[2023-06-13 14:34:03,681] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:34:03,683] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:34:03,683] [INFO] DQC Reference Directory: /var/lib/cwl/stg89c48714-38bf-4540-8bea-b0a2e34c789a/dqc_reference
[2023-06-13 14:34:04,881] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:34:04,882] [INFO] Task started: Prodigal
[2023-06-13 14:34:04,883] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c29e3d6-090b-4b78-b969-3d15bf42d0e0/GCA_947488545.1_ZE-13may13-207_genomic.fna.gz | prodigal -d GCA_947488545.1_ZE-13may13-207_genomic.fna/cds.fna -a GCA_947488545.1_ZE-13may13-207_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:34:11,689] [INFO] Task succeeded: Prodigal
[2023-06-13 14:34:11,689] [INFO] Task started: HMMsearch
[2023-06-13 14:34:11,689] [INFO] Running command: hmmsearch --tblout GCA_947488545.1_ZE-13may13-207_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89c48714-38bf-4540-8bea-b0a2e34c789a/dqc_reference/reference_markers.hmm GCA_947488545.1_ZE-13may13-207_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:34:11,918] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:34:11,919] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0c29e3d6-090b-4b78-b969-3d15bf42d0e0/GCA_947488545.1_ZE-13may13-207_genomic.fna.gz]
[2023-06-13 14:34:11,947] [INFO] Query marker FASTA was written to GCA_947488545.1_ZE-13may13-207_genomic.fna/markers.fasta
[2023-06-13 14:34:11,947] [INFO] Task started: Blastn
[2023-06-13 14:34:11,947] [INFO] Running command: blastn -query GCA_947488545.1_ZE-13may13-207_genomic.fna/markers.fasta -db /var/lib/cwl/stg89c48714-38bf-4540-8bea-b0a2e34c789a/dqc_reference/reference_markers.fasta -out GCA_947488545.1_ZE-13may13-207_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:34:12,618] [INFO] Task succeeded: Blastn
[2023-06-13 14:34:12,622] [INFO] Selected 25 target genomes.
[2023-06-13 14:34:12,623] [INFO] Target genome list was writen to GCA_947488545.1_ZE-13may13-207_genomic.fna/target_genomes.txt
[2023-06-13 14:34:12,626] [INFO] Task started: fastANI
[2023-06-13 14:34:12,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c29e3d6-090b-4b78-b969-3d15bf42d0e0/GCA_947488545.1_ZE-13may13-207_genomic.fna.gz --refList GCA_947488545.1_ZE-13may13-207_genomic.fna/target_genomes.txt --output GCA_947488545.1_ZE-13may13-207_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:34:27,430] [INFO] Task succeeded: fastANI
[2023-06-13 14:34:27,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89c48714-38bf-4540-8bea-b0a2e34c789a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:34:27,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89c48714-38bf-4540-8bea-b0a2e34c789a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:34:27,450] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:34:27,450] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 14:34:27,450] [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
Flavobacterium psychrotolerans	strain=RB1R5	GCA_003097635.1	2169410	2169410	type	True	77.9103	190	639	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	77.8874	196	639	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	77.8678	209	639	95	below_threshold
Flavobacterium weaverense	strain=DSM 19727	GCA_003688495.1	271156	271156	type	True	77.835	186	639	95	below_threshold
Flavobacterium soli	strain=DSM 19725	GCA_000422705.1	344881	344881	type	True	77.7159	173	639	95	below_threshold
Flavobacterium aquatile	strain=NBRC 15052	GCA_006539785.1	245	245	type	True	77.6432	224	639	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	77.6159	231	639	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	77.5803	225	639	95	below_threshold
Flavobacterium aquatile	strain=ATCC 11947	GCA_002217235.1	245	245	type	True	77.5741	231	639	95	below_threshold
Flavobacterium xanthum	strain=DSM 3661	GCA_900142695.1	69322	69322	type	True	77.5335	193	639	95	below_threshold
Flavobacterium glycines	strain=Gm-149	GCA_900100165.1	551990	551990	type	True	77.5208	146	639	95	below_threshold
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	77.5098	190	639	95	below_threshold
Flavobacterium glaciei	strain=CGMCC 1.5380	GCA_007994155.1	386300	386300	type	True	77.4851	215	639	95	below_threshold
Flavobacterium glycines	strain=NBRC 105008	GCA_007989005.1	551990	551990	type	True	77.4736	150	639	95	below_threshold
Flavobacterium turcicum	strain=F-339	GCA_011365745.1	2764718	2764718	type	True	77.4295	182	639	95	below_threshold
Flavobacterium glaciei	strain=DSM 19728	GCA_003350545.1	386300	386300	type	True	77.3891	218	639	95	below_threshold
Flavobacterium tegetincola	strain=DSM 22377	GCA_000425485.1	150172	150172	type	True	77.3837	150	639	95	below_threshold
Flavobacterium laiguense	strain=LB2P30	GCA_003097655.1	2169409	2169409	type	True	77.3731	196	639	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	77.3395	182	639	95	below_threshold
