[2024-01-25 20:13:21,070] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:21,072] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:21,072] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b11e859-5e4f-4e58-9f01-469b193e3a1e/dqc_reference
[2024-01-25 20:13:22,230] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:22,230] [INFO] Task started: Prodigal
[2024-01-25 20:13:22,231] [INFO] Running command: gunzip -c /var/lib/cwl/stgec2264f7-0fbe-4825-8eef-cd6602b369de/GCF_002954265.1_ASM295426v1_genomic.fna.gz | prodigal -d GCF_002954265.1_ASM295426v1_genomic.fna/cds.fna -a GCF_002954265.1_ASM295426v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:43,488] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:43,488] [INFO] Task started: HMMsearch
[2024-01-25 20:13:43,488] [INFO] Running command: hmmsearch --tblout GCF_002954265.1_ASM295426v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b11e859-5e4f-4e58-9f01-469b193e3a1e/dqc_reference/reference_markers.hmm GCF_002954265.1_ASM295426v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:43,761] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:43,762] [INFO] Found 6/6 markers.
[2024-01-25 20:13:43,805] [INFO] Query marker FASTA was written to GCF_002954265.1_ASM295426v1_genomic.fna/markers.fasta
[2024-01-25 20:13:43,805] [INFO] Task started: Blastn
[2024-01-25 20:13:43,805] [INFO] Running command: blastn -query GCF_002954265.1_ASM295426v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b11e859-5e4f-4e58-9f01-469b193e3a1e/dqc_reference/reference_markers.fasta -out GCF_002954265.1_ASM295426v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:44,328] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:44,331] [INFO] Selected 22 target genomes.
[2024-01-25 20:13:44,331] [INFO] Target genome list was writen to GCF_002954265.1_ASM295426v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:44,345] [INFO] Task started: fastANI
[2024-01-25 20:13:44,346] [INFO] Running command: fastANI --query /var/lib/cwl/stgec2264f7-0fbe-4825-8eef-cd6602b369de/GCF_002954265.1_ASM295426v1_genomic.fna.gz --refList GCF_002954265.1_ASM295426v1_genomic.fna/target_genomes.txt --output GCF_002954265.1_ASM295426v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:10,510] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:10,510] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b11e859-5e4f-4e58-9f01-469b193e3a1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:10,511] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b11e859-5e4f-4e58-9f01-469b193e3a1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:10,515] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:14:10,515] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:10,515] [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
Flavipsychrobacter stenotrophus	strain=RB1R16	GCA_002954265.1	2077091	2077091	type	True	100.0	1797	1800	95	conclusive
Taibaiella chishuiensis	strain=CGMCC 1.12700	GCA_003014535.1	1434707	1434707	type	True	76.2726	63	1800	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:10,517] [INFO] DFAST Taxonomy check result was written to GCF_002954265.1_ASM295426v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:10,518] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:10,518] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:10,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b11e859-5e4f-4e58-9f01-469b193e3a1e/dqc_reference/checkm_data
[2024-01-25 20:14:10,519] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:10,571] [INFO] Task started: CheckM
[2024-01-25 20:14:10,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002954265.1_ASM295426v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002954265.1_ASM295426v1_genomic.fna/checkm_input GCF_002954265.1_ASM295426v1_genomic.fna/checkm_result
[2024-01-25 20:15:08,816] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:08,817] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:08,835] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:08,835] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:08,836] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002954265.1_ASM295426v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:08,836] [INFO] Task started: Blastn
[2024-01-25 20:15:08,836] [INFO] Running command: blastn -query GCF_002954265.1_ASM295426v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b11e859-5e4f-4e58-9f01-469b193e3a1e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002954265.1_ASM295426v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:09,594] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:09,597] [INFO] Selected 20 target genomes.
[2024-01-25 20:15:09,597] [INFO] Target genome list was writen to GCF_002954265.1_ASM295426v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:09,625] [INFO] Task started: fastANI
[2024-01-25 20:15:09,625] [INFO] Running command: fastANI --query /var/lib/cwl/stgec2264f7-0fbe-4825-8eef-cd6602b369de/GCF_002954265.1_ASM295426v1_genomic.fna.gz --refList GCF_002954265.1_ASM295426v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002954265.1_ASM295426v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:26,666] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:26,677] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:26,678] [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_002954265.1	s__Flavipsychrobacter stenotrophus	100.0	1797	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903877645.1	s__Flavipsychrobacter sp903877645	76.8814	147	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	99.60	99.21	0.95	0.89	10	-
GCA_013285595.1	s__Flavipsychrobacter sp013285595	76.7513	93	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903903635.1	s__Flavipsychrobacter sp903903635	76.6426	114	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903905065.1	s__Flavipsychrobacter sp903905065	76.6145	133	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	99.97	99.97	0.97	0.97	2	-
GCA_002337045.1	s__Flavipsychrobacter sp002337045	76.5363	92	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903821975.1	s__Flavipsychrobacter sp903821975	76.5003	104	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903835145.1	s__Flavipsychrobacter sp903835145	76.4964	107	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	99.38	99.38	0.87	0.87	2	-
GCA_014377675.1	s__Flavipsychrobacter sp014377675	76.4341	106	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168085.1	s__Flavipsychrobacter sp902168085	76.4315	129	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004144175.1	s__Flavipsychrobacter sp004144175	76.362	100	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903906615.1	s__Flavipsychrobacter sp903906615	76.3532	93	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903881585.1	s__Flavipsychrobacter sp903881585	76.3218	127	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903887415.1	s__Flavipsychrobacter sp903887415	76.2656	124	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	99.97	99.94	0.98	0.97	4	-
GCA_903882965.1	s__Flavipsychrobacter sp903882965	76.2581	111	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786565.1	s__Flavipsychrobacter sp016786565	76.221	95	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786665.1	s__Flavipsychrobacter sp016786665	76.2168	68	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879545.1	s__Flavipsychrobacter sp014879545	76.2034	83	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839875.1	s__Flavipsychrobacter sp903839875	76.1299	87	1800	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	99.93	99.93	0.96	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:26,679] [INFO] GTDB search result was written to GCF_002954265.1_ASM295426v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:26,680] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:26,683] [INFO] DFAST_QC result json was written to GCF_002954265.1_ASM295426v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:26,683] [INFO] DFAST_QC completed!
[2024-01-25 20:15:26,683] [INFO] Total running time: 0h2m6s