[2024-01-24 13:55:14,687] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:14,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:14,689] [INFO] DQC Reference Directory: /var/lib/cwl/stg05877ce2-37c8-4c06-9893-893b1a6745a1/dqc_reference
[2024-01-24 13:55:15,984] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:15,985] [INFO] Task started: Prodigal
[2024-01-24 13:55:15,986] [INFO] Running command: gunzip -c /var/lib/cwl/stg4083cf28-fff7-4bc4-8866-88cc8099586f/GCF_014295415.1_ASM1429541v1_genomic.fna.gz | prodigal -d GCF_014295415.1_ASM1429541v1_genomic.fna/cds.fna -a GCF_014295415.1_ASM1429541v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:28,729] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:28,729] [INFO] Task started: HMMsearch
[2024-01-24 13:55:28,730] [INFO] Running command: hmmsearch --tblout GCF_014295415.1_ASM1429541v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05877ce2-37c8-4c06-9893-893b1a6745a1/dqc_reference/reference_markers.hmm GCF_014295415.1_ASM1429541v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:29,060] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:29,061] [INFO] Found 6/6 markers.
[2024-01-24 13:55:29,089] [INFO] Query marker FASTA was written to GCF_014295415.1_ASM1429541v1_genomic.fna/markers.fasta
[2024-01-24 13:55:29,090] [INFO] Task started: Blastn
[2024-01-24 13:55:29,090] [INFO] Running command: blastn -query GCF_014295415.1_ASM1429541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05877ce2-37c8-4c06-9893-893b1a6745a1/dqc_reference/reference_markers.fasta -out GCF_014295415.1_ASM1429541v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:29,801] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:29,805] [INFO] Selected 24 target genomes.
[2024-01-24 13:55:29,805] [INFO] Target genome list was writen to GCF_014295415.1_ASM1429541v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:29,821] [INFO] Task started: fastANI
[2024-01-24 13:55:29,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg4083cf28-fff7-4bc4-8866-88cc8099586f/GCF_014295415.1_ASM1429541v1_genomic.fna.gz --refList GCF_014295415.1_ASM1429541v1_genomic.fna/target_genomes.txt --output GCF_014295415.1_ASM1429541v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:44,987] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:44,988] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05877ce2-37c8-4c06-9893-893b1a6745a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:44,988] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05877ce2-37c8-4c06-9893-893b1a6745a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:45,001] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:45,001] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:45,001] [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
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	100.0	994	995	95	conclusive
Altibacter lentus	strain=JLT2010	GCA_000746845.1	1223410	1223410	type	True	78.0258	225	995	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.9988	53	995	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	77.8137	139	995	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	77.6785	130	995	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	77.597	135	995	95	below_threshold
Pukyongia salina	strain=RR4-38	GCA_002966125.1	2094025	2094025	type	True	77.4663	178	995	95	below_threshold
Aequorivita viscosa	strain=CGMCC 1.11023	GCA_900106795.1	797419	797419	type	True	77.3645	70	995	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	77.351	116	995	95	below_threshold
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	77.2339	169	995	95	below_threshold
Aequorivita viscosa	strain=DSM 26349	GCA_900141955.1	797419	797419	type	True	77.1668	71	995	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	77.1123	87	995	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	77.0574	50	995	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	77.0032	99	995	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:45,003] [INFO] DFAST Taxonomy check result was written to GCF_014295415.1_ASM1429541v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:45,003] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:45,004] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:45,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05877ce2-37c8-4c06-9893-893b1a6745a1/dqc_reference/checkm_data
[2024-01-24 13:55:45,005] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:45,045] [INFO] Task started: CheckM
[2024-01-24 13:55:45,046] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014295415.1_ASM1429541v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014295415.1_ASM1429541v1_genomic.fna/checkm_input GCF_014295415.1_ASM1429541v1_genomic.fna/checkm_result
[2024-01-24 13:56:25,776] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:25,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:25,795] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:25,796] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:25,796] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014295415.1_ASM1429541v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:25,797] [INFO] Task started: Blastn
[2024-01-24 13:56:25,797] [INFO] Running command: blastn -query GCF_014295415.1_ASM1429541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05877ce2-37c8-4c06-9893-893b1a6745a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014295415.1_ASM1429541v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:26,595] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:26,600] [INFO] Selected 21 target genomes.
[2024-01-24 13:56:26,600] [INFO] Target genome list was writen to GCF_014295415.1_ASM1429541v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:26,623] [INFO] Task started: fastANI
[2024-01-24 13:56:26,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg4083cf28-fff7-4bc4-8866-88cc8099586f/GCF_014295415.1_ASM1429541v1_genomic.fna.gz --refList GCF_014295415.1_ASM1429541v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014295415.1_ASM1429541v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:38,104] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:38,123] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:38,123] [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_014295415.1	s__Altibacter sp014295415	100.0	994	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002813135.1	s__Altibacter sp002813135	78.2834	218	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746845.1	s__Altibacter lentus	78.0334	226	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	77.8137	139	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102055.1	s__Ulvibacter litoralis	77.6785	130	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCA_002696485.1	s__Altibacter sp002696485	77.5751	167	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	99.86	99.86	0.91	0.91	2	-
GCF_003413745.1	s__Marixanthomonas ophiurae	77.351	116	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008501705.1	s__Pukyongia sp008501705	77.2524	164	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688405.1	s__Ulvibacter antarcticus	77.2488	168	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002631855.1	s__Marixanthomonas sp002631855	77.2347	132	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346335.1	s__Aequorivita sinensis	77.1123	87	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.40	96.22	0.90	0.88	3	-
GCF_003095375.1	s__Marixanthomonas sp003095375	77.0032	99	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337605.1	s__Marinirhabdus sp002337605	76.9983	137	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.69	98.69	0.95	0.95	2	-
GCA_002715485.1	s__Aequorivita sp002715485	76.9845	99	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCA_905479745.1	s__Pukyongia sp905479745	76.9681	143	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649715.1	s__Aequorivita sp016649715	76.7221	89	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016827595.1	s__Marixanthomonas sp016827595	76.623	92	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009901575.1	s__Leptobacterium sp009901575	76.6111	56	995	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:38,124] [INFO] GTDB search result was written to GCF_014295415.1_ASM1429541v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:38,125] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:38,131] [INFO] DFAST_QC result json was written to GCF_014295415.1_ASM1429541v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:38,132] [INFO] DFAST_QC completed!
[2024-01-24 13:56:38,132] [INFO] Total running time: 0h1m23s