[2023-03-14 10:55:58,911] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,936] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,936] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d76f465-9abc-4cbd-a333-a8a5cec71fb4/dqc_reference
[2023-03-14 10:56:00,758] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,758] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,758] [INFO] Running command: cat /var/lib/cwl/stgb76dba32-7bb4-4399-a9ae-f81e13979396/OceanDNA-b7279.fa | prodigal -d OceanDNA-b7279/cds.fna -a OceanDNA-b7279/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:12,019] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:12,019] [INFO] Task started: HMMsearch
[2023-03-14 10:56:12,019] [INFO] Running command: hmmsearch --tblout OceanDNA-b7279/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d76f465-9abc-4cbd-a333-a8a5cec71fb4/dqc_reference/reference_markers.hmm OceanDNA-b7279/protein.faa > /dev/null
[2023-03-14 10:56:12,245] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:12,246] [INFO] Found 6/6 markers.
[2023-03-14 10:56:12,258] [INFO] Query marker FASTA was written to OceanDNA-b7279/markers.fasta
[2023-03-14 10:56:12,258] [INFO] Task started: Blastn
[2023-03-14 10:56:12,258] [INFO] Running command: blastn -query OceanDNA-b7279/markers.fasta -db /var/lib/cwl/stg8d76f465-9abc-4cbd-a333-a8a5cec71fb4/dqc_reference/reference_markers.fasta -out OceanDNA-b7279/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:12,914] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:12,915] [INFO] Selected 31 target genomes.
[2023-03-14 10:56:12,915] [INFO] Target genome list was writen to OceanDNA-b7279/target_genomes.txt
[2023-03-14 10:56:12,927] [INFO] Task started: fastANI
[2023-03-14 10:56:12,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgb76dba32-7bb4-4399-a9ae-f81e13979396/OceanDNA-b7279.fa --refList OceanDNA-b7279/target_genomes.txt --output OceanDNA-b7279/fastani_result.tsv --threads 1
[2023-03-14 10:56:31,717] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:31,717] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d76f465-9abc-4cbd-a333-a8a5cec71fb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:31,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d76f465-9abc-4cbd-a333-a8a5cec71fb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:31,733] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:31,733] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 10:56:31,734] [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	76.7646	64	534	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.6859	62	534	95	below_threshold
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	76.6344	59	534	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.5486	73	534	95	below_threshold
Formosa agariphila	strain=type strain: KMM 3901	GCA_000723205.1	320324	320324	type	True	76.5336	59	534	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	76.4739	72	534	95	below_threshold
Bizionia argentinensis	strain=JUB59	GCA_000224335.2	456455	456455	type	True	76.3953	58	534	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	76.3741	76	534	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.3501	72	534	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	76.3074	60	534	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.2458	68	534	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	76.228	64	534	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	76.228	64	534	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.228	64	534	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	76.2188	66	534	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.211	82	534	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	76.1759	70	534	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.1259	70	534	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	76.1099	73	534	95	below_threshold
Mangrovimonas spongiae	strain=HN-E26	GCA_003944795.1	2494697	2494697	type	True	76.1064	58	534	95	below_threshold
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	76.0506	63	534	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.0396	59	534	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	75.9896	64	534	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	75.9831	64	534	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	75.9612	53	534	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	75.9398	60	534	95	below_threshold
Winogradskyella tangerina	strain=M1309	GCA_003260205.1	2023240	2023240	type	True	75.9344	50	534	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	75.9322	66	534	95	below_threshold
Gelidibacter mesophilus	strain=DSM 14095	GCA_000423005.1	169050	169050	type	True	75.7482	54	534	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	75.4721	51	534	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:31,734] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7279/tc_result.tsv
[2023-03-14 10:56:31,734] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:31,734] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:31,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d76f465-9abc-4cbd-a333-a8a5cec71fb4/dqc_reference/checkm_data
[2023-03-14 10:56:31,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:31,738] [INFO] Task started: CheckM
[2023-03-14 10:56:31,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7279/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7279/checkm_input OceanDNA-b7279/checkm_result
[2023-03-14 10:57:04,255] [INFO] Task succeeded: CheckM
[2023-03-14 10:57:04,255] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:57:04,257] [INFO] ===== Completeness check finished =====
[2023-03-14 10:57:04,257] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:57:04,258] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7279/markers.fasta)
[2023-03-14 10:57:04,258] [INFO] Task started: Blastn
[2023-03-14 10:57:04,258] [INFO] Running command: blastn -query OceanDNA-b7279/markers.fasta -db /var/lib/cwl/stg8d76f465-9abc-4cbd-a333-a8a5cec71fb4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7279/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:57:05,092] [INFO] Task succeeded: Blastn
[2023-03-14 10:57:05,093] [INFO] Selected 9 target genomes.
[2023-03-14 10:57:05,093] [INFO] Target genome list was writen to OceanDNA-b7279/target_genomes_gtdb.txt
[2023-03-14 10:57:05,132] [INFO] Task started: fastANI
[2023-03-14 10:57:05,133] [INFO] Running command: fastANI --query /var/lib/cwl/stgb76dba32-7bb4-4399-a9ae-f81e13979396/OceanDNA-b7279.fa --refList OceanDNA-b7279/target_genomes_gtdb.txt --output OceanDNA-b7279/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:57:08,692] [INFO] Task succeeded: fastANI
[2023-03-14 10:57:08,698] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 10:57:08,698] [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_905479095.1	s__Hel1-33-131 sp905479095	99.6959	479	534	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	conclusive
GCF_001735745.1	s__Hel1-33-131 sp001735745	81.7946	386	534	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_018608765.1	s__Hel1-33-131 sp018608765	80.3454	319	534	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	80.041	253	534	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	79.9811	303	534	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	79.8618	281	534	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	79.4968	189	534	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	78.9768	214	534	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	-
--------------------------------------------------------------------------------
[2023-03-14 10:57:08,698] [INFO] GTDB search result was written to OceanDNA-b7279/result_gtdb.tsv
[2023-03-14 10:57:08,699] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:57:08,701] [INFO] DFAST_QC result json was written to OceanDNA-b7279/dqc_result.json
[2023-03-14 10:57:08,701] [INFO] DFAST_QC completed!
[2023-03-14 10:57:08,701] [INFO] Total running time: 0h1m10s