1:an input cDNA file

input_1/test.fa

>BMgn002072|Gene000001
ATGTTTTTTCAGGCAGCCAGTGCGTTGTTCACGCTGGACGGTCCAAAGAGTCAGGCCTTA
TCACGTCGTCTGGCCCGGGGCGAGCGTCGCCGCAGACGGTGTCGAGTAGCCCTGGCGGTG
CTGGCGTTACTGCTGCTACTGGCGTCGGTGGGAGCCGTGGAGCTTATCATGTCGCGAGGA
CAGAGGGTCTTCGGAGCCGTCCTGCGATGA
>BMgn002071|Gene000002
GCAGTATCAGTTTGGAGTTGACATAAAGTGGCTTTCTCCGTGTTATCTTGTGCAACTAGG
AGGCAGAATGAGTCCAATAAAACCAAATCCAGCCAAAGCCTTGCTACGTAACGAAATTGC
CGCTAAAATCGCCGCCTTGACGAATGAAGAGAAAAAAAGACAATCGCAAATTGTTTATGA
AAAGGTTATCAACCACTCATGGTACAAATCATCAAGTCGTATTGCTCTCTACATGAGCAC

input_2:reference cDNA files for blastn

input_2/GenesetA.nt.fasta

>BMgn002072|Gene000001
ATGTTTTTTCAGGCAGCCAGTGCGTTGTTCACGCTGGACGGTCCAAAGAGTCAGGCCTTA
TCACGTCGTCTGGCCCGGGGCGAGCGTCGCCGCAGACGGTGTCGAGTAGCCCTGGCGGTG
CTGGCGTTACTGCTGCTACTGGCGTCGGTGGGAGCCGTGGAGCTTATCATGTCGCGAGGA
CAGAGGGTCTTCGGAGCCGTCCTGCGATGA
>BMgn002071|Gene000002
GCAGTATCAGTTTGGAGTTGACATAAAGTGGCTTTCTCCGTGTTATCTTGTGCAACTAGG
AGGCAGAATGAGTCCAATAAAACCAAATCCAGCCAAAGCCTTGCTACGTAACGAAATTGC
CGCTAAAATCGCCGCCTTGACGAATGAAGAGAAAAAAAGACAATCGCAAATTGTTTATGA
AAAGGTTATCAACCACTCATGGTACAAATCATCAAGTCGTATTGCTCTCTACATGAGCAC

input_3:reference protein files for blastx

input_3/Dm-r6.49.fasta

>FBgn0004907;CG17870-PD 14-3-3zeta~14-3-3zeta;14-3-3_protein
MSTVDKEELVQKAKLAEQSERYDDMAQAMKSVTETGVELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEASARKQQLAREYRERVEKELREICYEVLGLLDKYLIPKASNPESKVFYLKMKGDYYRYLAEVATGDARNTVVDDSQTAYQDAFDISKGKMQPTHPIRLGLALNFSVFYYEILNSPDKACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDEAEPQEGGDN
>FBgn0004907;CG17870-PB 14-3-3zeta~14-3-3zeta;14-3-3_protein
MSTVDKEELVQKAKLAEQSERYDDMAQAMKSVTETGVELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEASARKQQLAREYRERVEKELREICYEVLGLLDKYLIPKASNPESKVFYLKMKGDYYRYLAEVATGDARNTVVDDSKNAYQEAFDIAKTKMQPTHPIRLGLALNFSVFYYEILNSPDKACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDEAEPQEGGDN
>FBgn0004907;CG17870-PF 14-3-3zeta~14-3-3zeta;14-3-3_protein
MSTVDKEELVQKAKLAEQSERYDDMAQAMKSVTETGVELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEASARKQQLAREYRERVEKELREICYEVLGLLDKYLIPKASNPESKVFYLKMKGDYYRYLAEVATGDARNTVVEDSKKAYQEAFDIAKTKMQPTHPIRLGLALNFSVFYYEIINSPARACHLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDEAEPQEGGDN
>FBgn0020238;CG31196-PA 14-3-3epsilon~14-3-3epsilon;14-3-3_protein
MTERENNVYKAKLAEQAERYDEMVEAMKKVASMDVELTVEERNLLSVAYKNVIGARRASWRIITSIEQKEENKGAEEKLEMIKTYRGQVEKELRDICSDILNVLEKHLIPCATSGESKVFYYKMKGDYHRYLAEFATGSDRKDAAENSLIAYKAASDIAMNDLPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQAEEVDPNAGDGEPKEQIQDVEDQDVS
>FBgn0020238;CG31196-PB 14-3-3epsilon~14-3-3epsilon;14-3-3_protein
MTERENNVYKAKLAEQAERYDEMVEAMKKVASMDVELTVEERNLLSVAYKNVIGARRASWRIITSIEQKEENKGAEEKLEMIKTYRGQVEKELRDICSDILNVLEKHLIPCATSGESKVFYYKMKGDYHRYLAEFATGSDRKDAAENSLIAYKAASDIAMNDLPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQAEVDPNAGDGEPKEQIQDVEDQDVS

