[2023-03-15 03:14:16,456] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:14:16,456] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:14:16,456] [INFO] DQC Reference Directory: /var/lib/cwl/stgb48a70f7-9b65-4f02-bb40-18d777fcba3f/dqc_reference
[2023-03-15 03:14:17,653] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:14:17,653] [INFO] Task started: Prodigal
[2023-03-15 03:14:17,653] [INFO] Running command: cat /var/lib/cwl/stg0cb384dc-eef2-4d00-b705-1420575d84f1/OceanDNA-b6202.fa | prodigal -d OceanDNA-b6202/cds.fna -a OceanDNA-b6202/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:14:31,342] [INFO] Task succeeded: Prodigal
[2023-03-15 03:14:31,342] [INFO] Task started: HMMsearch
[2023-03-15 03:14:31,342] [INFO] Running command: hmmsearch --tblout OceanDNA-b6202/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb48a70f7-9b65-4f02-bb40-18d777fcba3f/dqc_reference/reference_markers.hmm OceanDNA-b6202/protein.faa > /dev/null
[2023-03-15 03:14:31,580] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:14:31,581] [INFO] Found 6/6 markers.
[2023-03-15 03:14:31,596] [INFO] Query marker FASTA was written to OceanDNA-b6202/markers.fasta
[2023-03-15 03:14:31,596] [INFO] Task started: Blastn
[2023-03-15 03:14:31,596] [INFO] Running command: blastn -query OceanDNA-b6202/markers.fasta -db /var/lib/cwl/stgb48a70f7-9b65-4f02-bb40-18d777fcba3f/dqc_reference/reference_markers.fasta -out OceanDNA-b6202/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:14:32,213] [INFO] Task succeeded: Blastn
[2023-03-15 03:14:32,214] [INFO] Selected 28 target genomes.
[2023-03-15 03:14:32,214] [INFO] Target genome list was writen to OceanDNA-b6202/target_genomes.txt
[2023-03-15 03:14:32,229] [INFO] Task started: fastANI
[2023-03-15 03:14:32,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cb384dc-eef2-4d00-b705-1420575d84f1/OceanDNA-b6202.fa --refList OceanDNA-b6202/target_genomes.txt --output OceanDNA-b6202/fastani_result.tsv --threads 1
[2023-03-15 03:14:49,000] [INFO] Task succeeded: fastANI
[2023-03-15 03:14:49,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb48a70f7-9b65-4f02-bb40-18d777fcba3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:14:49,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb48a70f7-9b65-4f02-bb40-18d777fcba3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:14:49,016] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:14:49,016] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:14:49,016] [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
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.3741	239	713	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	77.3205	172	713	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.1584	147	713	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	77.1422	133	713	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	77.1087	143	713	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	77.0697	160	713	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.9957	186	713	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	76.9556	159	713	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	76.9327	157	713	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.923	164	713	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.9209	171	713	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	76.9075	182	713	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	76.9074	182	713	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	76.8936	176	713	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	76.8936	176	713	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.8837	179	713	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.8638	152	713	95	below_threshold
Confluentibacter flavum	strain=3B	GCA_002843175.1	1909700	1909700	type	True	76.8522	156	713	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	76.8446	149	713	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.7686	116	713	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.719	115	713	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	76.7074	168	713	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.6453	61	713	95	below_threshold
Winogradskyella tangerina	strain=M1309	GCA_003260205.1	2023240	2023240	type	True	76.531	92	713	95	below_threshold
Hyunsoonleella pacifica	strain=CGMCC 1.11009	GCA_014636335.1	1080224	1080224	type	True	76.5256	148	713	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	76.4948	146	713	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.4841	119	713	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.4273	130	713	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:14:49,016] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6202/tc_result.tsv
[2023-03-15 03:14:49,016] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:14:49,016] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:14:49,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb48a70f7-9b65-4f02-bb40-18d777fcba3f/dqc_reference/checkm_data
[2023-03-15 03:14:49,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:14:49,021] [INFO] Task started: CheckM
[2023-03-15 03:14:49,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6202/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6202/checkm_input OceanDNA-b6202/checkm_result
[2023-03-15 03:15:26,153] [INFO] Task succeeded: CheckM
[2023-03-15 03:15:26,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:15:26,155] [INFO] ===== Completeness check finished =====
[2023-03-15 03:15:26,155] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:15:26,155] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6202/markers.fasta)
[2023-03-15 03:15:26,156] [INFO] Task started: Blastn
[2023-03-15 03:15:26,156] [INFO] Running command: blastn -query OceanDNA-b6202/markers.fasta -db /var/lib/cwl/stgb48a70f7-9b65-4f02-bb40-18d777fcba3f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6202/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:15:27,011] [INFO] Task succeeded: Blastn
[2023-03-15 03:15:27,012] [INFO] Selected 19 target genomes.
[2023-03-15 03:15:27,012] [INFO] Target genome list was writen to OceanDNA-b6202/target_genomes_gtdb.txt
[2023-03-15 03:15:27,027] [INFO] Task started: fastANI
[2023-03-15 03:15:27,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cb384dc-eef2-4d00-b705-1420575d84f1/OceanDNA-b6202.fa --refList OceanDNA-b6202/target_genomes_gtdb.txt --output OceanDNA-b6202/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:15:37,585] [INFO] Task succeeded: fastANI
[2023-03-15 03:15:37,596] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 03:15:37,596] [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
GCA_003709165.1	s__PRS1 sp003709165	98.499	597	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003650305.1	s__PRS1 sp003650305	81.2967	475	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151975.1	s__PRS1 sp013151975	78.7435	288	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	77.6103	204	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011777505.1	s__CAU-1491 sp011777505	77.5523	251	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	77.5064	194	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148645.1	s__Xanthomarina spongicola	77.5055	209	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003443635.1	s__AU392 sp003443635	77.4414	205	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__AU392	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000422365.1	s__Mesoflavibacter zeaxanthinifaciens	77.3903	147	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	97.07	97.05	0.91	0.91	3	-
GCF_900114265.1	s__Flaviramulus basaltis	77.3751	214	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005047595.1	s__CAU-1491 sp005047595	77.3741	239	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638915.1	s__Xanthomarina arctica	77.2382	178	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366675.1	s__Xanthomarina sp002366675	77.1821	153	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	77.129	166	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	77.1204	223	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744625.1	s__Winogradskyella sp016744625	77.0166	180	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259525.1	s__Olleya aquimaris	76.9951	174	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000941055.1	s__Siansivirga zeaxanthinifaciens	76.9683	167	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	76.8837	179	713	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2023-03-15 03:15:37,596] [INFO] GTDB search result was written to OceanDNA-b6202/result_gtdb.tsv
[2023-03-15 03:15:37,596] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:15:37,599] [INFO] DFAST_QC result json was written to OceanDNA-b6202/dqc_result.json
[2023-03-15 03:15:37,599] [INFO] DFAST_QC completed!
[2023-03-15 03:15:37,599] [INFO] Total running time: 0h1m21s