[2024-01-25 18:07:35,604] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:35,610] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:35,610] [INFO] DQC Reference Directory: /var/lib/cwl/stg31c92e09-66db-4102-9457-0df207895286/dqc_reference
[2024-01-25 18:07:36,775] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:36,776] [INFO] Task started: Prodigal
[2024-01-25 18:07:36,776] [INFO] Running command: gunzip -c /var/lib/cwl/stgcec08a31-5f17-448b-9b96-6b66234dc634/GCF_014332695.1_ASM1433269v1_genomic.fna.gz | prodigal -d GCF_014332695.1_ASM1433269v1_genomic.fna/cds.fna -a GCF_014332695.1_ASM1433269v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:07:57,317] [INFO] Task succeeded: Prodigal
[2024-01-25 18:07:57,317] [INFO] Task started: HMMsearch
[2024-01-25 18:07:57,318] [INFO] Running command: hmmsearch --tblout GCF_014332695.1_ASM1433269v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31c92e09-66db-4102-9457-0df207895286/dqc_reference/reference_markers.hmm GCF_014332695.1_ASM1433269v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:07:57,577] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:07:57,578] [INFO] Found 6/6 markers.
[2024-01-25 18:07:57,630] [INFO] Query marker FASTA was written to GCF_014332695.1_ASM1433269v1_genomic.fna/markers.fasta
[2024-01-25 18:07:57,630] [INFO] Task started: Blastn
[2024-01-25 18:07:57,630] [INFO] Running command: blastn -query GCF_014332695.1_ASM1433269v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31c92e09-66db-4102-9457-0df207895286/dqc_reference/reference_markers.fasta -out GCF_014332695.1_ASM1433269v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:58,181] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:58,185] [INFO] Selected 15 target genomes.
[2024-01-25 18:07:58,185] [INFO] Target genome list was writen to GCF_014332695.1_ASM1433269v1_genomic.fna/target_genomes.txt
[2024-01-25 18:07:58,203] [INFO] Task started: fastANI
[2024-01-25 18:07:58,203] [INFO] Running command: fastANI --query /var/lib/cwl/stgcec08a31-5f17-448b-9b96-6b66234dc634/GCF_014332695.1_ASM1433269v1_genomic.fna.gz --refList GCF_014332695.1_ASM1433269v1_genomic.fna/target_genomes.txt --output GCF_014332695.1_ASM1433269v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:13,697] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:13,698] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31c92e09-66db-4102-9457-0df207895286/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:13,698] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31c92e09-66db-4102-9457-0df207895286/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:13,707] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:08:13,707] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:13,707] [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
Flavihumibacter stibioxidans	strain=YS-17	GCA_014332695.1	1834163	1834163	type	True	100.0	1518	1521	95	conclusive
Flavihumibacter profundi	strain=KCTC 62290	GCA_020076305.1	2716883	2716883	type	True	77.9417	300	1521	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	77.8912	366	1521	95	below_threshold
Flavihumibacter rivuli	strain=IMCC34838	GCA_018595685.2	2838156	2838156	type	True	77.7899	338	1521	95	below_threshold
Flavihumibacter solisilvae	strain=3-3	GCA_000814475.1	1349421	1349421	type	True	77.7302	309	1521	95	below_threshold
Flavihumibacter fluminis	strain=IMCC34837	GCA_018595675.2	2838157	2838157	type	True	77.7057	330	1521	95	below_threshold
Flavihumibacter petaseus	strain=NBRC 106054	GCA_000974785.1	549295	549295	type	True	77.2098	285	1521	95	below_threshold
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	76.5214	120	1521	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	76.2646	69	1521	95	below_threshold
Niastella vici	strain=DJ57	GCA_002077945.1	1703345	1703345	type	True	76.2444	103	1521	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	76.1839	76	1521	95	below_threshold
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	76.1225	54	1521	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	75.9904	121	1521	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	75.8671	119	1521	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:13,709] [INFO] DFAST Taxonomy check result was written to GCF_014332695.1_ASM1433269v1_genomic.fna/tc_result.tsv
[2024-01-25 18:08:13,710] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:13,710] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:13,710] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31c92e09-66db-4102-9457-0df207895286/dqc_reference/checkm_data
[2024-01-25 18:08:13,711] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:13,754] [INFO] Task started: CheckM
[2024-01-25 18:08:13,755] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014332695.1_ASM1433269v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014332695.1_ASM1433269v1_genomic.fna/checkm_input GCF_014332695.1_ASM1433269v1_genomic.fna/checkm_result
[2024-01-25 18:09:11,338] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:11,340] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:11,359] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:11,360] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:11,361] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014332695.1_ASM1433269v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:11,361] [INFO] Task started: Blastn
[2024-01-25 18:09:11,361] [INFO] Running command: blastn -query GCF_014332695.1_ASM1433269v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31c92e09-66db-4102-9457-0df207895286/dqc_reference/reference_markers_gtdb.fasta -out GCF_014332695.1_ASM1433269v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:12,171] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:12,174] [INFO] Selected 18 target genomes.
[2024-01-25 18:09:12,174] [INFO] Target genome list was writen to GCF_014332695.1_ASM1433269v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:12,193] [INFO] Task started: fastANI
[2024-01-25 18:09:12,193] [INFO] Running command: fastANI --query /var/lib/cwl/stgcec08a31-5f17-448b-9b96-6b66234dc634/GCF_014332695.1_ASM1433269v1_genomic.fna.gz --refList GCF_014332695.1_ASM1433269v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014332695.1_ASM1433269v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:28,977] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:28,988] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:28,988] [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_014332695.1	s__Flavihumibacter stibioxidans	100.0	1517	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018595685.1	s__Flavihumibacter sp018595685	77.7622	338	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814475.1	s__Flavihumibacter solisilvae	77.7302	309	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018595675.1	s__Flavihumibacter sp018595675	77.6876	329	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001601815.1	s__Flavihumibacter sp001601815	77.6717	310	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787265.1	s__Flavihumibacter sp016787265	77.6543	334	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483205.1	s__Flavihumibacter sp002483205	77.614	304	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018993145.1	s__Flavihumibacter sp018993145	77.3978	173	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974785.1	s__Flavihumibacter petaseus	77.2011	285	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavihumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007970185.1	s__Pseudobacter ginsenosidimutans	76.5214	120	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002077945.1	s__Niastella vici	76.2444	103	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884665.1	s__VBAT01 sp005884665	76.1512	63	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__VBAT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744805.1	s__Pseudobacter sp017744805	75.9199	98	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Pseudobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110245.1	s__Niastella yeongjuensis	75.8671	119	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014879565.1	s__JJ008 sp014879565	75.8365	95	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786785.1	s__Flavitalea sp016786785	75.7549	60	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173255.1	s__46-32 sp004173255	75.7542	65	1521	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:28,990] [INFO] GTDB search result was written to GCF_014332695.1_ASM1433269v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:28,990] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:28,993] [INFO] DFAST_QC result json was written to GCF_014332695.1_ASM1433269v1_genomic.fna/dqc_result.json
[2024-01-25 18:09:28,994] [INFO] DFAST_QC completed!
[2024-01-25 18:09:28,994] [INFO] Total running time: 0h1m53s