input_4:reference protein files for diamond

input_4/Dm-r6.49.fasta

>FBgn0004907;CG17870-PD 14-3-3zeta~14-3-3zeta;14-3-3_protein
MSTVDKEELVQKAKLAEQSERYDDMAQAMKSVTETGVELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEASARKQQLAREYRERVEKELREICYEVLGLLDKYLIPKASNPESKVFYLKMKGDYYRYLAEVATGDARNTVVDDSQTAYQDAFDISKGKMQPTHPIRLGLALNFSVFYYEILNSPDKACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDEAEPQEGGDN
>FBgn0004907;CG17870-PB 14-3-3zeta~14-3-3zeta;14-3-3_protein
MSTVDKEELVQKAKLAEQSERYDDMAQAMKSVTETGVELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEASARKQQLAREYRERVEKELREICYEVLGLLDKYLIPKASNPESKVFYLKMKGDYYRYLAEVATGDARNTVVDDSKNAYQEAFDIAKTKMQPTHPIRLGLALNFSVFYYEILNSPDKACQLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDEAEPQEGGDN
>FBgn0004907;CG17870-PF 14-3-3zeta~14-3-3zeta;14-3-3_protein
MSTVDKEELVQKAKLAEQSERYDDMAQAMKSVTETGVELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEASARKQQLAREYRERVEKELREICYEVLGLLDKYLIPKASNPESKVFYLKMKGDYYRYLAEVATGDARNTVVEDSKKAYQEAFDIAKTKMQPTHPIRLGLALNFSVFYYEIINSPARACHLAKQAFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDEAEPQEGGDN
>FBgn0020238;CG31196-PA 14-3-3epsilon~14-3-3epsilon;14-3-3_protein
MTERENNVYKAKLAEQAERYDEMVEAMKKVASMDVELTVEERNLLSVAYKNVIGARRASWRIITSIEQKEENKGAEEKLEMIKTYRGQVEKELRDICSDILNVLEKHLIPCATSGESKVFYYKMKGDYHRYLAEFATGSDRKDAAENSLIAYKAASDIAMNDLPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQAEEVDPNAGDGEPKEQIQDVEDQDVS
>FBgn0020238;CG31196-PB 14-3-3epsilon~14-3-3epsilon;14-3-3_protein
MTERENNVYKAKLAEQAERYDEMVEAMKKVASMDVELTVEERNLLSVAYKNVIGARRASWRIITSIEQKEENKGAEEKLEMIKTYRGQVEKELRDICSDILNVLEKHLIPCATSGESKVFYYKMKGDYHRYLAEFATGSDRKDAAENSLIAYKAASDIAMNDLPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQAEVDPNAGDGEPKEQIQDVEDQDVS

Command

annotation~blast-diamond_for_cDNA -c 8 -m 32 -x input_2/ -y input_3/ -z input_4/ input_1/test.fa

Output

result.txt

qseqid	length	blastn.GenesetA.nt.fasta:sseqid	qlen	slen	pident	length	mismatch	gapopen	qstart	qend	sstart	send	qframe	evalue	bitscore	stitle	blastx.Dm-r6.49.fasta:sseqid	qlen	slen	pident	length	mismatch	gapopen	qstart	qend	sstart	send	qframe	evalue	bitscore	stitle	diamond.Dm-r6.49.fasta:sseqid	qlen	slen	pident	length	mismatch	gapopen	qstart	qend	sstart	send	qframe	evalue	bitscore	stitle
BMgn002071|Gene000002	781	BMgn002071|Gene000002	781	781	100.000	781	0	0	1	781	1	781	1	0.0	1443	BMgn002071|Gene000002	FBgn0085453;CG34424-PB	781	201	34.343	198	118	4	68	625	1	198	2	9.15e-32	116	FBgn0085453;CG34424-PB Methenyltetrahydrofolate_synthetase~Mthfs;CYCLO-LIGASES	FBgn0085453;CG34424-PB	781	201	34.4	192	114	4	86	625	7	198	2	7.23e-29	108	FBgn0085453;CG34424-PB Methenyltetrahydrofolate_synthetase~Mthfs;CYCLO-LIGASES
BMgn002072|Gene000001	210	BMgn002072|Gene000001	210	210	100.000	210	0	0	1	210	1	210	1	4.17e-108	388	BMgn002072|Gene000001																														
BMgn002073|Gene000003	4740	BMgn002073|Gene000003	4740	5525	100.000	4740	0	0	1	4740	1	4740	1	0.0	8754	BMgn002073|Gene000003	FBgn0036043;CG8177-PI	4740	1201	50.333	1200	492	19	63	3386	14	1201	3	0.0	1049	FBgn0036043;CG8177-PI Anion_exchanger_2~Ae2;SLC4:_Bicarbonate_transporter	FBgn0036043;CG8177-PI	4740	1201	50.6	1212	487	21	36	3383	5	1200	3	0.0	1016	FBgn0036043;CG8177-PI Anion_exchanger_2~Ae2;SLC4:_Bicarbonate_transporter

