[2024-01-24 11:34:38,739] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:38,743] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:38,743] [INFO] DQC Reference Directory: /var/lib/cwl/stg91a8eefc-08e5-403c-8d78-7df6a43510e4/dqc_reference
[2024-01-24 11:34:40,000] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:40,001] [INFO] Task started: Prodigal
[2024-01-24 11:34:40,001] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d8693fa-0992-4f34-9765-1638e54caf34/GCF_019249625.1_ASM1924962v1_genomic.fna.gz | prodigal -d GCF_019249625.1_ASM1924962v1_genomic.fna/cds.fna -a GCF_019249625.1_ASM1924962v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:54,462] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:54,462] [INFO] Task started: HMMsearch
[2024-01-24 11:34:54,462] [INFO] Running command: hmmsearch --tblout GCF_019249625.1_ASM1924962v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91a8eefc-08e5-403c-8d78-7df6a43510e4/dqc_reference/reference_markers.hmm GCF_019249625.1_ASM1924962v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:54,751] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:54,753] [INFO] Found 6/6 markers.
[2024-01-24 11:34:54,794] [INFO] Query marker FASTA was written to GCF_019249625.1_ASM1924962v1_genomic.fna/markers.fasta
[2024-01-24 11:34:54,795] [INFO] Task started: Blastn
[2024-01-24 11:34:54,795] [INFO] Running command: blastn -query GCF_019249625.1_ASM1924962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91a8eefc-08e5-403c-8d78-7df6a43510e4/dqc_reference/reference_markers.fasta -out GCF_019249625.1_ASM1924962v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:55,368] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:55,371] [INFO] Selected 20 target genomes.
[2024-01-24 11:34:55,371] [INFO] Target genome list was writen to GCF_019249625.1_ASM1924962v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:55,396] [INFO] Task started: fastANI
[2024-01-24 11:34:55,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d8693fa-0992-4f34-9765-1638e54caf34/GCF_019249625.1_ASM1924962v1_genomic.fna.gz --refList GCF_019249625.1_ASM1924962v1_genomic.fna/target_genomes.txt --output GCF_019249625.1_ASM1924962v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:12,929] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:12,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91a8eefc-08e5-403c-8d78-7df6a43510e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:12,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91a8eefc-08e5-403c-8d78-7df6a43510e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:12,941] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:12,941] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:35:12,941] [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 lipotrueae	strain=TMF_100	GCA_019249625.1	2803817	2803817	type	True	100.0	1117	1119	95	inconclusive
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	95.2838	944	1119	95	inconclusive
Hydrotalea sandarakina	strain=DSM 23241	GCA_003254115.1	1004304	1004304	type	True	79.5348	626	1119	95	below_threshold
Sediminibacterium salmoneum	strain=NBRC 103935	GCA_000511175.1	426421	426421	type	True	77.0798	95	1119	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	76.4993	130	1119	95	below_threshold
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	76.2491	106	1119	95	below_threshold
Foetidibacter luteolus	strain=YG09	GCA_009650435.1	2608880	2608880	type	True	75.9453	73	1119	95	below_threshold
Ilyomonas limi	strain=17mud1-8	GCA_005233845.1	2575867	2575867	type	True	75.9311	65	1119	95	below_threshold
Niastella vici	strain=DJ57	GCA_002077945.1	1703345	1703345	type	True	75.5991	56	1119	95	below_threshold
Filimonas zeae	strain=CGMCC 1.15290	GCA_014641615.1	1737353	1737353	type	True	75.4206	70	1119	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:12,945] [INFO] DFAST Taxonomy check result was written to GCF_019249625.1_ASM1924962v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:12,949] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:12,949] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:12,950] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91a8eefc-08e5-403c-8d78-7df6a43510e4/dqc_reference/checkm_data
[2024-01-24 11:35:12,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:12,986] [INFO] Task started: CheckM
[2024-01-24 11:35:12,987] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019249625.1_ASM1924962v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019249625.1_ASM1924962v1_genomic.fna/checkm_input GCF_019249625.1_ASM1924962v1_genomic.fna/checkm_result
[2024-01-24 11:35:56,335] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:56,336] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:56,354] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:56,355] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:56,355] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019249625.1_ASM1924962v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:56,356] [INFO] Task started: Blastn
[2024-01-24 11:35:56,356] [INFO] Running command: blastn -query GCF_019249625.1_ASM1924962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91a8eefc-08e5-403c-8d78-7df6a43510e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_019249625.1_ASM1924962v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:57,124] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:57,127] [INFO] Selected 17 target genomes.
[2024-01-24 11:35:57,128] [INFO] Target genome list was writen to GCF_019249625.1_ASM1924962v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:57,184] [INFO] Task started: fastANI
[2024-01-24 11:35:57,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d8693fa-0992-4f34-9765-1638e54caf34/GCF_019249625.1_ASM1924962v1_genomic.fna.gz --refList GCF_019249625.1_ASM1924962v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019249625.1_ASM1924962v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:07,023] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:07,036] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:07,037] [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	95.2838	944	1119	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	79.535	626	1119	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	79.4546	564	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Hydrotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075435.1	s__Agriterribacter sp003075435	79.2649	87	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Agriterribacter	95.0	97.00	96.97	0.82	0.82	3	-
GCA_903904335.1	s__CAILAF01 sp903904335	76.7553	131	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	97.62	96.62	0.83	0.78	4	-
GCA_903870685.1	s__CAILAF01 sp903870685	76.5426	150	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.70	99.46	0.92	0.91	5	-
GCA_004028795.1	s__CW01 sp004028795	76.535	168	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CW01	95.0	99.97	99.97	0.97	0.97	2	-
GCA_018267725.1	s__CW01 sp018267725	76.5101	166	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CW01	95.0	97.77	97.12	0.93	0.90	5	-
GCA_013391385.1	s__Sediminibacterium sp013391385	76.3898	98	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903881425.1	s__CAILAF01 sp903881425	76.3524	174	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.80	99.80	0.95	0.95	2	-
GCA_903841915.1	s__CAILAF01 sp903841915	76.2919	78	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304675.1	s__CW01 sp017304675	76.2644	147	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270485.1	s__Sediminibacterium sp012270485	76.1466	99	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913355.1	s__Sediminibacterium sp903913355	76.1071	90	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002390845.1	s__Panacibacter sp002390845	76.105	94	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256765.1	s__Sediminibacterium sp002256765	76.0666	86	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.72	99.72	0.88	0.88	2	-
GCA_903832075.1	s__CAILAF01 sp903832075	75.9409	116	1119	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:07,038] [INFO] GTDB search result was written to GCF_019249625.1_ASM1924962v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:07,039] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:07,042] [INFO] DFAST_QC result json was written to GCF_019249625.1_ASM1924962v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:07,042] [INFO] DFAST_QC completed!
[2024-01-24 11:36:07,042] [INFO] Total running time: 0h1m28s