[2023-06-28 16:22:32,458] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:22:32,460] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:22:32,460] [INFO] DQC Reference Directory: /var/lib/cwl/stg09515b9e-b744-4bb7-bf44-028da4b9c809/dqc_reference
[2023-06-28 16:22:33,728] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:22:33,729] [INFO] Task started: Prodigal
[2023-06-28 16:22:33,730] [INFO] Running command: gunzip -c /var/lib/cwl/stg0da5992b-d9d7-4fc5-923f-d2990a0cbc76/GCA_020059395.1_ASM2005939v1_genomic.fna.gz | prodigal -d GCA_020059395.1_ASM2005939v1_genomic.fna/cds.fna -a GCA_020059395.1_ASM2005939v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:22:48,119] [INFO] Task succeeded: Prodigal
[2023-06-28 16:22:48,119] [INFO] Task started: HMMsearch
[2023-06-28 16:22:48,119] [INFO] Running command: hmmsearch --tblout GCA_020059395.1_ASM2005939v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09515b9e-b744-4bb7-bf44-028da4b9c809/dqc_reference/reference_markers.hmm GCA_020059395.1_ASM2005939v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:22:48,408] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:22:48,410] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0da5992b-d9d7-4fc5-923f-d2990a0cbc76/GCA_020059395.1_ASM2005939v1_genomic.fna.gz]
[2023-06-28 16:22:48,446] [INFO] Query marker FASTA was written to GCA_020059395.1_ASM2005939v1_genomic.fna/markers.fasta
[2023-06-28 16:22:48,446] [INFO] Task started: Blastn
[2023-06-28 16:22:48,446] [INFO] Running command: blastn -query GCA_020059395.1_ASM2005939v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09515b9e-b744-4bb7-bf44-028da4b9c809/dqc_reference/reference_markers.fasta -out GCA_020059395.1_ASM2005939v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:22:49,055] [INFO] Task succeeded: Blastn
[2023-06-28 16:22:49,059] [INFO] Selected 21 target genomes.
[2023-06-28 16:22:49,060] [INFO] Target genome list was writen to GCA_020059395.1_ASM2005939v1_genomic.fna/target_genomes.txt
[2023-06-28 16:22:49,064] [INFO] Task started: fastANI
[2023-06-28 16:22:49,065] [INFO] Running command: fastANI --query /var/lib/cwl/stg0da5992b-d9d7-4fc5-923f-d2990a0cbc76/GCA_020059395.1_ASM2005939v1_genomic.fna.gz --refList GCA_020059395.1_ASM2005939v1_genomic.fna/target_genomes.txt --output GCA_020059395.1_ASM2005939v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:23:05,407] [INFO] Task succeeded: fastANI
[2023-06-28 16:23:05,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09515b9e-b744-4bb7-bf44-028da4b9c809/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:23:05,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09515b9e-b744-4bb7-bf44-028da4b9c809/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:23:05,420] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:23:05,420] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:23:05,420] [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
Ferruginibacter albus	strain=KIS38-8	GCA_020042285.1	2875540	2875540	type	True	76.2225	83	973	95	below_threshold
Foetidibacter luteolus	strain=YG09	GCA_009650435.1	2608880	2608880	type	True	75.9762	74	973	95	below_threshold
Niabella ginsengisoli	strain=GR10-1	GCA_022513635.1	522298	522298	type	True	75.9012	50	973	95	below_threshold
Ilyomonas limi	strain=17mud1-8	GCA_005233845.1	2575867	2575867	type	True	75.6288	55	973	95	below_threshold
Hydrotalea lipotrueae	strain=TMF_100	GCA_019249625.1	2803817	2803817	type	True	75.5386	58	973	95	below_threshold
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	75.4092	52	973	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:23:05,422] [INFO] DFAST Taxonomy check result was written to GCA_020059395.1_ASM2005939v1_genomic.fna/tc_result.tsv
[2023-06-28 16:23:05,423] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:23:05,423] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:23:05,423] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09515b9e-b744-4bb7-bf44-028da4b9c809/dqc_reference/checkm_data
[2023-06-28 16:23:05,424] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:23:05,468] [INFO] Task started: CheckM
[2023-06-28 16:23:05,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020059395.1_ASM2005939v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020059395.1_ASM2005939v1_genomic.fna/checkm_input GCA_020059395.1_ASM2005939v1_genomic.fna/checkm_result