view all outputs

Log

pp annotation~diamond -c 8 -m 32 -x input_2/ -y input_3/ -z input_4/ input_1/test.fa
Checking the realpath of input files.
0 input_1/test.fa
0 input_2/
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt.njs
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt.ndb
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt.ntf
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt.nin
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt.nhr
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt.nsq
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt.not
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt.nto
0 input_3/
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt.pjs
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt.pdb
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt.ptf
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt.pin
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt.phr
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt.psq
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt.pot
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt.pto
0 input_4/
1 /yoshitake/test/annotation~diamond/input_4/Dm-r6.49.fasta
1 /yoshitake/test/annotation~diamond/input_4/Dm-r6.49.fasta.formatted.txt
1 /yoshitake/test/annotation~diamond/input_4/Dm-r6.49.fasta.formatted.txt.dmnd
c2997108/centos7:3-java centos:centos6 ncbi/blast:2.13.0 quay.io/biocontainers/diamond:2.1.4--hb97b32f_0 quay.io/biocontainers/exonerate:2.2.0--1
using docker
+ set -o pipefail
+ find input_1/test.fa input_2/ input_3/ input_4/
+ grep -E '(fa|fasta|fsa|fna|faa)[.]gz$'
+ read i
+ xargs '-d\n' -I '{}' -P 8 bash -c '{}'
+ true
+ find input_1/test.fa input_2/ input_3/ input_4/
+ grep -E '(fa|fasta|fsa|fna|faa)$'
+ read i
+ xargs '-d\n' -I '{}' -P 8 bash -c '{}'
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1  fastareformat "input_1/test.fa" |sed '\''s/\r//g'\'' > "input_1/test.fa".formatted.txt'
+ read i
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1  fastareformat "input_2/GenesetA.nt.fasta" |sed '\''s/\r//g'\'' > "input_2/GenesetA.nt.fasta".formatted.txt'
+ read i
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1  fastareformat "input_3/Dm-r6.49.fasta" |sed '\''s/\r//g'\'' > "input_3/Dm-r6.49.fasta".formatted.txt'
+ read i
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1  fastareformat "input_4/Dm-r6.49.fasta" |sed '\''s/\r//g'\'' > "input_4/Dm-r6.49.fasta".formatted.txt'
+ read i
++ echo input_1/test.fa
++ sed 's/[.]gz$//'
+ input=input_1/test.fa.formatted.txt
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
+ grep -E '(fa|fasta|fsa|fna|faa)[.]formatted[.]txt$'
+ find input_2/
+ read i
++ basename input_2/GenesetA.nt.fasta.formatted.txt
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm ncbi/blast:2.13.0  makeblastdb -in "input_2/GenesetA.nt.fasta.formatted.txt" -dbtype nucl; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm ncbi/blast:2.13.0  blastn -db "input_2/GenesetA.nt.fasta.formatted.txt" -query "input_1/test.fa.formatted.txt" -num_threads 8 -outfmt "6 qseqid sseqid qlen slen pident length mismatch gapopen qstart qend sstart send qframe evalue bitscore stitle" -out "input_1/test.fa.formatted.txt.blastn.GenesetA.nt.fasta.formatted.txt.tsv" '
+ read i
+ find input_3/
+ grep -E '(fa|fasta|fsa|fna|faa)[.]formatted[.]txt$'
+ read i
++ basename input_3/Dm-r6.49.fasta.formatted.txt
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm ncbi/blast:2.13.0  makeblastdb -in "input_3/Dm-r6.49.fasta.formatted.txt" -dbtype prot; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm ncbi/blast:2.13.0  blastx -db "input_3/Dm-r6.49.fasta.formatted.txt" -query "input_1/test.fa.formatted.txt" -num_threads 8 -outfmt "6 qseqid sseqid qlen slen pident length mismatch gapopen qstart qend sstart send qframe evalue bitscore stitle" -out "input_1/test.fa.formatted.txt.blastx.Dm-r6.49.fasta.formatted.txt.tsv" '
+ read i
+ find input_4/
+ grep -E '(fa|fasta|fsa|fna|faa)[.]formatted[.]txt$'
+ read i
++ basename input_4/Dm-r6.49.fasta.formatted.txt
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm quay.io/biocontainers/diamond:2.1.4--hb97b32f_0  diamond makedb --in "input_4/Dm-r6.49.fasta.formatted.txt" -d "input_4/Dm-r6.49.fasta.formatted.txt"; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm quay.io/biocontainers/diamond:2.1.4--hb97b32f_0  diamond blastx -d "input_4/Dm-r6.49.fasta.formatted.txt" -q "input_1/test.fa.formatted.txt" --threads 8 --outfmt 6 qseqid sseqid qlen slen pident length mismatch gapopen qstart qend sstart send qframe evalue bitscore salltitles -o "input_1/test.fa.formatted.txt.diamond.Dm-r6.49.fasta.formatted.txt.tsv" --sensitive'
+ read i


Building a new DB, current time: 03/07/2023 17:51:34
New DB name:   /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt
New DB title:  input_2/GenesetA.nt.fasta.formatted.txt
Sequence type: Nucleotide
Deleted existing Nucleotide BLAST database named /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt
Keep MBits: T
Maximum file size: 3000000000B
Adding sequences from FASTA; added 16823 sequences in 0.536334 seconds.




