[2024-01-25 18:13:05,753] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:05,755] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:05,755] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf4224ee-0818-43ed-a540-33d7f817c850/dqc_reference
[2024-01-25 18:13:06,868] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:06,873] [INFO] Task started: Prodigal
[2024-01-25 18:13:06,874] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfaec9c9-1adb-4a36-9e2d-f3f6d49708b3/GCF_018967865.2_ASM1896786v2_genomic.fna.gz | prodigal -d GCF_018967865.2_ASM1896786v2_genomic.fna/cds.fna -a GCF_018967865.2_ASM1896786v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:31,538] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:31,539] [INFO] Task started: HMMsearch
[2024-01-25 18:13:31,539] [INFO] Running command: hmmsearch --tblout GCF_018967865.2_ASM1896786v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf4224ee-0818-43ed-a540-33d7f817c850/dqc_reference/reference_markers.hmm GCF_018967865.2_ASM1896786v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:31,796] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:31,797] [INFO] Found 6/6 markers.
[2024-01-25 18:13:31,835] [INFO] Query marker FASTA was written to GCF_018967865.2_ASM1896786v2_genomic.fna/markers.fasta
[2024-01-25 18:13:31,835] [INFO] Task started: Blastn
[2024-01-25 18:13:31,835] [INFO] Running command: blastn -query GCF_018967865.2_ASM1896786v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf4224ee-0818-43ed-a540-33d7f817c850/dqc_reference/reference_markers.fasta -out GCF_018967865.2_ASM1896786v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:32,444] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:32,447] [INFO] Selected 16 target genomes.
[2024-01-25 18:13:32,447] [INFO] Target genome list was writen to GCF_018967865.2_ASM1896786v2_genomic.fna/target_genomes.txt
[2024-01-25 18:13:32,462] [INFO] Task started: fastANI
[2024-01-25 18:13:32,462] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfaec9c9-1adb-4a36-9e2d-f3f6d49708b3/GCF_018967865.2_ASM1896786v2_genomic.fna.gz --refList GCF_018967865.2_ASM1896786v2_genomic.fna/target_genomes.txt --output GCF_018967865.2_ASM1896786v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:51,455] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:51,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf4224ee-0818-43ed-a540-33d7f817c850/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:51,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf4224ee-0818-43ed-a540-33d7f817c850/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:51,464] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:13:51,465] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:13:51,465] [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
Hymenobacter artigasi	strain=1B	GCA_012275535.1	2719616	2719616	type	True	93.4736	1403	1609	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	84.9281	1206	1609	95	below_threshold
Hymenobacter rubidus	strain=DG7B	GCA_016734815.1	1441626	1441626	type	True	84.3055	1119	1609	95	below_threshold
Hymenobacter ruricola	strain=BT662	GCA_015694525.1	2791023	2791023	type	True	84.1392	1128	1609	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	84.1254	1168	1609	95	below_threshold
Hymenobacter frigidus	strain=CGMCC 1.14966	GCA_014640435.1	1524095	1524095	type	True	83.68	1093	1609	95	below_threshold
Hymenobacter properus	strain=BT439	GCA_015694735.1	2791026	2791026	type	True	83.6214	1139	1609	95	below_threshold
Hymenobacter lapidarius	strain=CCM 8643	GCA_001816145.1	1908237	1908237	type	True	83.216	1006	1609	95	below_threshold
Hymenobacter glacialis	strain=CCM 8648	GCA_001816165.1	1908236	1908236	type	True	83.0437	993	1609	95	below_threshold
Hymenobacter jeongseonensis	strain=BT683	GCA_015694725.1	2791027	2791027	type	True	82.3268	1027	1609	95	below_threshold
Hymenobacter montanus	strain=BT664	GCA_014699115.1	2771359	2771359	type	True	80.8923	898	1609	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	78.8694	663	1609	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	78.7241	649	1609	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:51,466] [INFO] DFAST Taxonomy check result was written to GCF_018967865.2_ASM1896786v2_genomic.fna/tc_result.tsv
[2024-01-25 18:13:51,467] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:51,467] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:51,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf4224ee-0818-43ed-a540-33d7f817c850/dqc_reference/checkm_data
[2024-01-25 18:13:51,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:51,516] [INFO] Task started: CheckM
[2024-01-25 18:13:51,516] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018967865.2_ASM1896786v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018967865.2_ASM1896786v2_genomic.fna/checkm_input GCF_018967865.2_ASM1896786v2_genomic.fna/checkm_result
[2024-01-25 18:14:55,720] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:55,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:55,744] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:55,744] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:55,745] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018967865.2_ASM1896786v2_genomic.fna/markers.fasta)
[2024-01-25 18:14:55,745] [INFO] Task started: Blastn
[2024-01-25 18:14:55,746] [INFO] Running command: blastn -query GCF_018967865.2_ASM1896786v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf4224ee-0818-43ed-a540-33d7f817c850/dqc_reference/reference_markers_gtdb.fasta -out GCF_018967865.2_ASM1896786v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:56,631] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:56,633] [INFO] Selected 15 target genomes.
[2024-01-25 18:14:56,634] [INFO] Target genome list was writen to GCF_018967865.2_ASM1896786v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:56,657] [INFO] Task started: fastANI
[2024-01-25 18:14:56,657] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfaec9c9-1adb-4a36-9e2d-f3f6d49708b3/GCF_018967865.2_ASM1896786v2_genomic.fna.gz --refList GCF_018967865.2_ASM1896786v2_genomic.fna/target_genomes_gtdb.txt --output GCF_018967865.2_ASM1896786v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:17,424] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:17,433] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:17,434] [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_018967845.1	s__Hymenobacter sp018967845	98.9797	1516	1609	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	99.02	98.98	0.94	0.93	3	conclusive
GCF_012275535.1	s__Hymenobacter artigasi	93.4669	1403	1609	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016056375.1	s__Hymenobacter negativus_A	87.1117	1234	1609	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	97.78	97.78	0.95	0.95	3	-
GCF_016734815.1	s__Hymenobacter rubidus	84.2997	1120	1609	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694525.1	s__Hymenobacter ruricola	84.1391	1128	1609	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640435.1	s__Hymenobacter frigidus	83.6864	1094	1609	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694735.1	s__Hymenobacter properus	83.6304	1138	1609	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001816145.1	s__Hymenobacter lapidarius	83.2131	1008	1609	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816165.1	s__Hymenobacter glacialis	83.0375	994	1609	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507645.1	s__Hymenobacter sedentarius	82.9601	1065	1609	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000715495.1	s__Hymenobacter sp000715495	82.9149	1039	1609	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017571495.1	s__Hymenobacter negativus	82.8319	1127	1609	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694725.1	s__Hymenobacter jeongseonensis	82.3293	1026	1609	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699115.1	s__Hymenobacter sp014699115	80.8752	901	1609	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745955.1	s__Hymenobacter elongatus	78.614	618	1609	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:17,435] [INFO] GTDB search result was written to GCF_018967865.2_ASM1896786v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:17,436] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:17,438] [INFO] DFAST_QC result json was written to GCF_018967865.2_ASM1896786v2_genomic.fna/dqc_result.json
[2024-01-25 18:15:17,439] [INFO] DFAST_QC completed!
[2024-01-25 18:15:17,439] [INFO] Total running time: 0h2m12s