Flavobacterium daejeonense	strain=DSM 17708	GCA_000425425.1	350893	350893	type	True	77.2972	158	639	95	below_threshold
Flavobacterium faecale	strain=WV33	GCA_003076455.1	1355330	1355330	type	True	77.2844	143	639	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	77.2803	205	639	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.2554	174	639	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.2608	53	639	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	75.8083	66	639	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:34:27,452] [INFO] DFAST Taxonomy check result was written to GCA_947488545.1_ZE-13may13-207_genomic.fna/tc_result.tsv
[2023-06-13 14:34:27,453] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:34:27,453] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:34:27,453] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89c48714-38bf-4540-8bea-b0a2e34c789a/dqc_reference/checkm_data
[2023-06-13 14:34:27,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:34:27,481] [INFO] Task started: CheckM
[2023-06-13 14:34:27,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947488545.1_ZE-13may13-207_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947488545.1_ZE-13may13-207_genomic.fna/checkm_input GCA_947488545.1_ZE-13may13-207_genomic.fna/checkm_result
[2023-06-13 14:34:53,267] [INFO] Task succeeded: CheckM
[2023-06-13 14:34:53,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:34:53,289] [INFO] ===== Completeness check finished =====
[2023-06-13 14:34:53,289] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:34:53,289] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947488545.1_ZE-13may13-207_genomic.fna/markers.fasta)
[2023-06-13 14:34:53,290] [INFO] Task started: Blastn
[2023-06-13 14:34:53,290] [INFO] Running command: blastn -query GCA_947488545.1_ZE-13may13-207_genomic.fna/markers.fasta -db /var/lib/cwl/stg89c48714-38bf-4540-8bea-b0a2e34c789a/dqc_reference/reference_markers_gtdb.fasta -out GCA_947488545.1_ZE-13may13-207_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:34:54,353] [INFO] Task succeeded: Blastn
[2023-06-13 14:34:54,358] [INFO] Selected 12 target genomes.
[2023-06-13 14:34:54,358] [INFO] Target genome list was writen to GCA_947488545.1_ZE-13may13-207_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:34:54,364] [INFO] Task started: fastANI
[2023-06-13 14:34:54,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c29e3d6-090b-4b78-b969-3d15bf42d0e0/GCA_947488545.1_ZE-13may13-207_genomic.fna.gz --refList GCA_947488545.1_ZE-13may13-207_genomic.fna/target_genomes_gtdb.txt --output GCA_947488545.1_ZE-13may13-207_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:35:01,215] [INFO] Task succeeded: fastANI
[2023-06-13 14:35:01,228] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 14:35:01,229] [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_009926065.1	s__Flavobacterium sp009926065	89.9879	522	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903819815.1	s__Flavobacterium sp903819815	87.2049	405	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000439025.2	s__Flavobacterium sp000439025	86.2393	495	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693635.1	s__Flavobacterium sp009693635	81.593	345	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839195.1	s__Flavobacterium sp903839195	78.6101	246	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.63	96.46	0.85	0.82	4	-
GCF_003634825.1	s__Flavobacterium sp003634825	78.0939	210	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920895.1	s__Flavobacterium alvei	77.8708	197	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298525.1	s__Flavobacterium sp013298525	77.8316	186	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464475.1	s__Flavobacterium sp001464475	77.6654	217	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097385.1	s__Flavobacterium sp007097385	77.6406	175	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013284035.1	s__Flavobacterium sp003096795	77.6376	186	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.66	97.66	0.93	0.93	2	-
GCA_903838055.1	s__Flavobacterium sp903838055	77.2622	184	639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.97	99.95	0.98	0.97	3	-
--------------------------------------------------------------------------------
[2023-06-13 14:35:01,231] [INFO] GTDB search result was written to GCA_947488545.1_ZE-13may13-207_genomic.fna/result_gtdb.tsv
[2023-06-13 14:35:01,232] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:35:01,236] [INFO] DFAST_QC result json was written to GCA_947488545.1_ZE-13may13-207_genomic.fna/dqc_result.json
[2023-06-13 14:35:01,237] [INFO] DFAST_QC completed!
[2023-06-13 14:35:01,237] [INFO] Total running time: 0h0m58s