Building a new DB, current time: 03/07/2023 17:51:38
New DB name:   /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt
New DB title:  input_3/Dm-r6.49.fasta.formatted.txt
Sequence type: Protein
Deleted existing Protein BLAST database named /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt
Keep MBits: T
Maximum file size: 3000000000B
Adding sequences from FASTA; added 22449 sequences in 0.638087 seconds.


diamond v2.1.4.158 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 16
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Database input file: input_4/Dm-r6.49.fasta.formatted.txt
Opening the database file...  [0.009s]
Loading sequences...  [0.115s]
Masking sequences...  [0.229s]
Writing sequences...  [0.012s]
Hashing sequences...  [0.005s]
Loading sequences...  [0s]
Writing trailer...  [0s]
Closing the input file...  [0s]
Closing the database file...  [0.004s]

Database sequences  22449
  Database letters  15508912
     Database hash  a5438a99987074936422a8c4d8ca0151
        Total time  0.377000s
diamond v2.1.4.158 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 8
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: input_1
#Target sequences to report alignments for: 25
Opening the database...  [0.014s]
Database: input_4/Dm-r6.49.fasta.formatted.txt (type: Diamond database, sequences: 22449, letters: 15508912)
Block size = 2000000000
Algorithm: Double-indexed
Building query histograms...  [0.002s]
Loading reference sequences...  [0.026s]
Masking reference...  [0.273s]
Initializing temporary storage...  [0s]
Building reference histograms...  [0.726s]
Allocating buffers...  [0s]
Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4.
Building reference seed array...  [0.07s]
Building query seed array...  [0.002s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.004s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4.
Building reference seed array...  [0.076s]
Building query seed array...  [0.002s]
Computing hash join...  [0.01s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4.
Building reference seed array...  [0.07s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4.
Building reference seed array...  [0.059s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4.
Building reference seed array...  [0.054s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4.
Building reference seed array...  [0.063s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4.
Building reference seed array...  [0.07s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4.
Building reference seed array...  [0.054s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4.
Building reference seed array...  [0.051s]
Building query seed array...  [0.001s]
Computing hash join...  [0.006s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4.
Building reference seed array...  [0.065s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4.
Building reference seed array...  [0.065s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4.
Building reference seed array...  [0.057s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4.
Building reference seed array...  [0.058s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4.
Building reference seed array...  [0.07s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4.
Building reference seed array...  [0.067s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4.
Building reference seed array...  [0.056s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4.
Building reference seed array...  [0.064s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4.
Building reference seed array...  [0.069s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4.
Building reference seed array...  [0.064s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4.
Building reference seed array...  [0.053s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4.
Building reference seed array...  [0.055s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4.
Building reference seed array...  [0.067s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4.
Building reference seed array...  [0.068s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4.
Building reference seed array...  [0.054s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4.
Building reference seed array...  [0.058s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4.
Building reference seed array...  [0.068s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4.
Building reference seed array...  [0.068s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4.
Building reference seed array...  [0.057s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4.
Building reference seed array...  [0.053s]
Building query seed array...  [0.001s]
Computing hash join...  [0.006s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4.
Building reference seed array...  [0.064s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4.
Building reference seed array...  [0.07s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4.
Building reference seed array...  [0.051s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4.
Building reference seed array...  [0.061s]
Building query seed array...  [0.001s]
Computing hash join...  [0.01s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4.
Building reference seed array...  [0.07s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4.
Building reference seed array...  [0.073s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4.
Building reference seed array...  [0.051s]
Building query seed array...  [0.002s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4.
Building reference seed array...  [0.065s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4.
Building reference seed array...  [0.076s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4.
Building reference seed array...  [0.068s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4.
Building reference seed array...  [0.05s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4.
Building reference seed array...  [0.055s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4.
Building reference seed array...  [0.069s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4.
Building reference seed array...  [0.076s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4.
Building reference seed array...  [0.062s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4.
Building reference seed array...  [0.059s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4.
Building reference seed array...  [0.066s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4.
Building reference seed array...  [0.069s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4.
Building reference seed array...  [0.061s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4.
Building reference seed array...  [0.056s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4.
Building reference seed array...  [0.071s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4.
Building reference seed array...  [0.066s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4.
Building reference seed array...  [0.055s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4.
Building reference seed array...  [0.059s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4.
Building reference seed array...  [0.065s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4.
Building reference seed array...  [0.072s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4.
Building reference seed array...  [0.053s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4.
Building reference seed array...  [0.056s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4.
Building reference seed array...  [0.067s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4.
Building reference seed array...  [0.074s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4.
Building reference seed array...  [0.067s]
Building query seed array...  [0.002s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4.
Building reference seed array...  [0.058s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4.
Building reference seed array...  [0.073s]
