[2023-03-17 07:01:49,598] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:01:49,598] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:01:49,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ef090bd-14f6-4294-8b58-1a2fc14c7eca/dqc_reference
[2023-03-17 07:01:51,533] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:01:51,533] [INFO] Task started: Prodigal
[2023-03-17 07:01:51,533] [INFO] Running command: cat /var/lib/cwl/stg8f5c8128-7fdf-4dcd-a5f2-b76877e54562/OceanDNA-b7344.fa | prodigal -d OceanDNA-b7344/cds.fna -a OceanDNA-b7344/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:02:03,069] [INFO] Task succeeded: Prodigal
[2023-03-17 07:02:03,069] [INFO] Task started: HMMsearch
[2023-03-17 07:02:03,069] [INFO] Running command: hmmsearch --tblout OceanDNA-b7344/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ef090bd-14f6-4294-8b58-1a2fc14c7eca/dqc_reference/reference_markers.hmm OceanDNA-b7344/protein.faa > /dev/null
[2023-03-17 07:02:03,288] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:02:03,289] [INFO] Found 6/6 markers.
[2023-03-17 07:02:03,301] [INFO] Query marker FASTA was written to OceanDNA-b7344/markers.fasta
[2023-03-17 07:02:03,302] [INFO] Task started: Blastn
[2023-03-17 07:02:03,302] [INFO] Running command: blastn -query OceanDNA-b7344/markers.fasta -db /var/lib/cwl/stg1ef090bd-14f6-4294-8b58-1a2fc14c7eca/dqc_reference/reference_markers.fasta -out OceanDNA-b7344/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:03,902] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:03,903] [INFO] Selected 31 target genomes.
[2023-03-17 07:02:03,903] [INFO] Target genome list was writen to OceanDNA-b7344/target_genomes.txt
[2023-03-17 07:02:03,919] [INFO] Task started: fastANI
[2023-03-17 07:02:03,920] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f5c8128-7fdf-4dcd-a5f2-b76877e54562/OceanDNA-b7344.fa --refList OceanDNA-b7344/target_genomes.txt --output OceanDNA-b7344/fastani_result.tsv --threads 1
[2023-03-17 07:02:22,306] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:22,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ef090bd-14f6-4294-8b58-1a2fc14c7eca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:02:22,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ef090bd-14f6-4294-8b58-1a2fc14c7eca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:02:22,322] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:02:22,322] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:02:22,322] [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
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.6188	73	572	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	76.5631	72	572	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	76.5217	53	572	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	76.4356	77	572	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	76.384	86	572	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.3496	79	572	95	below_threshold
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	76.3393	73	572	95	below_threshold
Bizionia paragorgiae	strain=DSM 23842	GCA_900107625.1	283786	283786	type	True	76.3221	65	572	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.3195	103	572	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	76.2989	74	572	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.2715	72	572	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	76.2709	83	572	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	76.2485	73	572	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.2384	90	572	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	76.2205	67	572	95	below_threshold
Hyunsoonleella pacifica	strain=CGMCC 1.11009	GCA_014636335.1	1080224	1080224	type	True	76.2205	67	572	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.2199	86	572	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.1539	78	572	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	76.1345	93	572	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	76.1325	95	572	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	76.1302	80	572	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.0627	81	572	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	75.9787	75	572	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	75.9634	57	572	95	below_threshold
Kordia jejudonensis	strain=SSK3-3	GCA_001005315.1	1348245	1348245	type	True	75.9552	76	572	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	75.9267	76	572	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	75.8366	52	572	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	75.6112	62	572	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:02:22,323] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7344/tc_result.tsv
[2023-03-17 07:02:22,324] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:02:22,324] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:02:22,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ef090bd-14f6-4294-8b58-1a2fc14c7eca/dqc_reference/checkm_data
[2023-03-17 07:02:22,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:02:22,328] [INFO] Task started: CheckM
[2023-03-17 07:02:22,328] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7344/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7344/checkm_input OceanDNA-b7344/checkm_result
[2023-03-17 07:02:55,397] [INFO] Task succeeded: CheckM
[2023-03-17 07:02:55,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:02:55,399] [INFO] ===== Completeness check finished =====
[2023-03-17 07:02:55,399] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:02:55,399] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7344/markers.fasta)
[2023-03-17 07:02:55,399] [INFO] Task started: Blastn
[2023-03-17 07:02:55,399] [INFO] Running command: blastn -query OceanDNA-b7344/markers.fasta -db /var/lib/cwl/stg1ef090bd-14f6-4294-8b58-1a2fc14c7eca/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7344/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:56,278] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:56,279] [INFO] Selected 8 target genomes.
[2023-03-17 07:02:56,279] [INFO] Target genome list was writen to OceanDNA-b7344/target_genomes_gtdb.txt
[2023-03-17 07:02:56,372] [INFO] Task started: fastANI
[2023-03-17 07:02:56,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f5c8128-7fdf-4dcd-a5f2-b76877e54562/OceanDNA-b7344.fa --refList OceanDNA-b7344/target_genomes_gtdb.txt --output OceanDNA-b7344/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:02:59,709] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:59,715] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:02:59,715] [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_018608765.1	s__Hel1-33-131 sp018608765	81.1438	399	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735745.1	s__Hel1-33-131 sp001735745	80.9882	421	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608735.1	s__Hel1-33-131 sp018608735	80.7775	310	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608725.1	s__Hel1-33-131 sp018608725	80.5887	356	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673215.1	s__Hel1-33-131 sp018673215	80.2449	389	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479095.1	s__Hel1-33-131 sp905479095	79.9534	338	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181825.1	s__Hel1-33-131 sp905181825	78.4017	212	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.01	99.01	0.77	0.77	2	-
GCA_018608625.1	s__Hel1-33-131 sp018608625	78.1957	228	572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	98.93	97.98	0.88	0.82	3	-
--------------------------------------------------------------------------------
[2023-03-17 07:02:59,715] [INFO] GTDB search result was written to OceanDNA-b7344/result_gtdb.tsv
[2023-03-17 07:02:59,715] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:02:59,717] [INFO] DFAST_QC result json was written to OceanDNA-b7344/dqc_result.json
[2023-03-17 07:02:59,718] [INFO] DFAST_QC completed!
[2023-03-17 07:02:59,718] [INFO] Total running time: 0h1m10s