[2023-07-01 01:37:48,640] [INFO] DFAST_QC pipeline started.
[2023-07-01 01:37:48,642] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 01:37:48,642] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e9b1863-4568-49d5-a26b-835e5c6694e2/dqc_reference
[2023-07-01 01:37:49,871] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 01:37:49,872] [INFO] Task started: Prodigal
[2023-07-01 01:37:49,872] [INFO] Running command: gunzip -c /var/lib/cwl/stg8842e455-9e4b-4480-a835-af1f758a59c5/GCA_016708275.1_ASM1670827v1_genomic.fna.gz | prodigal -d GCA_016708275.1_ASM1670827v1_genomic.fna/cds.fna -a GCA_016708275.1_ASM1670827v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 01:38:03,790] [INFO] Task succeeded: Prodigal
[2023-07-01 01:38:03,791] [INFO] Task started: HMMsearch
[2023-07-01 01:38:03,791] [INFO] Running command: hmmsearch --tblout GCA_016708275.1_ASM1670827v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e9b1863-4568-49d5-a26b-835e5c6694e2/dqc_reference/reference_markers.hmm GCA_016708275.1_ASM1670827v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 01:38:04,012] [INFO] Task succeeded: HMMsearch
[2023-07-01 01:38:04,013] [INFO] Found 6/6 markers.
[2023-07-01 01:38:04,040] [INFO] Query marker FASTA was written to GCA_016708275.1_ASM1670827v1_genomic.fna/markers.fasta
[2023-07-01 01:38:04,041] [INFO] Task started: Blastn
[2023-07-01 01:38:04,041] [INFO] Running command: blastn -query GCA_016708275.1_ASM1670827v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e9b1863-4568-49d5-a26b-835e5c6694e2/dqc_reference/reference_markers.fasta -out GCA_016708275.1_ASM1670827v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:38:04,629] [INFO] Task succeeded: Blastn
[2023-07-01 01:38:04,633] [INFO] Selected 32 target genomes.
[2023-07-01 01:38:04,633] [INFO] Target genome list was writen to GCA_016708275.1_ASM1670827v1_genomic.fna/target_genomes.txt
[2023-07-01 01:38:04,634] [INFO] Task started: fastANI
[2023-07-01 01:38:04,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg8842e455-9e4b-4480-a835-af1f758a59c5/GCA_016708275.1_ASM1670827v1_genomic.fna.gz --refList GCA_016708275.1_ASM1670827v1_genomic.fna/target_genomes.txt --output GCA_016708275.1_ASM1670827v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 01:38:27,716] [INFO] Task succeeded: fastANI
[2023-07-01 01:38:27,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e9b1863-4568-49d5-a26b-835e5c6694e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 01:38:27,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e9b1863-4568-49d5-a26b-835e5c6694e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 01:38:27,725] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 01:38:27,725] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 01:38:27,725] [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	76.4633	92	1084	95	below_threshold
Hydrotalea sandarakina	strain=DSM 23241	GCA_003254115.1	1004304	1004304	type	True	76.4028	54	1084	95	below_threshold
Ginsengibacter hankyongi	strain=BR5-29	GCA_008710285.1	2607284	2607284	type	True	76.3035	87	1084	95	below_threshold
Hydrotalea lipotrueae	strain=TMF_100	GCA_019249625.1	2803817	2803817	type	True	76.2876	71	1084	95	below_threshold
Agriterribacter humi	strain=YJ03	GCA_009192765.1	1104781	1104781	type	True	76.2558	71	1084	95	below_threshold
Hanamia caeni	strain=BO-59	GCA_003721595.1	2294116	2294116	type	True	76.0452	51	1084	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	75.8573	80	1084	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	75.7797	59	1084	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 01:38:27,727] [INFO] DFAST Taxonomy check result was written to GCA_016708275.1_ASM1670827v1_genomic.fna/tc_result.tsv
[2023-07-01 01:38:27,728] [INFO] ===== Taxonomy check completed =====
[2023-07-01 01:38:27,728] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 01:38:27,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e9b1863-4568-49d5-a26b-835e5c6694e2/dqc_reference/checkm_data
[2023-07-01 01:38:27,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 01:38:27,762] [INFO] Task started: CheckM
[2023-07-01 01:38:27,763] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708275.1_ASM1670827v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708275.1_ASM1670827v1_genomic.fna/checkm_input GCA_016708275.1_ASM1670827v1_genomic.fna/checkm_result
[2023-07-01 01:39:07,504] [INFO] Task succeeded: CheckM
[2023-07-01 01:39:07,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 01:39:07,518] [INFO] ===== Completeness check finished =====
[2023-07-01 01:39:07,518] [INFO] ===== Start GTDB Search =====
[2023-07-01 01:39:07,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708275.1_ASM1670827v1_genomic.fna/markers.fasta)
[2023-07-01 01:39:07,519] [INFO] Task started: Blastn
[2023-07-01 01:39:07,519] [INFO] Running command: blastn -query GCA_016708275.1_ASM1670827v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e9b1863-4568-49d5-a26b-835e5c6694e2/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708275.1_ASM1670827v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:39:08,252] [INFO] Task succeeded: Blastn
[2023-07-01 01:39:08,255] [INFO] Selected 21 target genomes.
[2023-07-01 01:39:08,256] [INFO] Target genome list was writen to GCA_016708275.1_ASM1670827v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 01:39:08,257] [INFO] Task started: fastANI
[2023-07-01 01:39:08,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg8842e455-9e4b-4480-a835-af1f758a59c5/GCA_016708275.1_ASM1670827v1_genomic.fna.gz --refList GCA_016708275.1_ASM1670827v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708275.1_ASM1670827v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 01:39:20,407] [INFO] Task succeeded: fastANI
[2023-07-01 01:39:20,417] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 01:39:20,417] [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_016699815.1	s__Ferruginibacter sp002381005	99.7233	1007	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	99.75	99.14	0.99	0.94	20	conclusive
GCA_018266715.1	s__Ferruginibacter sp018266715	80.9341	521	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	99.51	99.51	0.88	0.88	2	-
GCA_016710595.1	s__Ferruginibacter sp016710595	77.4569	242	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898465.1	s__Ferruginibacter sp001898465	77.0544	226	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	99.99	99.99	0.99	0.97	3	-
GCA_018268155.1	s__Ferruginibacter sp018268155	76.9338	198	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983695.1	s__Ferruginibacter sp017983695	76.7307	176	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713965.1	s__Ferruginibacter sp016713965	76.6946	109	1084	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	76.685	173	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379905.1	s__Ferruginibacter sp014379905	76.5156	147	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268135.1	s__Ferruginibacter sp018268135	76.3919	192	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	99.79	99.79	0.93	0.93	2	-
GCA_903858475.1	s__Ferruginibacter sp903858475	76.365	73	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	99.60	99.32	0.91	0.84	6	-
GCA_014379625.1	s__Ferruginibacter sp014379625	75.8831	94	1084	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 01:39:20,419] [INFO] GTDB search result was written to GCA_016708275.1_ASM1670827v1_genomic.fna/result_gtdb.tsv
[2023-07-01 01:39:20,420] [INFO] ===== GTDB Search completed =====
[2023-07-01 01:39:20,423] [INFO] DFAST_QC result json was written to GCA_016708275.1_ASM1670827v1_genomic.fna/dqc_result.json
[2023-07-01 01:39:20,423] [INFO] DFAST_QC completed!
[2023-07-01 01:39:20,423] [INFO] Total running time: 0h1m32s