Building query seed array...  [0.002s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4.
Building reference seed array...  [0.066s]
Building query seed array...  [0.001s]
Computing hash join...  [0.006s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4.
Building reference seed array...  [0.062s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Deallocating buffers...  [0s]
Clearing query masking...  [0s]
Computing alignments... Loading trace points...  [0.001s]
Sorting trace points...  [0s]
Computing alignments...  [0.014s]
Deallocating buffers...  [0s]
Loading trace points...  [0s]
 [0.016s]
Deallocating reference...  [0.001s]
Loading reference sequences...  [0s]
Deallocating buffers...  [0s]
Deallocating queries...  [0s]
Total time = 6.07s
Reported 19 pairwise alignments, 19 HSPs.
2 queries aligned.
+ for i in '"$input".*.tsv'
++ basename input_1/test.fa.formatted.txt.blastn.GenesetA.nt.fasta.formatted.txt.tsv
++ sed 's/.*[.]formatted[.]txt[.]\(.*\)[.]formatted[.]txt[.]tsv$/\1/'
+ awk '-F\t' -v name=blastn.GenesetA.nt.fasta 'BEGIN{print "qseqid\t"name":sseqid\tqlen\tslen\tpident\tlength\tmismatch\tgapopen\tqstart\tqend\tsstart\tsend\tqframe\tevalue\tbitscore\tstitle"} {if($1!=old){print $0; old=$1}}' input_1/test.fa.formatted.txt.blastn.GenesetA.nt.fasta.formatted.txt.tsv
+ for i in '"$input".*.tsv'
++ basename input_1/test.fa.formatted.txt.blastx.Dm-r6.49.fasta.formatted.txt.tsv
++ sed 's/.*[.]formatted[.]txt[.]\(.*\)[.]formatted[.]txt[.]tsv$/\1/'
+ awk '-F\t' -v name=blastx.Dm-r6.49.fasta 'BEGIN{print "qseqid\t"name":sseqid\tqlen\tslen\tpident\tlength\tmismatch\tgapopen\tqstart\tqend\tsstart\tsend\tqframe\tevalue\tbitscore\tstitle"} {if($1!=old){print $0; old=$1}}' input_1/test.fa.formatted.txt.blastx.Dm-r6.49.fasta.formatted.txt.tsv
+ for i in '"$input".*.tsv'
++ basename input_1/test.fa.formatted.txt.diamond.Dm-r6.49.fasta.formatted.txt.tsv
++ sed 's/.*[.]formatted[.]txt[.]\(.*\)[.]formatted[.]txt[.]tsv$/\1/'
+ awk '-F\t' -v name=diamond.Dm-r6.49.fasta 'BEGIN{print "qseqid\t"name":sseqid\tqlen\tslen\tpident\tlength\tmismatch\tgapopen\tqstart\tqend\tsstart\tsend\tqframe\tevalue\tbitscore\tstitle"} {if($1!=old){print $0; old=$1}}' input_1/test.fa.formatted.txt.diamond.Dm-r6.49.fasta.formatted.txt.tsv
+ FUNC_RUN_DOCKER c2997108/centos7:3-java merge_table.pl -k input_1/test.fa.formatted.txt.blastn.GenesetA.nt.fasta.formatted.txt.tsv.txt input_1/test.fa.formatted.txt.blastx.Dm-r6.49.fasta.formatted.txt.tsv.txt input_1/test.fa.formatted.txt.diamond.Dm-r6.49.fasta.formatted.txt.tsv.txt
+ PP_RUN_IMAGE=c2997108/centos7:3-java
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230308_025150_268_30256
+ echo pp20230308_025150_268_30256
++ id -u
++ id -g
+ docker run --name pp20230308_025150_268_30256 -v /yoshitake/test/annotation~diamond:/yoshitake/test/annotation~diamond -w /yoshitake/test/annotation~diamond -u 2007:600 -i --rm c2997108/centos7:3-java merge_table.pl -k input_1/test.fa.formatted.txt.blastn.GenesetA.nt.fasta.formatted.txt.tsv.txt input_1/test.fa.formatted.txt.blastx.Dm-r6.49.fasta.formatted.txt.tsv.txt input_1/test.fa.formatted.txt.diamond.Dm-r6.49.fasta.formatted.txt.tsv.txt
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /yoshitake/test/annotation~diamond/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit
PID: 413167
Checking the realpath of input files.
0 input_1/test.fa
0 input_2/
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt.njs
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt.ndb
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt.ntf
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt.nin
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt.nhr
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt.nsq
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt.not
1 /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt.nto
0 input_3/
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt.pjs
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt.pdb
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt.ptf
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt.pin
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt.phr
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt.psq
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt.pot
1 /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt.pto
0 input_4/
1 /yoshitake/test/annotation~diamond/input_4/Dm-r6.49.fasta
1 /yoshitake/test/annotation~diamond/input_4/Dm-r6.49.fasta.formatted.txt
1 /yoshitake/test/annotation~diamond/input_4/Dm-r6.49.fasta.formatted.txt.dmnd
c2997108/centos7:3-java centos:centos6 ncbi/blast:2.13.0 quay.io/biocontainers/diamond:2.1.4--hb97b32f_0 quay.io/biocontainers/exonerate:2.2.0--1
using docker
+ set -o pipefail
+ find input_1/test.fa input_2/ input_3/ input_4/
+ grep -E '(fa|fasta|fsa|fna|faa)[.]gz$'
+ read i
+ xargs '-d\n' -I '{}' -P 8 bash -c '{}'
+ true
+ find input_1/test.fa input_2/ input_3/ input_4/
+ grep -E '(fa|fasta|fsa|fna|faa)$'
+ read i
+ xargs '-d\n' -I '{}' -P 8 bash -c '{}'
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1  fastareformat "input_1/test.fa" |sed '\''s/\r//g'\'' > "input_1/test.fa".formatted.txt'
+ read i
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1  fastareformat "input_2/GenesetA.nt.fasta" |sed '\''s/\r//g'\'' > "input_2/GenesetA.nt.fasta".formatted.txt'
+ read i
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1  fastareformat "input_3/Dm-r6.49.fasta" |sed '\''s/\r//g'\'' > "input_3/Dm-r6.49.fasta".formatted.txt'
+ read i
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm quay.io/biocontainers/exonerate:2.2.0--1  fastareformat "input_4/Dm-r6.49.fasta" |sed '\''s/\r//g'\'' > "input_4/Dm-r6.49.fasta".formatted.txt'
+ read i
++ echo input_1/test.fa
++ sed 's/[.]gz$//'
+ input=input_1/test.fa.formatted.txt
+ xargs '-d\n' -I '{}' -P 1 bash -c '{}'
+ find input_2/
+ grep -E '(fa|fasta|fsa|fna|faa)[.]formatted[.]txt$'
+ read i
++ basename input_2/GenesetA.nt.fasta.formatted.txt
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm ncbi/blast:2.13.0  makeblastdb -in "input_2/GenesetA.nt.fasta.formatted.txt" -dbtype nucl; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm ncbi/blast:2.13.0  blastn -db "input_2/GenesetA.nt.fasta.formatted.txt" -query "input_1/test.fa.formatted.txt" -num_threads 8 -outfmt "6 qseqid sseqid qlen slen pident length mismatch gapopen qstart qend sstart send qframe evalue bitscore stitle" -out "input_1/test.fa.formatted.txt.blastn.GenesetA.nt.fasta.formatted.txt.tsv" '
+ read i
+ find input_3/
+ grep -E '(fa|fasta|fsa|fna|faa)[.]formatted[.]txt$'
+ read i
++ basename input_3/Dm-r6.49.fasta.formatted.txt
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm ncbi/blast:2.13.0  makeblastdb -in "input_3/Dm-r6.49.fasta.formatted.txt" -dbtype prot; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm ncbi/blast:2.13.0  blastx -db "input_3/Dm-r6.49.fasta.formatted.txt" -query "input_1/test.fa.formatted.txt" -num_threads 8 -outfmt "6 qseqid sseqid qlen slen pident length mismatch gapopen qstart qend sstart send qframe evalue bitscore stitle" -out "input_1/test.fa.formatted.txt.blastx.Dm-r6.49.fasta.formatted.txt.tsv" '
+ read i
+ find input_4/
+ grep -E '(fa|fasta|fsa|fna|faa)[.]formatted[.]txt$'
+ read i
++ basename input_4/Dm-r6.49.fasta.formatted.txt
+ echo 'PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm quay.io/biocontainers/diamond:2.1.4--hb97b32f_0  diamond makedb --in "input_4/Dm-r6.49.fasta.formatted.txt" -d "input_4/Dm-r6.49.fasta.formatted.txt"; PPDOCNAME=pp`date +%Y%m%d_%H%M%S_%3N`_$RANDOM; echo $PPDOCNAME >> /yoshitake/test/annotation~diamond/pp-docker-list; docker run --name ${PPDOCNAME} -v $PWD:$PWD -w $PWD  -u 2007:600 -i --rm quay.io/biocontainers/diamond:2.1.4--hb97b32f_0  diamond blastx -d "input_4/Dm-r6.49.fasta.formatted.txt" -q "input_1/test.fa.formatted.txt" --threads 8 --outfmt 6 qseqid sseqid qlen slen pident length mismatch gapopen qstart qend sstart send qframe evalue bitscore salltitles -o "input_1/test.fa.formatted.txt.diamond.Dm-r6.49.fasta.formatted.txt.tsv" --sensitive'
+ read i


