[2023-03-16 04:20:43,486] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:20:43,486] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:20:43,486] [INFO] DQC Reference Directory: /var/lib/cwl/stg860851a5-d0ba-498f-bd76-6547ccd77c9b/dqc_reference
[2023-03-16 04:20:44,608] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:20:44,609] [INFO] Task started: Prodigal
[2023-03-16 04:20:44,609] [INFO] Running command: cat /var/lib/cwl/stge035834e-b648-44e3-b0b9-aa9c4c0aba69/OceanDNA-b7132.fa | prodigal -d OceanDNA-b7132/cds.fna -a OceanDNA-b7132/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:20:55,282] [INFO] Task succeeded: Prodigal
[2023-03-16 04:20:55,282] [INFO] Task started: HMMsearch
[2023-03-16 04:20:55,283] [INFO] Running command: hmmsearch --tblout OceanDNA-b7132/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg860851a5-d0ba-498f-bd76-6547ccd77c9b/dqc_reference/reference_markers.hmm OceanDNA-b7132/protein.faa > /dev/null
[2023-03-16 04:20:55,456] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:20:55,457] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge035834e-b648-44e3-b0b9-aa9c4c0aba69/OceanDNA-b7132.fa]
[2023-03-16 04:20:55,471] [INFO] Query marker FASTA was written to OceanDNA-b7132/markers.fasta
[2023-03-16 04:20:55,471] [INFO] Task started: Blastn
[2023-03-16 04:20:55,471] [INFO] Running command: blastn -query OceanDNA-b7132/markers.fasta -db /var/lib/cwl/stg860851a5-d0ba-498f-bd76-6547ccd77c9b/dqc_reference/reference_markers.fasta -out OceanDNA-b7132/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:20:56,016] [INFO] Task succeeded: Blastn
[2023-03-16 04:20:56,016] [INFO] Selected 29 target genomes.
[2023-03-16 04:20:56,017] [INFO] Target genome list was writen to OceanDNA-b7132/target_genomes.txt
[2023-03-16 04:20:56,032] [INFO] Task started: fastANI
[2023-03-16 04:20:56,032] [INFO] Running command: fastANI --query /var/lib/cwl/stge035834e-b648-44e3-b0b9-aa9c4c0aba69/OceanDNA-b7132.fa --refList OceanDNA-b7132/target_genomes.txt --output OceanDNA-b7132/fastani_result.tsv --threads 1
[2023-03-16 04:21:11,149] [INFO] Task succeeded: fastANI
[2023-03-16 04:21:11,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg860851a5-d0ba-498f-bd76-6547ccd77c9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:21:11,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg860851a5-d0ba-498f-bd76-6547ccd77c9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:21:11,164] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:21:11,164] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:21:11,165] [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 amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	76.5142	79	578	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	76.5142	79	578	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.5101	78	578	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.4598	85	578	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.3521	91	578	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	76.3046	68	578	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.286	88	578	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	76.2514	107	578	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.196	89	578	95	below_threshold
Flavobacterium cheniae	strain=CGMCC 1.6844	GCA_007830415.1	295428	295428	type	True	76.1853	67	578	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	76.1579	80	578	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	76.1349	63	578	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	76.1282	87	578	95	below_threshold
Formosa sediminum	strain=PS13	GCA_007197735.1	2594004	2594004	type	True	76.1272	94	578	95	below_threshold
Aureivirga marina	strain=LMG 26721	GCA_015767265.1	1182451	1182451	type	True	76.1181	56	578	95	below_threshold
Flavobacterium cheniae	strain=DSM 22462	GCA_004363695.1	295428	295428	type	True	76.1124	70	578	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	76.0927	90	578	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.0879	83	578	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	76.0327	104	578	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	75.9215	84	578	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	75.8888	74	578	95	below_threshold
Kordia zhangzhouensis	strain=MCCC 1A00726	GCA_001005305.1	1620405	1620405	type	True	75.8836	74	578	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	75.8801	88	578	95	below_threshold
Urechidicola croceus	strain=LPB0138	GCA_001761325.1	1850246	1850246	type	True	75.8351	85	578	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	75.797	79	578	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	75.7761	63	578	95	below_threshold
Formosa agariphila	strain=type strain: KMM 3901	GCA_000723205.1	320324	320324	type	True	75.7593	90	578	95	below_threshold
Lutibacter profundi	strain=LP1	GCA_001543325.1	1622118	1622118	type	True	75.6814	75	578	95	below_threshold
Mesonia algae	strain=DSM 15361	GCA_003253545.1	213248	213248	type	True	75.3932	72	578	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:21:11,165] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7132/tc_result.tsv
