[2023-03-17 05:26:45,784] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:26:45,789] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:26:45,789] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ccb8621-9636-4f6e-b7d4-01a344b74b9f/dqc_reference
[2023-03-17 05:26:46,921] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:26:46,921] [INFO] Task started: Prodigal
[2023-03-17 05:26:46,921] [INFO] Running command: cat /var/lib/cwl/stgcf865d40-b7c8-4a4b-9d8f-e264638c2d1b/OceanDNA-b7184.fa | prodigal -d OceanDNA-b7184/cds.fna -a OceanDNA-b7184/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:27:04,746] [INFO] Task succeeded: Prodigal
[2023-03-17 05:27:04,746] [INFO] Task started: HMMsearch
[2023-03-17 05:27:04,746] [INFO] Running command: hmmsearch --tblout OceanDNA-b7184/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ccb8621-9636-4f6e-b7d4-01a344b74b9f/dqc_reference/reference_markers.hmm OceanDNA-b7184/protein.faa > /dev/null
[2023-03-17 05:27:04,949] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:27:04,949] [INFO] Found 6/6 markers.
[2023-03-17 05:27:04,967] [INFO] Query marker FASTA was written to OceanDNA-b7184/markers.fasta
[2023-03-17 05:27:04,969] [INFO] Task started: Blastn
[2023-03-17 05:27:04,969] [INFO] Running command: blastn -query OceanDNA-b7184/markers.fasta -db /var/lib/cwl/stg7ccb8621-9636-4f6e-b7d4-01a344b74b9f/dqc_reference/reference_markers.fasta -out OceanDNA-b7184/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:27:05,630] [INFO] Task succeeded: Blastn
[2023-03-17 05:27:05,631] [INFO] Selected 29 target genomes.
[2023-03-17 05:27:05,631] [INFO] Target genome list was writen to OceanDNA-b7184/target_genomes.txt
[2023-03-17 05:27:05,698] [INFO] Task started: fastANI
[2023-03-17 05:27:05,698] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf865d40-b7c8-4a4b-9d8f-e264638c2d1b/OceanDNA-b7184.fa --refList OceanDNA-b7184/target_genomes.txt --output OceanDNA-b7184/fastani_result.tsv --threads 1
[2023-03-17 05:27:24,067] [INFO] Task succeeded: fastANI
[2023-03-17 05:27:24,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ccb8621-9636-4f6e-b7d4-01a344b74b9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:27:24,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ccb8621-9636-4f6e-b7d4-01a344b74b9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:27:24,084] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:27:24,084] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:27:24,084] [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
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	78.2118	376	971	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	78.1511	318	971	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	78.105	355	971	95	below_threshold
Gelidibacter mesophilus	strain=DSM 14095	GCA_000423005.1	169050	169050	type	True	78.0717	272	971	95	below_threshold
Gelidibacter sediminis	strain=DSM 28135	GCA_004364975.1	1608710	1608710	type	True	77.9918	298	971	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.909	310	971	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.8846	330	971	95	below_threshold
Gelidibacter salicanalis	strain=IC162	GCA_007997285.1	291193	291193	type	True	77.8769	220	971	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	77.825	286	971	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.8168	292	971	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	77.7838	302	971	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.7807	273	971	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.7511	325	971	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.7173	357	971	95	below_threshold
Gelidibacter japonicus	strain=Bio7-1	GCA_010725055.1	1962232	1962232	type	True	77.6733	255	971	95	below_threshold
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	77.6598	283	971	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.65	289	971	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	77.6295	290	971	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	77.6025	232	971	95	below_threshold
Gelidibacter pelagius	strain=DF109	GCA_017581925.1	2819985	2819985	type	True	77.5694	248	971	95	below_threshold
Tamlana carrageenivorans	strain=UJ94	GCA_002893765.1	2069432	2069432	type	True	77.5611	191	971	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.5109	268	971	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	77.4939	269	971	95	below_threshold
Confluentibacter lentus	strain=HJM-3	GCA_002806995.1	1699412	1699412	type	True	77.3908	213	971	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	77.378	231	971	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.3468	228	971	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	77.3028	248	971	95	below_threshold
Hyunsoonleella pacifica	strain=CGMCC 1.11009	GCA_014636335.1	1080224	1080224	type	True	77.2972	248	971	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.112	213	971	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:27:24,084] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7184/tc_result.tsv
[2023-03-17 05:27:24,085] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:27:24,085] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:27:24,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ccb8621-9636-4f6e-b7d4-01a344b74b9f/dqc_reference/checkm_data
[2023-03-17 05:27:24,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:27:24,115] [INFO] Task started: CheckM
[2023-03-17 05:27:24,116] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7184/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7184/checkm_input OceanDNA-b7184/checkm_result
[2023-03-17 05:28:10,253] [INFO] Task succeeded: CheckM
[2023-03-17 05:28:10,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:28:10,301] [INFO] ===== Completeness check finished =====
[2023-03-17 05:28:10,301] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:28:10,301] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7184/markers.fasta)
[2023-03-17 05:28:10,302] [INFO] Task started: Blastn
[2023-03-17 05:28:10,303] [INFO] Running command: blastn -query OceanDNA-b7184/markers.fasta -db /var/lib/cwl/stg7ccb8621-9636-4f6e-b7d4-01a344b74b9f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7184/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:28:11,291] [INFO] Task succeeded: Blastn
[2023-03-17 05:28:11,292] [INFO] Selected 17 target genomes.
[2023-03-17 05:28:11,292] [INFO] Target genome list was writen to OceanDNA-b7184/target_genomes_gtdb.txt
[2023-03-17 05:28:11,425] [INFO] Task started: fastANI
[2023-03-17 05:28:11,425] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf865d40-b7c8-4a4b-9d8f-e264638c2d1b/OceanDNA-b7184.fa --refList OceanDNA-b7184/target_genomes_gtdb.txt --output OceanDNA-b7184/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:28:22,332] [INFO] Task succeeded: fastANI
[2023-03-17 05:28:22,342] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:28:22,342] [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_014641635.1	s__Aquaticitalea lipolytica	97.7325	885	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002426015.1	s__Aquaticitalea sp002426015	83.8169	607	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	79.1883	440	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	78.814	429	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_900114265.1	s__Flaviramulus basaltis	78.6883	402	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	78.688	332	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162685.1	s__Psychroserpens sp002162685	78.2926	394	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002426755.1	s__Aquaticitalea sp002426755	78.253	372	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	78.2085	377	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162765.1	s__MAAR01 sp002162765	78.2053	328	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366675.1	s__Xanthomarina sp002366675	78.1253	262	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014764305.1	s__Mesoflavibacter profundi	77.9537	317	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	99.53	99.53	0.98	0.98	3	-
GCF_000799465.1	s__Psychroserpens sp000799465	77.8356	326	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638915.1	s__Xanthomarina arctica	77.7716	324	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414705.1	s__Algorimicrobium sp002414705	77.7089	286	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171875.1	s__Winogradskyella sp000171875	77.6984	337	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441545.1	s__Yeosuana sp002441545	77.5702	304	971	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:28:22,342] [INFO] GTDB search result was written to OceanDNA-b7184/result_gtdb.tsv
[2023-03-17 05:28:22,342] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:28:22,344] [INFO] DFAST_QC result json was written to OceanDNA-b7184/dqc_result.json
[2023-03-17 05:28:22,345] [INFO] DFAST_QC completed!
[2023-03-17 05:28:22,345] [INFO] Total running time: 0h1m37s