[2024-01-25 20:27:20,508] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:27:20,510] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:27:20,510] [INFO] DQC Reference Directory: /var/lib/cwl/stgd43b79bb-0b54-49c8-b584-0996242da04d/dqc_reference
[2024-01-25 20:27:21,768] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:27:21,769] [INFO] Task started: Prodigal
[2024-01-25 20:27:21,769] [INFO] Running command: gunzip -c /var/lib/cwl/stgd569fc54-6384-488c-a3be-1845310c5902/GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/cds.fna -a GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:27:33,960] [INFO] Task succeeded: Prodigal
[2024-01-25 20:27:33,960] [INFO] Task started: HMMsearch
[2024-01-25 20:27:33,960] [INFO] Running command: hmmsearch --tblout GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd43b79bb-0b54-49c8-b584-0996242da04d/dqc_reference/reference_markers.hmm GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:27:34,196] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:27:34,197] [INFO] Found 6/6 markers.
[2024-01-25 20:27:34,236] [INFO] Query marker FASTA was written to GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:27:34,236] [INFO] Task started: Blastn
[2024-01-25 20:27:34,236] [INFO] Running command: blastn -query GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd43b79bb-0b54-49c8-b584-0996242da04d/dqc_reference/reference_markers.fasta -out GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:34,874] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:34,876] [INFO] Selected 16 target genomes.
[2024-01-25 20:27:34,876] [INFO] Target genome list was writen to GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:27:34,904] [INFO] Task started: fastANI
[2024-01-25 20:27:34,905] [INFO] Running command: fastANI --query /var/lib/cwl/stgd569fc54-6384-488c-a3be-1845310c5902/GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna.gz --refList GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:27:47,066] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:47,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd43b79bb-0b54-49c8-b584-0996242da04d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:27:47,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd43b79bb-0b54-49c8-b584-0996242da04d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:27:47,076] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:27:47,076] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:27:47,076] [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
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	99.9988	1390	1392	95	conclusive
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	89.8578	1103	1392	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	80.5084	748	1392	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	80.4823	751	1392	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	80.4695	751	1392	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	80.4215	729	1392	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	80.1475	736	1392	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	80.0414	755	1392	95	below_threshold
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	79.921	683	1392	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	76.8509	178	1392	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	76.8146	145	1392	95	below_threshold
Saonia flava	strain=DSM 29762	GCA_011927795.1	523696	523696	type	True	76.6794	169	1392	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	76.131	56	1392	95	below_threshold
Haloflavibacter putidus	strain=PLHSN227	GCA_006546625.1	2576776	2576776	type	True	75.9179	55	1392	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	75.7693	59	1392	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:27:47,078] [INFO] DFAST Taxonomy check result was written to GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:27:47,079] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:27:47,079] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:27:47,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd43b79bb-0b54-49c8-b584-0996242da04d/dqc_reference/checkm_data
[2024-01-25 20:27:47,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:27:47,124] [INFO] Task started: CheckM
[2024-01-25 20:27:47,124] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/checkm_input GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:28:24,667] [INFO] Task succeeded: CheckM
[2024-01-25 20:28:24,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:28:24,689] [INFO] ===== Completeness check finished =====
[2024-01-25 20:28:24,689] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:28:24,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:28:24,690] [INFO] Task started: Blastn
[2024-01-25 20:28:24,690] [INFO] Running command: blastn -query GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd43b79bb-0b54-49c8-b584-0996242da04d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:28:25,656] [INFO] Task succeeded: Blastn
[2024-01-25 20:28:25,658] [INFO] Selected 13 target genomes.
[2024-01-25 20:28:25,659] [INFO] Target genome list was writen to GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:28:25,674] [INFO] Task started: fastANI
[2024-01-25 20:28:25,674] [INFO] Running command: fastANI --query /var/lib/cwl/stgd569fc54-6384-488c-a3be-1845310c5902/GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna.gz --refList GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:28:37,252] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:37,262] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:28:37,262] [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_900167935.1	s__Maribacter arcticus	99.9988	1390	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900109345.1	s__Maribacter orientalis	89.8728	1102	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771495.1	s__Maribacter sp005771495	81.2066	828	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	80.6586	765	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900112245.1	s__Maribacter stanieri	80.5081	749	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_001913155.1	s__Maribacter hydrothermalis	80.4867	750	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142175.1	s__Maribacter aquivivus	80.418	729	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364165.1	s__Maribacter spongiicola	80.1517	735	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744105.1	s__Maribacter forsetii	79.921	683	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155985.1	s__Maribacter ulvicola	79.5568	642	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885635.1	s__RZ26 sp005885635	76.8495	178	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RZ26	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927795.1	s__Saonia flava	76.7273	168	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Saonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001401755.1	s__Aquimarina longa	76.2288	93	1392	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:28:37,271] [INFO] GTDB search result was written to GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:28:37,272] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:28:37,275] [INFO] DFAST_QC result json was written to GCF_900167935.1_IMG-taxon_2595698209_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:28:37,275] [INFO] DFAST_QC completed!
[2024-01-25 20:28:37,275] [INFO] Total running time: 0h1m17s