Building a new DB, current time: 03/07/2023 17:53:08
New DB name:   /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt
New DB title:  input_2/GenesetA.nt.fasta.formatted.txt
Sequence type: Nucleotide
Deleted existing Nucleotide BLAST database named /yoshitake/test/annotation~diamond/input_2/GenesetA.nt.fasta.formatted.txt
Keep MBits: T
Maximum file size: 3000000000B
Adding sequences from FASTA; added 16823 sequences in 0.516625 seconds.




Building a new DB, current time: 03/07/2023 17:53:12
New DB name:   /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt
New DB title:  input_3/Dm-r6.49.fasta.formatted.txt
Sequence type: Protein
Deleted existing Protein BLAST database named /yoshitake/test/annotation~diamond/input_3/Dm-r6.49.fasta.formatted.txt
Keep MBits: T
Maximum file size: 3000000000B
Adding sequences from FASTA; added 22449 sequences in 0.631008 seconds.


diamond v2.1.4.158 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 16
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Database input file: input_4/Dm-r6.49.fasta.formatted.txt
Opening the database file...  [0.01s]
Loading sequences...  [0.113s]
Masking sequences...  [0.229s]
Writing sequences...  [0.012s]
Hashing sequences...  [0.005s]
Loading sequences...  [0s]
Writing trailer...  [0s]
Closing the input file...  [0s]
Closing the database file...  [0.004s]