[2023-06-28 16:23:48,193] [INFO] Task succeeded: CheckM
[2023-06-28 16:23:48,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:23:48,219] [INFO] ===== Completeness check finished =====
[2023-06-28 16:23:48,220] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:23:48,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020059395.1_ASM2005939v1_genomic.fna/markers.fasta)
[2023-06-28 16:23:48,221] [INFO] Task started: Blastn
[2023-06-28 16:23:48,221] [INFO] Running command: blastn -query GCA_020059395.1_ASM2005939v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09515b9e-b744-4bb7-bf44-028da4b9c809/dqc_reference/reference_markers_gtdb.fasta -out GCA_020059395.1_ASM2005939v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:23:49,048] [INFO] Task succeeded: Blastn
[2023-06-28 16:23:49,053] [INFO] Selected 19 target genomes.
[2023-06-28 16:23:49,053] [INFO] Target genome list was writen to GCA_020059395.1_ASM2005939v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:23:49,064] [INFO] Task started: fastANI
[2023-06-28 16:23:49,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg0da5992b-d9d7-4fc5-923f-d2990a0cbc76/GCA_020059395.1_ASM2005939v1_genomic.fna.gz --refList GCA_020059395.1_ASM2005939v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020059395.1_ASM2005939v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:24:02,658] [INFO] Task succeeded: fastANI
[2023-06-28 16:24:02,674] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 16:24:02,674] [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_017983695.1	s__Ferruginibacter sp017983695	78.5839	386	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141115.1	s__Ferruginibacter sp013141115	78.2335	373	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266775.1	s__Ferruginibacter sp018266775	77.0277	240	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710935.1	s__Ferruginibacter sp016710935	76.9319	190	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786725.1	s__Ferruginibacter sp016786725	76.9234	185	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721385.1	s__Ferruginibacter sp016721385	76.9211	153	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715365.1	s__Ferruginibacter sp016715365	76.9126	198	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	98.79	98.54	0.91	0.89	5	-
GCA_016722465.1	s__Ferruginibacter sp016722465	76.8719	115	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017988335.1	s__Ferruginibacter sp017988335	76.6083	163	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268155.1	s__Ferruginibacter sp018268155	76.5991	153	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710745.1	s__Ferruginibacter sp016710745	76.3987	120	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377975.1	s__Ferruginibacter sp014377975	76.3098	110	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003455235.1	s__Ferruginibacter sp003455235	76.1812	61	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963365.1	s__AWTP1-9 sp003963365	76.0054	84	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__AWTP1-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710165.1	s__Ferruginibacter sp016710165	75.9842	114	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	99.37	99.37	0.98	0.98	3	-
GCA_018267725.1	s__CW01 sp018267725	75.972	69	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CW01	95.0	97.77	97.12	0.93	0.90	5	-
GCA_005882315.1	s__VBAR01 sp005882315	75.8643	51	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__VBAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005233845.1	s__Ilyomonas limi	75.6504	54	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ilyomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:24:02,677] [INFO] GTDB search result was written to GCA_020059395.1_ASM2005939v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:24:02,678] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:24:02,681] [INFO] DFAST_QC result json was written to GCA_020059395.1_ASM2005939v1_genomic.fna/dqc_result.json
[2023-06-28 16:24:02,682] [INFO] DFAST_QC completed!
[2023-06-28 16:24:02,682] [INFO] Total running time: 0h1m30s