[2023-03-18 09:53:10,280] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:53:10,280] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:53:10,280] [INFO] DQC Reference Directory: /var/lib/cwl/stge2eb8d01-52b5-403a-b9eb-193b1eda6ac3/dqc_reference
[2023-03-18 09:53:11,365] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:53:11,366] [INFO] Task started: Prodigal
[2023-03-18 09:53:11,366] [INFO] Running command: cat /var/lib/cwl/stg2b5ec152-e7da-402e-8b9b-974e74a095c4/OceanDNA-b10092.fa | prodigal -d OceanDNA-b10092/cds.fna -a OceanDNA-b10092/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:53:32,730] [INFO] Task succeeded: Prodigal
[2023-03-18 09:53:32,730] [INFO] Task started: HMMsearch
[2023-03-18 09:53:32,730] [INFO] Running command: hmmsearch --tblout OceanDNA-b10092/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2eb8d01-52b5-403a-b9eb-193b1eda6ac3/dqc_reference/reference_markers.hmm OceanDNA-b10092/protein.faa > /dev/null
[2023-03-18 09:53:32,943] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:53:32,943] [INFO] Found 6/6 markers.
[2023-03-18 09:53:32,962] [INFO] Query marker FASTA was written to OceanDNA-b10092/markers.fasta
[2023-03-18 09:53:32,963] [INFO] Task started: Blastn
[2023-03-18 09:53:32,963] [INFO] Running command: blastn -query OceanDNA-b10092/markers.fasta -db /var/lib/cwl/stge2eb8d01-52b5-403a-b9eb-193b1eda6ac3/dqc_reference/reference_markers.fasta -out OceanDNA-b10092/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:53:33,557] [INFO] Task succeeded: Blastn
[2023-03-18 09:53:33,558] [INFO] Selected 24 target genomes.
[2023-03-18 09:53:33,558] [INFO] Target genome list was writen to OceanDNA-b10092/target_genomes.txt
[2023-03-18 09:53:33,574] [INFO] Task started: fastANI
[2023-03-18 09:53:33,574] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b5ec152-e7da-402e-8b9b-974e74a095c4/OceanDNA-b10092.fa --refList OceanDNA-b10092/target_genomes.txt --output OceanDNA-b10092/fastani_result.tsv --threads 1
[2023-03-18 09:53:47,341] [INFO] Task succeeded: fastANI
[2023-03-18 09:53:47,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2eb8d01-52b5-403a-b9eb-193b1eda6ac3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:53:47,342] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2eb8d01-52b5-403a-b9eb-193b1eda6ac3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:53:47,354] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:53:47,354] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:53:47,355] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Subsaximicrobium wynnwilliamsii	strain=G#7(T)	GCA_007997225.1	291179	291179	type	True	78.7669	471	928	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	77.0256	157	928	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.9939	162	928	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	76.9257	144	928	95	below_threshold
Gelidibacter mesophilus	strain=DSM 14095	GCA_000423005.1	169050	169050	type	True	76.5026	122	928	95	below_threshold
Tamlana crocina	strain=HST1-43	GCA_012037625.1	393006	393006	type	True	76.321	85	928	95	below_threshold
Gelidibacter pelagius	strain=DF109	GCA_017581925.1	2819985	2819985	type	True	76.2979	139	928	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	76.2611	118	928	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	76.2611	118	928	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	76.2601	103	928	95	below_threshold
Bizionia paragorgiae	strain=DSM 23842	GCA_900107625.1	283786	283786	type	True	76.2487	76	928	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.1922	111	928	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	76.1488	91	928	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	76.113	128	928	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	76.1064	91	928	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	76.096	84	928	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.0664	78	928	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	76.0511	107	928	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	75.9352	72	928	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	75.7843	86	928	95	below_threshold
Mangrovimonas yunxiaonensis	strain=CGMCC 1.12280	GCA_014636995.1	1197477	1197477	type	True	75.7688	92	928	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	75.6794	68	928	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:53:47,355] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10092/tc_result.tsv
