[2024-01-24 11:35:23,405] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:23,407] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:23,407] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc8c5d0f-6b6d-4174-9bfa-a4b2c2bb3456/dqc_reference
[2024-01-24 11:35:26,245] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,246] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,247] [INFO] Running command: gunzip -c /var/lib/cwl/stg0df0fd77-c0b0-4c56-bcad-b2b733fdc32e/GCF_001623405.1_ASM162340v1_genomic.fna.gz | prodigal -d GCF_001623405.1_ASM162340v1_genomic.fna/cds.fna -a GCF_001623405.1_ASM162340v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:40,871] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:40,872] [INFO] Task started: HMMsearch
[2024-01-24 11:35:40,872] [INFO] Running command: hmmsearch --tblout GCF_001623405.1_ASM162340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc8c5d0f-6b6d-4174-9bfa-a4b2c2bb3456/dqc_reference/reference_markers.hmm GCF_001623405.1_ASM162340v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:41,201] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:41,202] [INFO] Found 6/6 markers.
[2024-01-24 11:35:41,233] [INFO] Query marker FASTA was written to GCF_001623405.1_ASM162340v1_genomic.fna/markers.fasta
[2024-01-24 11:35:41,233] [INFO] Task started: Blastn
[2024-01-24 11:35:41,233] [INFO] Running command: blastn -query GCF_001623405.1_ASM162340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc8c5d0f-6b6d-4174-9bfa-a4b2c2bb3456/dqc_reference/reference_markers.fasta -out GCF_001623405.1_ASM162340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:41,817] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:41,820] [INFO] Selected 16 target genomes.
[2024-01-24 11:35:41,820] [INFO] Target genome list was writen to GCF_001623405.1_ASM162340v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:41,826] [INFO] Task started: fastANI
[2024-01-24 11:35:41,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg0df0fd77-c0b0-4c56-bcad-b2b733fdc32e/GCF_001623405.1_ASM162340v1_genomic.fna.gz --refList GCF_001623405.1_ASM162340v1_genomic.fna/target_genomes.txt --output GCF_001623405.1_ASM162340v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:55,481] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:55,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc8c5d0f-6b6d-4174-9bfa-a4b2c2bb3456/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:55,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc8c5d0f-6b6d-4174-9bfa-a4b2c2bb3456/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:55,491] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:55,491] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:35:55,492] [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
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	100.0	1079	1084	95	inconclusive
Hydrotalea lipotrueae	strain=TMF_100	GCA_019249625.1	2803817	2803817	type	True	95.4024	939	1084	95	inconclusive
Hydrotalea sandarakina	strain=DSM 23241	GCA_003254115.1	1004304	1004304	type	True	79.0372	624	1084	95	below_threshold
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	76.4228	106	1084	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	76.3966	129	1084	95	below_threshold
Filimonas zeae	strain=CGMCC 1.15290	GCA_014641615.1	1737353	1737353	type	True	75.9444	64	1084	95	below_threshold
Foetidibacter luteolus	strain=YG09	GCA_009650435.1	2608880	2608880	type	True	75.9103	76	1084	95	below_threshold
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	75.8645	64	1084	95	below_threshold
Ilyomonas limi	strain=17mud1-8	GCA_005233845.1	2575867	2575867	type	True	75.8448	73	1084	95	below_threshold
Ginsengibacter hankyongi	strain=BR5-29	GCA_008710285.1	2607284	2607284	type	True	75.7166	65	1084	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:55,493] [INFO] DFAST Taxonomy check result was written to GCF_001623405.1_ASM162340v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:55,494] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:55,494] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:55,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc8c5d0f-6b6d-4174-9bfa-a4b2c2bb3456/dqc_reference/checkm_data
[2024-01-24 11:35:55,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:55,536] [INFO] Task started: CheckM
[2024-01-24 11:35:55,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001623405.1_ASM162340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001623405.1_ASM162340v1_genomic.fna/checkm_input GCF_001623405.1_ASM162340v1_genomic.fna/checkm_result
[2024-01-24 11:36:39,990] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:39,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:40,012] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:40,012] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:40,013] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001623405.1_ASM162340v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:40,013] [INFO] Task started: Blastn
[2024-01-24 11:36:40,013] [INFO] Running command: blastn -query GCF_001623405.1_ASM162340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc8c5d0f-6b6d-4174-9bfa-a4b2c2bb3456/dqc_reference/reference_markers_gtdb.fasta -out GCF_001623405.1_ASM162340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:40,815] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:40,819] [INFO] Selected 16 target genomes.
[2024-01-24 11:36:40,820] [INFO] Target genome list was writen to GCF_001623405.1_ASM162340v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:40,859] [INFO] Task started: fastANI
[2024-01-24 11:36:40,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg0df0fd77-c0b0-4c56-bcad-b2b733fdc32e/GCF_001623405.1_ASM162340v1_genomic.fna.gz --refList GCF_001623405.1_ASM162340v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001623405.1_ASM162340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:50,070] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:50,094] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:50,094] [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_001623405.1	s__Hydrotalea flava	100.0	1079	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Hydrotalea	95.0	95.88	95.18	0.90	0.86	13	conclusive
GCF_003254115.1	s__Hydrotalea sandarakina	79.0517	622	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Hydrotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011362875.1	s__Hydrotalea flava_A	78.9031	569	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Hydrotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903870685.1	s__CAILAF01 sp903870685	76.6081	149	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.70	99.46	0.92	0.91	5	-
GCA_903904335.1	s__CAILAF01 sp903904335	76.5676	141	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	97.62	96.62	0.83	0.78	4	-
GCA_903881425.1	s__CAILAF01 sp903881425	76.5223	173	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.80	99.80	0.95	0.95	2	-
GCA_018267725.1	s__CW01 sp018267725	76.478	169	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CW01	95.0	97.77	97.12	0.93	0.90	5	-
GCF_013106755.1	s__Panacibacter sp013106755	76.3966	129	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304675.1	s__CW01 sp017304675	76.3589	151	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004028795.1	s__CW01 sp004028795	76.3429	158	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CW01	95.0	99.97	99.97	0.97	0.97	2	-
GCA_013391385.1	s__Sediminibacterium sp013391385	76.3056	101	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270485.1	s__Sediminibacterium sp012270485	76.1749	97	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699815.1	s__Ferruginibacter sp002381005	76.0315	61	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	99.75	99.14	0.99	0.94	20	-
GCA_016721385.1	s__Ferruginibacter sp016721385	76.0248	75	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650435.1	s__Foetidibacter luteolus	75.9103	76	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Foetidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837525.1	s__Ferruginibacter sp903837525	75.6566	51	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:50,096] [INFO] GTDB search result was written to GCF_001623405.1_ASM162340v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:50,097] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:50,102] [INFO] DFAST_QC result json was written to GCF_001623405.1_ASM162340v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:50,103] [INFO] DFAST_QC completed!
[2024-01-24 11:36:50,103] [INFO] Total running time: 0h1m27s