Database sequences  22449
  Database letters  15508912
     Database hash  a5438a99987074936422a8c4d8ca0151
        Total time  0.375000s
diamond v2.1.4.158 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 8
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: input_1
#Target sequences to report alignments for: 25
Opening the database...  [0.016s]
Database: input_4/Dm-r6.49.fasta.formatted.txt (type: Diamond database, sequences: 22449, letters: 15508912)
Block size = 2000000000
Algorithm: Double-indexed
Building query histograms...  [0.002s]
Loading reference sequences...  [0.025s]
Masking reference...  [0.239s]
Initializing temporary storage...  [0s]
Building reference histograms...  [0.726s]
Allocating buffers...  [0.001s]
Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4.
Building reference seed array...  [0.07s]
Building query seed array...  [0.002s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.004s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4.
Building reference seed array...  [0.074s]
Building query seed array...  [0.002s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4.
Building reference seed array...  [0.068s]
Building query seed array...  [0.002s]
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Searching alignments...  [0.001s]
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Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4.
Building reference seed array...  [0.056s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
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Searching alignments...  [0s]
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Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4.
Building reference seed array...  [0.056s]
Building query seed array...  [0.001s]
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Searching alignments...  [0.001s]
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Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4.
Building reference seed array...  [0.066s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4.
Building reference seed array...  [0.068s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
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Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4.
Building reference seed array...  [0.06s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4.
Building reference seed array...  [0.061s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
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Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4.
Building reference seed array...  [0.064s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4.
Building reference seed array...  [0.07s]
Building query seed array...  [0.002s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4.
Building reference seed array...  [0.057s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
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Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4.
Building reference seed array...  [0.052s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
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Searching alignments...  [0s]
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Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4.
Building reference seed array...  [0.066s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
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Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4.
Building reference seed array...  [0.07s]
Building query seed array...  [0.001s]
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Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4.
Building reference seed array...  [0.061s]
Building query seed array...  [0.001s]
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Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4.
Building reference seed array...  [0.061s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
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Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4.
Building reference seed array...  [0.07s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4.
Building reference seed array...  [0.074s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4.
Building reference seed array...  [0.058s]
Building query seed array...  [0.001s]
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Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4.
Building reference seed array...  [0.056s]
Building query seed array...  [0.002s]
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Searching alignments...  [0.001s]
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Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4.
Building reference seed array...  [0.064s]
Building query seed array...  [0.002s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4.
Building reference seed array...  [0.071s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
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Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4.
Building reference seed array...  [0.053s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4.
Building reference seed array...  [0.058s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
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Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4.
Building reference seed array...  [0.07s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
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Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4.
Building reference seed array...  [0.064s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4.
Building reference seed array...  [0.051s]
Building query seed array...  [0.001s]
Computing hash join...  [0.006s]
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Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4.
Building reference seed array...  [0.051s]
Building query seed array...  [0.001s]
Computing hash join...  [0.006s]
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Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4.
Building reference seed array...  [0.063s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
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Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4.
Building reference seed array...  [0.07s]
Building query seed array...  [0.001s]
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Searching alignments...  [0.001s]
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Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4.
Building reference seed array...  [0.055s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
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Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4.
Building reference seed array...  [0.058s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4.
Building reference seed array...  [0.07s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4.