[2023-03-16 04:21:11,165] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:21:11,165] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:21:11,165] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg860851a5-d0ba-498f-bd76-6547ccd77c9b/dqc_reference/checkm_data
[2023-03-16 04:21:11,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:21:11,169] [INFO] Task started: CheckM
[2023-03-16 04:21:11,169] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7132/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7132/checkm_input OceanDNA-b7132/checkm_result
[2023-03-16 04:21:41,632] [INFO] Task succeeded: CheckM
[2023-03-16 04:21:41,633] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:21:41,634] [INFO] ===== Completeness check finished =====
[2023-03-16 04:21:41,634] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:21:41,635] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7132/markers.fasta)
[2023-03-16 04:21:41,635] [INFO] Task started: Blastn
[2023-03-16 04:21:41,635] [INFO] Running command: blastn -query OceanDNA-b7132/markers.fasta -db /var/lib/cwl/stg860851a5-d0ba-498f-bd76-6547ccd77c9b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7132/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:21:42,437] [INFO] Task succeeded: Blastn
[2023-03-16 04:21:42,438] [INFO] Selected 27 target genomes.
[2023-03-16 04:21:42,438] [INFO] Target genome list was writen to OceanDNA-b7132/target_genomes_gtdb.txt
[2023-03-16 04:21:42,512] [INFO] Task started: fastANI
[2023-03-16 04:21:42,512] [INFO] Running command: fastANI --query /var/lib/cwl/stge035834e-b648-44e3-b0b9-aa9c4c0aba69/OceanDNA-b7132.fa --refList OceanDNA-b7132/target_genomes_gtdb.txt --output OceanDNA-b7132/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:21:57,351] [INFO] Task succeeded: fastANI
[2023-03-16 04:21:57,366] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:21:57,366] [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_002733415.1	s__GCA-2733415 sp002733415	78.2588	267	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2733415	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214625.1	s__GCA-2733415 sp013214625	78.0796	249	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2733415	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105985.1	s__Tenacibaculum sp900105985	76.3888	98	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.69	98.69	0.93	0.93	2	-
GCF_005047595.1	s__CAU-1491 sp005047595	76.3469	90	578	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_011777505.1	s__CAU-1491 sp011777505	76.261	72	578	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_014764305.1	s__Mesoflavibacter profundi	76.2514	107	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	99.53	99.53	0.98	0.98	3	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	76.211	113	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889045.1	s__Tenacibaculum_A todarodis	76.196	89	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403985.1	s__Winogradskyella ludwigii	76.1579	80	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635865.1	s__Winogradskyella haliclonae	76.1349	63	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767265.1	s__Aureivirga marina	76.1181	56	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151975.1	s__PRS1 sp013151975	76.1158	75	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363695.1	s__Flavobacterium cheniae	76.1124	70	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007997385.1	s__Seonamhaeicola algicola	76.0999	109	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	76.0929	104	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427335.1	s__Winogradskyella psychrotolerans	76.0927	90	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	76.0879	83	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741275.1	s__Winogradskyella endarachnes	76.0327	104	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004337695.1	s__Tenacibaculum sp004337695	76.0108	100	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104785.1	s__Psychroserpens sp900104785	75.9229	66	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003709165.1	s__PRS1 sp003709165	75.8841	57	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	75.8801	88	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005305.1	s__Kordia zhangzhouensis	75.8708	73	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019090365.1	s__GCA-002733185 sp019090365	75.8367	59	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761325.1	s__Urechidicola croceus	75.8351	85	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017985075.1	s__Flavobacterium sp017985075	75.6489	52	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253545.1	s__Mesonia algae	75.3932	72	578	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	95.16	95.16	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-03-16 04:21:57,366] [INFO] GTDB search result was written to OceanDNA-b7132/result_gtdb.tsv
[2023-03-16 04:21:57,366] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:21:57,369] [INFO] DFAST_QC result json was written to OceanDNA-b7132/dqc_result.json
[2023-03-16 04:21:57,369] [INFO] DFAST_QC completed!
[2023-03-16 04:21:57,369] [INFO] Total running time: 0h1m14s