[2024-01-24 13:27:45,732] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:45,740] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:45,740] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc291c12-529d-4e31-ba1a-da6258a23b03/dqc_reference
[2024-01-24 13:27:47,165] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:47,166] [INFO] Task started: Prodigal
[2024-01-24 13:27:47,166] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc07a452-a17e-47ae-a4d5-65ba22549aec/GCF_000430665.1_ASM43066v1_genomic.fna.gz | prodigal -d GCF_000430665.1_ASM43066v1_genomic.fna/cds.fna -a GCF_000430665.1_ASM43066v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:01,273] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:01,273] [INFO] Task started: HMMsearch
[2024-01-24 13:28:01,273] [INFO] Running command: hmmsearch --tblout GCF_000430665.1_ASM43066v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc291c12-529d-4e31-ba1a-da6258a23b03/dqc_reference/reference_markers.hmm GCF_000430665.1_ASM43066v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:01,649] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:01,651] [INFO] Found 6/6 markers.
[2024-01-24 13:28:01,703] [INFO] Query marker FASTA was written to GCF_000430665.1_ASM43066v1_genomic.fna/markers.fasta
[2024-01-24 13:28:01,703] [INFO] Task started: Blastn
[2024-01-24 13:28:01,703] [INFO] Running command: blastn -query GCF_000430665.1_ASM43066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc291c12-529d-4e31-ba1a-da6258a23b03/dqc_reference/reference_markers.fasta -out GCF_000430665.1_ASM43066v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:02,446] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:02,449] [INFO] Selected 15 target genomes.
[2024-01-24 13:28:02,450] [INFO] Target genome list was writen to GCF_000430665.1_ASM43066v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:02,465] [INFO] Task started: fastANI
[2024-01-24 13:28:02,465] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc07a452-a17e-47ae-a4d5-65ba22549aec/GCF_000430665.1_ASM43066v1_genomic.fna.gz --refList GCF_000430665.1_ASM43066v1_genomic.fna/target_genomes.txt --output GCF_000430665.1_ASM43066v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:17,192] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:17,193] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc291c12-529d-4e31-ba1a-da6258a23b03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:17,193] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc291c12-529d-4e31-ba1a-da6258a23b03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:17,213] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:17,213] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:17,213] [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
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	100.0	1580	1583	95	conclusive
Aquimarina muelleri	strain=KCTC 12285	GCA_014651355.1	279356	279356	type	True	99.9833	1553	1583	95	conclusive
Aquimarina macrocephali	strain=JAMB N27	GCA_000520995.1	666563	666563	type	True	80.0922	852	1583	95	below_threshold
Aquimarina megaterium	strain=XH134	GCA_000520975.1	1443666	1443666	type	True	79.9561	836	1583	95	below_threshold
Aquimarina atlantica	strain=22II-S11-z7	GCA_000626715.1	1317122	1317122	type	True	79.9198	829	1583	95	below_threshold
Aquimarina longa	strain=SW024	GCA_001401755.1	1080221	1080221	type	True	79.7882	755	1583	95	below_threshold
Aquimarina sediminis	strain=w01	GCA_002895435.1	2070536	2070536	type	True	79.337	741	1583	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	78.3759	557	1583	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	76.7512	62	1583	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.3847	115	1583	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.2397	147	1583	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.1588	111	1583	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.0056	127	1583	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	75.9342	119	1583	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	75.8553	124	1583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:17,215] [INFO] DFAST Taxonomy check result was written to GCF_000430665.1_ASM43066v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:17,215] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:17,216] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:17,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc291c12-529d-4e31-ba1a-da6258a23b03/dqc_reference/checkm_data
[2024-01-24 13:28:17,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:17,268] [INFO] Task started: CheckM
[2024-01-24 13:28:17,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430665.1_ASM43066v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430665.1_ASM43066v1_genomic.fna/checkm_input GCF_000430665.1_ASM43066v1_genomic.fna/checkm_result
[2024-01-24 13:29:01,683] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:01,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:01,706] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:01,706] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:01,707] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430665.1_ASM43066v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:01,707] [INFO] Task started: Blastn
[2024-01-24 13:29:01,707] [INFO] Running command: blastn -query GCF_000430665.1_ASM43066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc291c12-529d-4e31-ba1a-da6258a23b03/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430665.1_ASM43066v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:02,618] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:02,621] [INFO] Selected 14 target genomes.
[2024-01-24 13:29:02,621] [INFO] Target genome list was writen to GCF_000430665.1_ASM43066v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:02,637] [INFO] Task started: fastANI
[2024-01-24 13:29:02,638] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc07a452-a17e-47ae-a4d5-65ba22549aec/GCF_000430665.1_ASM43066v1_genomic.fna.gz --refList GCF_000430665.1_ASM43066v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430665.1_ASM43066v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:18,180] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:18,191] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:18,191] [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_000430665.1	s__Aquimarina muelleri	100.0	1580	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_000520995.1	s__Aquimarina macrocephali	80.0924	852	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299525.1	s__Aquimarina sp900299525	80.0387	859	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000520975.1	s__Aquimarina megaterium	79.9549	835	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.79	98.77	0.92	0.92	4	-
GCF_000626715.1	s__Aquimarina atlantica	79.9198	829	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900312745.1	s__Aquimarina sp900312745	79.918	827	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.61	95.54	0.91	0.91	4	-
GCF_002846555.1	s__Aquimarina sp002846555	79.9141	817	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001401755.1	s__Aquimarina longa	79.7952	754	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299535.1	s__Aquimarina sp900299535	79.4271	649	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.11	95.11	0.81	0.81	2	-
GCF_002895435.1	s__Aquimarina sediminis	79.3305	742	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007489275.1	s__Aquimarina algiphila	79.3232	683	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.78	98.78	0.88	0.88	2	-
GCF_001632745.1	s__Aquimarina aggregata	78.3688	558	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.64	98.63	0.93	0.92	3	-
GCF_003384935.1	s__Lutibacter oceani	76.0266	115	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003449015.1	s__Aureibaculum sp003449015	75.8785	122	1583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:18,193] [INFO] GTDB search result was written to GCF_000430665.1_ASM43066v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:18,193] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:18,197] [INFO] DFAST_QC result json was written to GCF_000430665.1_ASM43066v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:18,197] [INFO] DFAST_QC completed!
[2024-01-24 13:29:18,197] [INFO] Total running time: 0h1m32s