Building reference seed array...  [0.068s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4.
Building reference seed array...  [0.058s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4.
Building reference seed array...  [0.06s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4.
Building reference seed array...  [0.069s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4.
Building reference seed array...  [0.075s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4.
Building reference seed array...  [0.06s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4.
Building reference seed array...  [0.064s]
Building query seed array...  [0.002s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4.
Building reference seed array...  [0.071s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4.
Building reference seed array...  [0.07s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4.
Building reference seed array...  [0.06s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4.
Building reference seed array...  [0.057s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4.
Building reference seed array...  [0.076s]
Building query seed array...  [0.001s]
Computing hash join...  [0.01s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4.
Building reference seed array...  [0.075s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4.
Building reference seed array...  [0.058s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4.
Building reference seed array...  [0.064s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4.
Building reference seed array...  [0.074s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4.
Building reference seed array...  [0.068s]
Building query seed array...  [0.002s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4.
Building reference seed array...  [0.057s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4.
Building reference seed array...  [0.054s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4.
Building reference seed array...  [0.063s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4.
Building reference seed array...  [0.075s]
Building query seed array...  [0.001s]
Computing hash join...  [0.01s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4.
Building reference seed array...  [0.061s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4.
Building reference seed array...  [0.064s]
Building query seed array...  [0.001s]
Computing hash join...  [0.009s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4.
Building reference seed array...  [0.073s]
Building query seed array...  [0.001s]
Computing hash join...  [0.01s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4.
Building reference seed array...  [0.069s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4.
Building reference seed array...  [0.058s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4.
Building reference seed array...  [0.051s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4.
Building reference seed array...  [0.065s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4.
Building reference seed array...  [0.071s]
Building query seed array...  [0.001s]
Computing hash join...  [0.008s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0.001s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4.
Building reference seed array...  [0.056s]
Building query seed array...  [0.001s]
Computing hash join...  [0.007s]
Masking low complexity seeds...  [0s]
Searching alignments...  [0s]
Deallocating memory...  [0s]
Deallocating buffers...  [0s]
Clearing query masking...  [0s]
Computing alignments... Loading trace points...  [0.001s]
Sorting trace points...  [0s]
Computing alignments...  [0.011s]
Deallocating buffers...  [0s]
Loading trace points...  [0s]
 [0.013s]
Deallocating reference...  [0.001s]
Loading reference sequences...  [0s]
Deallocating buffers...  [0s]
Deallocating queries...  [0s]
Total time = 6.09s
Reported 19 pairwise alignments, 19 HSPs.
2 queries aligned.
+ for i in '"$input".*.tsv'
++ basename input_1/test.fa.formatted.txt.blastn.GenesetA.nt.fasta.formatted.txt.tsv
++ sed 's/.*[.]formatted[.]txt[.]\(.*\)[.]formatted[.]txt[.]tsv$/\1/'
+ awk '-F\t' -v name=blastn.GenesetA.nt.fasta 'BEGIN{print "qseqid\t"name":sseqid\tqlen\tslen\tpident\tlength\tmismatch\tgapopen\tqstart\tqend\tsstart\tsend\tqframe\tevalue\tbitscore\tstitle"} {if($1!=old){print $0; old=$1}}' input_1/test.fa.formatted.txt.blastn.GenesetA.nt.fasta.formatted.txt.tsv
+ for i in '"$input".*.tsv'
++ basename input_1/test.fa.formatted.txt.blastx.Dm-r6.49.fasta.formatted.txt.tsv
++ sed 's/.*[.]formatted[.]txt[.]\(.*\)[.]formatted[.]txt[.]tsv$/\1/'
+ awk '-F\t' -v name=blastx.Dm-r6.49.fasta 'BEGIN{print "qseqid\t"name":sseqid\tqlen\tslen\tpident\tlength\tmismatch\tgapopen\tqstart\tqend\tsstart\tsend\tqframe\tevalue\tbitscore\tstitle"} {if($1!=old){print $0; old=$1}}' input_1/test.fa.formatted.txt.blastx.Dm-r6.49.fasta.formatted.txt.tsv
+ for i in '"$input".*.tsv'
++ basename input_1/test.fa.formatted.txt.diamond.Dm-r6.49.fasta.formatted.txt.tsv
++ sed 's/.*[.]formatted[.]txt[.]\(.*\)[.]formatted[.]txt[.]tsv$/\1/'
+ awk '-F\t' -v name=diamond.Dm-r6.49.fasta 'BEGIN{print "qseqid\t"name":sseqid\tqlen\tslen\tpident\tlength\tmismatch\tgapopen\tqstart\tqend\tsstart\tsend\tqframe\tevalue\tbitscore\tstitle"} {if($1!=old){print $0; old=$1}}' input_1/test.fa.formatted.txt.diamond.Dm-r6.49.fasta.formatted.txt.tsv
+ FUNC_RUN_DOCKER c2997108/centos7:3-java merge_table.pl -k input_1/test.fa.formatted.txt.blastn.GenesetA.nt.fasta.formatted.txt.tsv.txt input_1/test.fa.formatted.txt.blastx.Dm-r6.49.fasta.formatted.txt.tsv.txt input_1/test.fa.formatted.txt.diamond.Dm-r6.49.fasta.formatted.txt.tsv.txt
+ PP_RUN_IMAGE=c2997108/centos7:3-java
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230308_025324_830_6197
+ echo pp20230308_025324_830_6197
++ id -u
++ id -g
+ docker run --name pp20230308_025324_830_6197 -v /yoshitake/test/annotation~diamond:/yoshitake/test/annotation~diamond -w /yoshitake/test/annotation~diamond -u 2007:600 -i --rm c2997108/centos7:3-java merge_table.pl -k input_1/test.fa.formatted.txt.blastn.GenesetA.nt.fasta.formatted.txt.tsv.txt input_1/test.fa.formatted.txt.blastx.Dm-r6.49.fasta.formatted.txt.tsv.txt input_1/test.fa.formatted.txt.diamond.Dm-r6.49.fasta.formatted.txt.tsv.txt
+ FUNC_RUN_DOCKER c2997108/centos7:3-java java -Xmx1G -jar /usr/local/bin/excel2.jar result.txt result.xlsx
+ PP_RUN_IMAGE=c2997108/centos7:3-java
+ shift
+ PP_RUN_DOCKER_CMD=("${@}")
++ date +%Y%m%d_%H%M%S_%3N
+ PPDOCNAME=pp20230308_025325_546_29793
+ echo pp20230308_025325_546_29793
++ id -u
++ id -g
+ docker run --name pp20230308_025325_546_29793 -v /yoshitake/test/annotation~diamond:/yoshitake/test/annotation~diamond -w /yoshitake/test/annotation~diamond -u 2007:600 -i --rm c2997108/centos7:3-java java -Xmx1G -jar /usr/local/bin/excel2.jar result.txt result.xlsx
Start converting
+ post_processing
+ '[' 1 = 1 ']'
+ rm -f /yoshitake/test/annotation~diamond/pp-singularity-flag
+ '[' '' = y ']'
+ echo 0
+ exit
PID: 418384