[2023-06-05 12:23:10,637] [INFO] DFAST_QC pipeline started.
[2023-06-05 12:23:10,640] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 12:23:10,640] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8194144-21f0-494f-806c-fdec2331ce33/dqc_reference
[2023-06-05 12:23:11,828] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 12:23:11,829] [INFO] Task started: Prodigal
[2023-06-05 12:23:11,829] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ce37f3c-b198-4b95-be57-77ee2371cb46/GCA_001769035.1_ASM176903v1_genomic.fna.gz | prodigal -d GCA_001769035.1_ASM176903v1_genomic.fna/cds.fna -a GCA_001769035.1_ASM176903v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 12:23:25,619] [INFO] Task succeeded: Prodigal
[2023-06-05 12:23:25,620] [INFO] Task started: HMMsearch
[2023-06-05 12:23:25,620] [INFO] Running command: hmmsearch --tblout GCA_001769035.1_ASM176903v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8194144-21f0-494f-806c-fdec2331ce33/dqc_reference/reference_markers.hmm GCA_001769035.1_ASM176903v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 12:23:25,898] [INFO] Task succeeded: HMMsearch
[2023-06-05 12:23:25,900] [INFO] Found 6/6 markers.
[2023-06-05 12:23:25,941] [INFO] Query marker FASTA was written to GCA_001769035.1_ASM176903v1_genomic.fna/markers.fasta
[2023-06-05 12:23:25,941] [INFO] Task started: Blastn
[2023-06-05 12:23:25,942] [INFO] Running command: blastn -query GCA_001769035.1_ASM176903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8194144-21f0-494f-806c-fdec2331ce33/dqc_reference/reference_markers.fasta -out GCA_001769035.1_ASM176903v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:23:26,522] [INFO] Task succeeded: Blastn
[2023-06-05 12:23:26,528] [INFO] Selected 27 target genomes.
[2023-06-05 12:23:26,529] [INFO] Target genome list was writen to GCA_001769035.1_ASM176903v1_genomic.fna/target_genomes.txt
[2023-06-05 12:23:26,531] [INFO] Task started: fastANI
[2023-06-05 12:23:26,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ce37f3c-b198-4b95-be57-77ee2371cb46/GCA_001769035.1_ASM176903v1_genomic.fna.gz --refList GCA_001769035.1_ASM176903v1_genomic.fna/target_genomes.txt --output GCA_001769035.1_ASM176903v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 12:23:42,429] [INFO] Task succeeded: fastANI
[2023-06-05 12:23:42,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8194144-21f0-494f-806c-fdec2331ce33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 12:23:42,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8194144-21f0-494f-806c-fdec2331ce33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 12:23:42,438] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 12:23:42,438] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 12:23:42,439] [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
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	74.7838	53	1472	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	74.7577	65	1472	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	74.6228	50	1472	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 12:23:42,441] [INFO] DFAST Taxonomy check result was written to GCA_001769035.1_ASM176903v1_genomic.fna/tc_result.tsv
[2023-06-05 12:23:42,442] [INFO] ===== Taxonomy check completed =====
[2023-06-05 12:23:42,442] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 12:23:42,443] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8194144-21f0-494f-806c-fdec2331ce33/dqc_reference/checkm_data
[2023-06-05 12:23:42,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 12:23:42,491] [INFO] Task started: CheckM
[2023-06-05 12:23:42,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001769035.1_ASM176903v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001769035.1_ASM176903v1_genomic.fna/checkm_input GCA_001769035.1_ASM176903v1_genomic.fna/checkm_result
[2023-06-05 12:24:25,312] [INFO] Task succeeded: CheckM
[2023-06-05 12:24:25,313] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 12:24:25,335] [INFO] ===== Completeness check finished =====
[2023-06-05 12:24:25,336] [INFO] ===== Start GTDB Search =====
[2023-06-05 12:24:25,336] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001769035.1_ASM176903v1_genomic.fna/markers.fasta)
[2023-06-05 12:24:25,337] [INFO] Task started: Blastn
[2023-06-05 12:24:25,337] [INFO] Running command: blastn -query GCA_001769035.1_ASM176903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8194144-21f0-494f-806c-fdec2331ce33/dqc_reference/reference_markers_gtdb.fasta -out GCA_001769035.1_ASM176903v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:24:26,093] [INFO] Task succeeded: Blastn
[2023-06-05 12:24:26,098] [INFO] Selected 21 target genomes.
[2023-06-05 12:24:26,098] [INFO] Target genome list was writen to GCA_001769035.1_ASM176903v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 12:24:26,223] [INFO] Task started: fastANI
[2023-06-05 12:24:26,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ce37f3c-b198-4b95-be57-77ee2371cb46/GCA_001769035.1_ASM176903v1_genomic.fna.gz --refList GCA_001769035.1_ASM176903v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001769035.1_ASM176903v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 12:24:41,826] [INFO] Task succeeded: fastANI
[2023-06-05 12:24:41,841] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 12:24:41,841] [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_001769035.1	s__GWA2-32-17 sp001769035	99.9999	1452	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__GWA2-32-17;g__GWA2-32-17	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002771395.1	s__GWA2-32-17 sp002771395	79.0841	278	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__GWA2-32-17;g__GWA2-32-17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837285.1	s__GWA2-32-17 sp903837285	77.3225	371	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__GWA2-32-17;g__GWA2-32-17	95.0	99.88	99.88	0.97	0.97	2	-
GCA_903872185.1	s__GWA2-32-17 sp903872185	77.2871	350	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__GWA2-32-17;g__GWA2-32-17	95.0	99.61	99.56	0.90	0.90	3	-
GCA_016218155.1	s__GWA2-32-17 sp016218155	77.1686	373	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__GWA2-32-17;g__GWA2-32-17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001769505.1	s__GWF2-33-38 sp001769505	75.5005	91	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__GWF2-33-38;g__GWF2-33-38	95.0	99.92	99.84	0.98	0.98	4	-
GCA_001768975.1	s__GWA2-31-9 sp001768975	75.4921	168	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__GWF2-33-38;g__GWA2-31-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001768235.1	s__UBA12077 sp001768235	75.3413	61	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA12077;g__UBA12077	95.0	99.99	99.99	0.99	0.99	5	-
GCA_001769125.1	s__GWF2-35-48 sp001769125	75.0665	102	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__GWF2-35-48;g__GWF2-35-48	95.0	99.91	99.85	0.95	0.91	4	-
GCA_001768565.1	s__UBA12077 sp001768565	74.8991	65	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA12077;g__UBA12077	95.0	100.00	100.00	0.99	0.99	2	-
GCA_903928655.1	s__UBA4416 sp903928655	74.852	52	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__B-17BO;g__UBA4416	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002084355.1	s__4572-128 sp002084355	74.6432	119	1472	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__4572-128;g__4572-128	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 12:24:41,843] [INFO] GTDB search result was written to GCA_001769035.1_ASM176903v1_genomic.fna/result_gtdb.tsv
[2023-06-05 12:24:41,844] [INFO] ===== GTDB Search completed =====
[2023-06-05 12:24:41,847] [INFO] DFAST_QC result json was written to GCA_001769035.1_ASM176903v1_genomic.fna/dqc_result.json
[2023-06-05 12:24:41,848] [INFO] DFAST_QC completed!
[2023-06-05 12:24:41,848] [INFO] Total running time: 0h1m31s