[2024-01-24 14:31:14,624] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:14,626] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:14,626] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e08cb70-d777-4bf6-9ad0-574c380e78c6/dqc_reference
[2024-01-24 14:31:16,057] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:16,058] [INFO] Task started: Prodigal
[2024-01-24 14:31:16,058] [INFO] Running command: gunzip -c /var/lib/cwl/stg39cfafaa-ab2d-4a40-a6b3-f7835b638e68/GCF_004343705.1_ASM434370v1_genomic.fna.gz | prodigal -d GCF_004343705.1_ASM434370v1_genomic.fna/cds.fna -a GCF_004343705.1_ASM434370v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:43,412] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:43,412] [INFO] Task started: HMMsearch
[2024-01-24 14:31:43,413] [INFO] Running command: hmmsearch --tblout GCF_004343705.1_ASM434370v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e08cb70-d777-4bf6-9ad0-574c380e78c6/dqc_reference/reference_markers.hmm GCF_004343705.1_ASM434370v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:43,720] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:43,721] [INFO] Found 6/6 markers.
[2024-01-24 14:31:43,765] [INFO] Query marker FASTA was written to GCF_004343705.1_ASM434370v1_genomic.fna/markers.fasta
[2024-01-24 14:31:43,766] [INFO] Task started: Blastn
[2024-01-24 14:31:43,766] [INFO] Running command: blastn -query GCF_004343705.1_ASM434370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e08cb70-d777-4bf6-9ad0-574c380e78c6/dqc_reference/reference_markers.fasta -out GCF_004343705.1_ASM434370v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:44,447] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:44,450] [INFO] Selected 18 target genomes.
[2024-01-24 14:31:44,451] [INFO] Target genome list was writen to GCF_004343705.1_ASM434370v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:44,457] [INFO] Task started: fastANI
[2024-01-24 14:31:44,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg39cfafaa-ab2d-4a40-a6b3-f7835b638e68/GCF_004343705.1_ASM434370v1_genomic.fna.gz --refList GCF_004343705.1_ASM434370v1_genomic.fna/target_genomes.txt --output GCF_004343705.1_ASM434370v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:32:00,168] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:00,169] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e08cb70-d777-4bf6-9ad0-574c380e78c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:32:00,169] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e08cb70-d777-4bf6-9ad0-574c380e78c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:32:00,182] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:32:00,182] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:32:00,182] [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
Flaviaesturariibacter aridisoli	strain=17J68-15	GCA_004343705.1	2545761	2545761	type	True	100.0	1417	1420	95	conclusive
Flaviaesturariibacter flavus	strain=17J68-12	GCA_004337505.1	2502780	2502780	type	True	80.8853	725	1420	95	below_threshold
Cnuella takakiae	strain=RG1-1	GCA_001953305.1	1302690	1302690	type	True	76.7866	203	1420	95	below_threshold
Cnuella takakiae	strain=DSM 26897	GCA_900129015.1	1302690	1302690	type	True	76.7527	198	1420	95	below_threshold
Flavisolibacter nicotianae	strain=X7X	GCA_003628535.1	2364882	2364882	type	True	76.6291	185	1420	95	below_threshold
Dinghuibacter silviterrae	strain=DSM 100059	GCA_004366355.1	1539049	1539049	type	True	76.0691	92	1420	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	76.0471	105	1420	95	below_threshold
Chitinophaga chungangae	strain=MAH-28	GCA_017742215.1	2821488	2821488	type	True	75.9172	134	1420	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	75.862	50	1420	95	below_threshold
Chitinophaga japonensis	strain=DSM 13484	GCA_007830125.1	104662	104662	type	True	75.849	105	1420	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:32:00,184] [INFO] DFAST Taxonomy check result was written to GCF_004343705.1_ASM434370v1_genomic.fna/tc_result.tsv
[2024-01-24 14:32:00,185] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:32:00,185] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:32:00,185] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e08cb70-d777-4bf6-9ad0-574c380e78c6/dqc_reference/checkm_data
[2024-01-24 14:32:00,186] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:32:00,229] [INFO] Task started: CheckM
[2024-01-24 14:32:00,230] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004343705.1_ASM434370v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004343705.1_ASM434370v1_genomic.fna/checkm_input GCF_004343705.1_ASM434370v1_genomic.fna/checkm_result
[2024-01-24 14:33:09,459] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:09,460] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:09,482] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:09,482] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:09,483] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004343705.1_ASM434370v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:09,483] [INFO] Task started: Blastn
[2024-01-24 14:33:09,483] [INFO] Running command: blastn -query GCF_004343705.1_ASM434370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e08cb70-d777-4bf6-9ad0-574c380e78c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_004343705.1_ASM434370v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:10,400] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:10,404] [INFO] Selected 14 target genomes.
[2024-01-24 14:33:10,404] [INFO] Target genome list was writen to GCF_004343705.1_ASM434370v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:10,415] [INFO] Task started: fastANI
[2024-01-24 14:33:10,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg39cfafaa-ab2d-4a40-a6b3-f7835b638e68/GCF_004343705.1_ASM434370v1_genomic.fna.gz --refList GCF_004343705.1_ASM434370v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004343705.1_ASM434370v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:22,777] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:22,795] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:22,795] [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_004343705.1	s__Flaviaesturariibacter aridisoli	100.0	1417	1420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004337505.1	s__Flaviaesturariibacter flavus	80.9046	722	1420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173235.1	s__Flaviaesturariibacter sp004173235	80.7139	817	1420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013327885.1	s__Flavisolibacter sp013327885	76.8804	137	1420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953305.1	s__Cnuella takakiae	76.7866	203	1420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Cnuella	95.0	99.98	99.98	1.00	1.00	2	-
GCA_014163555.1	s__Flavisolibacter sp014163555	76.6558	115	1420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628535.1	s__Flavisolibacter nicotianae	76.6291	185	1420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003332885.2	s__Paracnuella aquatica	76.5132	171	1420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paracnuella	95.0	95.63	95.63	0.92	0.92	2	-
GCA_016720745.1	s__JJ008 sp016720745	76.2202	51	1420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	98.76	98.76	0.93	0.93	2	-
GCF_007970805.1	s__Flavisolibacter ginsenosidimutans	76.1482	98	1420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267545.1	s__Puia sp018267545	76.1294	85	1420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Puia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992715.1	s__Chitinophaga cymbidii	75.8198	114	1420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:22,797] [INFO] GTDB search result was written to GCF_004343705.1_ASM434370v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:22,798] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:22,802] [INFO] DFAST_QC result json was written to GCF_004343705.1_ASM434370v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:22,802] [INFO] DFAST_QC completed!
[2024-01-24 14:33:22,802] [INFO] Total running time: 0h2m8s