[2023-03-18 09:53:47,355] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:53:47,355] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:53:47,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2eb8d01-52b5-403a-b9eb-193b1eda6ac3/dqc_reference/checkm_data
[2023-03-18 09:53:47,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:53:47,384] [INFO] Task started: CheckM
[2023-03-18 09:53:47,385] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10092/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10092/checkm_input OceanDNA-b10092/checkm_result
[2023-03-18 09:54:41,727] [INFO] Task succeeded: CheckM
[2023-03-18 09:54:41,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:54:41,730] [INFO] ===== Completeness check finished =====
[2023-03-18 09:54:41,730] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:54:41,730] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10092/markers.fasta)
[2023-03-18 09:54:41,732] [INFO] Task started: Blastn
[2023-03-18 09:54:41,732] [INFO] Running command: blastn -query OceanDNA-b10092/markers.fasta -db /var/lib/cwl/stge2eb8d01-52b5-403a-b9eb-193b1eda6ac3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10092/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:54:42,535] [INFO] Task succeeded: Blastn
[2023-03-18 09:54:42,536] [INFO] Selected 21 target genomes.
[2023-03-18 09:54:42,536] [INFO] Target genome list was writen to OceanDNA-b10092/target_genomes_gtdb.txt
[2023-03-18 09:54:42,573] [INFO] Task started: fastANI
[2023-03-18 09:54:42,574] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b5ec152-e7da-402e-8b9b-974e74a095c4/OceanDNA-b10092.fa --refList OceanDNA-b10092/target_genomes_gtdb.txt --output OceanDNA-b10092/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:54:55,200] [INFO] Task succeeded: fastANI
[2023-03-18 09:54:55,212] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:54:55,212] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_007997225.1	s__Subsaximicrobium wynnwilliamsii	78.7854	469	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Subsaximicrobium	95.0	100.00	99.99	0.99	0.99	3	-
GCA_002162685.1	s__Psychroserpens sp002162685	77.1925	154	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799465.1	s__Psychroserpens sp000799465	77.0622	207	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	77.0419	156	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	77.0283	209	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688335.1	s__Subsaximicrobium sp000688335	77.0103	248	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Subsaximicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826655.1	s__Psychroserpens damuponensis	76.9611	198	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014526325.1	s__Psychroserpens algicola	76.9119	191	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	76.5856	121	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423005.1	s__Gelidibacter mesophilus	76.5026	122	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012931685.1	s__Pseudobizionia ponticola	76.384	112	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudobizionia	95.0	97.35	97.35	0.92	0.92	2	-
GCA_016744625.1	s__Winogradskyella sp016744625	76.2429	102	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806375.1	s__Tamlana_A haliotis	76.2332	84	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971725.1	s__Winogradskyella sp001971725	76.0931	77	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685485.1	s__Formosa haliotis	76.0335	87	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002973595.1	s__Jejuia pallidilutea	75.9659	81	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	98.03	97.97	0.83	0.83	4	-
GCF_005869935.1	s__Winogradskyella algicola	75.9352	72	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001275.1	s__Flaviramulus sp013001275	75.9004	79	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213835.1	s__Winogradskyella sp013213835	75.7892	84	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310325.1	s__Jejuia sp004310325	75.7843	86	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016827605.1	s__Jejuia sp016827605	75.6618	69	928	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:54:55,212] [INFO] GTDB search result was written to OceanDNA-b10092/result_gtdb.tsv
[2023-03-18 09:54:55,212] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:54:55,215] [INFO] DFAST_QC result json was written to OceanDNA-b10092/dqc_result.json
[2023-03-18 09:54:55,215] [INFO] DFAST_QC completed!
[2023-03-18 09:54:55,215] [INFO] Total running time: 0h1m45s