[2024-01-24 13:22:31,853] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:31,855] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:31,856] [INFO] DQC Reference Directory: /var/lib/cwl/stg06c4cb19-6e5c-4ce4-a982-38f55feb0dae/dqc_reference
[2024-01-24 13:22:33,220] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:33,221] [INFO] Task started: Prodigal
[2024-01-24 13:22:33,221] [INFO] Running command: gunzip -c /var/lib/cwl/stg26e2b07b-19c7-4fc6-8a6a-f6fe837cd344/GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/cds.fna -a GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:52,954] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:52,954] [INFO] Task started: HMMsearch
[2024-01-24 13:22:52,955] [INFO] Running command: hmmsearch --tblout GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06c4cb19-6e5c-4ce4-a982-38f55feb0dae/dqc_reference/reference_markers.hmm GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:53,223] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:53,224] [INFO] Found 6/6 markers.
[2024-01-24 13:22:53,275] [INFO] Query marker FASTA was written to GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:22:53,276] [INFO] Task started: Blastn
[2024-01-24 13:22:53,276] [INFO] Running command: blastn -query GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg06c4cb19-6e5c-4ce4-a982-38f55feb0dae/dqc_reference/reference_markers.fasta -out GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:53,891] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:53,896] [INFO] Selected 14 target genomes.
[2024-01-24 13:22:53,897] [INFO] Target genome list was writen to GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:22:54,324] [INFO] Task started: fastANI
[2024-01-24 13:22:54,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg26e2b07b-19c7-4fc6-8a6a-f6fe837cd344/GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna.gz --refList GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:04,536] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:04,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06c4cb19-6e5c-4ce4-a982-38f55feb0dae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:04,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06c4cb19-6e5c-4ce4-a982-38f55feb0dae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:04,547] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:23:04,547] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:04,548] [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
Flavobacterium akiainvivens	strain=DSM 25510	GCA_900115875.1	1202724	1202724	type	True	100.0	1474	1477	95	conclusive
Flavobacterium akiainvivens	strain=IK-1	GCA_001278115.1	1202724	1202724	type	True	99.998	1477	1477	95	conclusive
Flavobacterium subsaxonicum	strain=DSM 21790	GCA_000422725.1	426226	426226	type	True	78.5576	541	1477	95	below_threshold
Flavobacterium subsaxonicum	strain=WB 4.1-42	GCA_000769935.1	426226	426226	type	True	78.5419	533	1477	95	below_threshold
Flavobacterium zepuense	strain=ZT4R6	GCA_007097145.1	2593302	2593302	type	True	78.522	527	1477	95	below_threshold
Flavobacterium rivuli	strain=WB 3.3-2	GCA_000769825.1	498301	498301	type	True	78.1375	453	1477	95	below_threshold
Flavobacterium rivuli	strain=DSM 21788	GCA_000378485.1	498301	498301	type	True	78.1363	455	1477	95	below_threshold
Flavobacterium coralii	strain=D11R37	GCA_019891545.1	2838017	2838017	type	True	78.0206	303	1477	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	77.6418	241	1477	95	below_threshold
Flavobacterium salilacus subsp. altitudinum	strain=LaA7.5	GCA_010078225.1	2691899	2898423	type	True	77.4284	239	1477	95	below_threshold
Flavobacterium salilacus subsp. salilacus	strain=SaA2.12	GCA_004634195.1	2545633	2898423	type	True	77.3892	240	1477	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	76.7332	156	1477	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:04,549] [INFO] DFAST Taxonomy check result was written to GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:23:04,550] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:04,550] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:04,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06c4cb19-6e5c-4ce4-a982-38f55feb0dae/dqc_reference/checkm_data
[2024-01-24 13:23:04,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:04,600] [INFO] Task started: CheckM
[2024-01-24 13:23:04,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/checkm_input GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:23:58,859] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:58,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:58,882] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:58,882] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:58,882] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:23:58,883] [INFO] Task started: Blastn
[2024-01-24 13:23:58,883] [INFO] Running command: blastn -query GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg06c4cb19-6e5c-4ce4-a982-38f55feb0dae/dqc_reference/reference_markers_gtdb.fasta -out GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:59,683] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:59,687] [INFO] Selected 13 target genomes.
[2024-01-24 13:23:59,687] [INFO] Target genome list was writen to GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:59,714] [INFO] Task started: fastANI
[2024-01-24 13:23:59,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg26e2b07b-19c7-4fc6-8a6a-f6fe837cd344/GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna.gz --refList GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:09,226] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:09,243] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:09,243] [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_001278115.1	s__Flavobacterium akiainvivens	99.998	1477	1477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009826935.1	s__Flavobacterium sp009826935	78.9524	438	1477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403075.1	s__Flavobacterium sp003403075	78.9086	516	1477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270005.1	s__Flavobacterium sp012270005	78.6143	405	1477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422725.1	s__Flavobacterium subsaxonicum	78.5436	544	1477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009915155.1	s__Flavobacterium sp009915155	78.5204	74	1477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097145.1	s__Flavobacterium sp007097145	78.5143	528	1477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714575.1	s__Flavobacterium sp002714575	78.2438	323	1477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378485.1	s__Flavobacterium rivuli	78.112	458	1477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009848495.1	s__Flavobacterium sp009848495	77.8216	245	1477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002251835.1	s__Flavobacterium cyanobacteriorum	77.68	208	1477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008000935.1	s__Flavobacterium alkalisoli	77.653	242	1477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004634195.1	s__Flavobacterium sp004634195	77.3892	240	1477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.56	97.13	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:09,245] [INFO] GTDB search result was written to GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:09,245] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:09,249] [INFO] DFAST_QC result json was written to GCF_900115875.1_IMG-taxon_2693429907_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:24:09,249] [INFO] DFAST_QC completed!
[2024-01-24 13:24:09,249] [INFO] Total running time: 0h1m37s