[2024-01-24 13:32:41,204] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,206] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,206] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bd7cff1-e6b5-4360-9c63-716390cca97e/dqc_reference
[2024-01-24 13:32:42,466] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,467] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,467] [INFO] Running command: gunzip -c /var/lib/cwl/stg53877fdc-f44e-4943-88c3-fa2972b42251/GCF_002269385.1_ASM226938v1_genomic.fna.gz | prodigal -d GCF_002269385.1_ASM226938v1_genomic.fna/cds.fna -a GCF_002269385.1_ASM226938v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:04,989] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:04,990] [INFO] Task started: HMMsearch
[2024-01-24 13:33:04,990] [INFO] Running command: hmmsearch --tblout GCF_002269385.1_ASM226938v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bd7cff1-e6b5-4360-9c63-716390cca97e/dqc_reference/reference_markers.hmm GCF_002269385.1_ASM226938v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:05,279] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:05,281] [INFO] Found 6/6 markers.
[2024-01-24 13:33:05,323] [INFO] Query marker FASTA was written to GCF_002269385.1_ASM226938v1_genomic.fna/markers.fasta
[2024-01-24 13:33:05,323] [INFO] Task started: Blastn
[2024-01-24 13:33:05,323] [INFO] Running command: blastn -query GCF_002269385.1_ASM226938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bd7cff1-e6b5-4360-9c63-716390cca97e/dqc_reference/reference_markers.fasta -out GCF_002269385.1_ASM226938v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:05,936] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:05,940] [INFO] Selected 17 target genomes.
[2024-01-24 13:33:05,941] [INFO] Target genome list was writen to GCF_002269385.1_ASM226938v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:05,949] [INFO] Task started: fastANI
[2024-01-24 13:33:05,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg53877fdc-f44e-4943-88c3-fa2972b42251/GCF_002269385.1_ASM226938v1_genomic.fna.gz --refList GCF_002269385.1_ASM226938v1_genomic.fna/target_genomes.txt --output GCF_002269385.1_ASM226938v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:20,283] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:20,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bd7cff1-e6b5-4360-9c63-716390cca97e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:20,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bd7cff1-e6b5-4360-9c63-716390cca97e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:20,298] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:33:20,298] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:20,298] [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
Maribacter cobaltidurans	strain=B1	GCA_002269385.1	1178778	1178778	type	True	100.0	1543	1546	95	conclusive
Maribacter cobaltidurans	strain=CGMCC 1.15508	GCA_014643435.1	1178778	1178778	type	True	99.98	1495	1546	95	conclusive
Maribacter algicola	strain=PoM-212	GCA_003933245.1	2498892	2498892	type	True	82.5687	809	1546	95	below_threshold
Maribacter aurantiacus	strain=KCTC 52409	GCA_005780245.1	1882343	1882343	type	True	80.5765	712	1546	95	below_threshold
Maribacter flavus	strain=KCTC 42508	GCA_008386635.1	1658664	1658664	type	True	80.404	716	1546	95	below_threshold
Euzebyella saccharophila	strain=7SM30	GCA_014855495.1	679664	679664	type	True	79.6152	195	1546	95	below_threshold
Maribacter thermophilus	strain=HT7-2	GCA_001020565.1	1197874	1197874	type	True	78.0942	349	1546	95	below_threshold
Pareuzebyella sediminis	strain=S2-4-21	GCA_008367235.1	2607998	2607998	type	True	77.5053	158	1546	95	below_threshold
Arenibacter hampyeongensis	strain=JCM 17788	GCA_002909255.1	1028743	1028743	type	True	77.1523	174	1546	95	below_threshold
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	77.0728	213	1546	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.6983	52	1546	95	below_threshold
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	76.6103	140	1546	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	76.465	100	1546	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:20,301] [INFO] DFAST Taxonomy check result was written to GCF_002269385.1_ASM226938v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:20,301] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:20,302] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:20,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bd7cff1-e6b5-4360-9c63-716390cca97e/dqc_reference/checkm_data
[2024-01-24 13:33:20,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:20,352] [INFO] Task started: CheckM
[2024-01-24 13:33:20,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002269385.1_ASM226938v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002269385.1_ASM226938v1_genomic.fna/checkm_input GCF_002269385.1_ASM226938v1_genomic.fna/checkm_result
[2024-01-24 13:34:23,172] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:23,174] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:23,194] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:23,195] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:23,195] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002269385.1_ASM226938v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:23,196] [INFO] Task started: Blastn
[2024-01-24 13:34:23,196] [INFO] Running command: blastn -query GCF_002269385.1_ASM226938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bd7cff1-e6b5-4360-9c63-716390cca97e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002269385.1_ASM226938v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:24,000] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:24,004] [INFO] Selected 16 target genomes.
[2024-01-24 13:34:24,004] [INFO] Target genome list was writen to GCF_002269385.1_ASM226938v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:24,035] [INFO] Task started: fastANI
[2024-01-24 13:34:24,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg53877fdc-f44e-4943-88c3-fa2972b42251/GCF_002269385.1_ASM226938v1_genomic.fna.gz --refList GCF_002269385.1_ASM226938v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002269385.1_ASM226938v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:36,603] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:36,623] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:36,623] [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
GCF_002269385.1	s__Maribacter cobaltidurans	100.0	1542	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_002742265.1	s__Maribacter sp002742265	84.0654	896	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003933245.1	s__Maribacter algicola	82.5687	809	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386635.1	s__Maribacter flavus	80.4009	716	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.59	96.59	0.88	0.88	2	-
GCF_018100785.1	s__Maribacter sp018100785	78.059	349	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001020565.1	s__Maribacter thermophilus	78.0571	347	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008367235.1	s__Pareuzebyella sediminis	77.5066	158	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pareuzebyella	95.0	99.39	99.39	0.97	0.97	2	-
GCF_005771495.1	s__Maribacter sp005771495	77.4061	220	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167935.1	s__Maribacter arcticus	77.0709	214	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153165.2	s__Maribacter_A sp000153165	77.0374	127	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002909235.1	s__Arenibacter catalasegens	76.9407	150	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014397245.1	s__Arenibacter arenosicollis	76.609	139	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002514735.1	s__Sediminicola_A luteus	76.4177	78	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sediminicola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001935.1	s__Maribacter_A sp013001935	76.3645	70	1546	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	96.76	96.72	0.66	0.66	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:36,625] [INFO] GTDB search result was written to GCF_002269385.1_ASM226938v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:36,626] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:36,629] [INFO] DFAST_QC result json was written to GCF_002269385.1_ASM226938v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:36,629] [INFO] DFAST_QC completed!
[2024-01-24 13:34:36,630] [INFO] Total running time: 0h1m55s