[2024-01-25 18:58:05,708] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:05,709] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:05,709] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fe837fc-842e-4700-a801-25303e25dd27/dqc_reference
[2024-01-25 18:58:06,844] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:06,845] [INFO] Task started: Prodigal
[2024-01-25 18:58:06,845] [INFO] Running command: gunzip -c /var/lib/cwl/stgab56a24c-3003-4d22-a983-b8b024fb93d3/GCF_003122385.1_ASM312238v1_genomic.fna.gz | prodigal -d GCF_003122385.1_ASM312238v1_genomic.fna/cds.fna -a GCF_003122385.1_ASM312238v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:23,834] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:23,835] [INFO] Task started: HMMsearch
[2024-01-25 18:58:23,835] [INFO] Running command: hmmsearch --tblout GCF_003122385.1_ASM312238v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fe837fc-842e-4700-a801-25303e25dd27/dqc_reference/reference_markers.hmm GCF_003122385.1_ASM312238v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:24,096] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:24,097] [INFO] Found 6/6 markers.
[2024-01-25 18:58:24,144] [INFO] Query marker FASTA was written to GCF_003122385.1_ASM312238v1_genomic.fna/markers.fasta
[2024-01-25 18:58:24,144] [INFO] Task started: Blastn
[2024-01-25 18:58:24,144] [INFO] Running command: blastn -query GCF_003122385.1_ASM312238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fe837fc-842e-4700-a801-25303e25dd27/dqc_reference/reference_markers.fasta -out GCF_003122385.1_ASM312238v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:24,808] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:24,811] [INFO] Selected 16 target genomes.
[2024-01-25 18:58:24,812] [INFO] Target genome list was writen to GCF_003122385.1_ASM312238v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:24,824] [INFO] Task started: fastANI
[2024-01-25 18:58:24,825] [INFO] Running command: fastANI --query /var/lib/cwl/stgab56a24c-3003-4d22-a983-b8b024fb93d3/GCF_003122385.1_ASM312238v1_genomic.fna.gz --refList GCF_003122385.1_ASM312238v1_genomic.fna/target_genomes.txt --output GCF_003122385.1_ASM312238v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:45,162] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:45,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fe837fc-842e-4700-a801-25303e25dd27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:45,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fe837fc-842e-4700-a801-25303e25dd27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:45,173] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:58:45,173] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:58:45,173] [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 crocinum	strain=HYN0056	GCA_003122385.1	2183896	2183896	type	True	100.0	1956	1959	95	conclusive
Flavobacterium quisquiliarum	strain=EA-12	GCA_019308285.1	1834436	1834436	type	True	90.0782	1571	1959	95	below_threshold
Flavobacterium phragmitis	strain=CGMCC 1.10370	GCA_900112575.1	739143	739143	type	True	89.6959	1545	1959	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	85.6306	1473	1959	95	below_threshold
Flavobacterium tistrianum	strain=GB 56.1	GCA_003254545.1	1685414	1685414	type	True	85.4511	1218	1959	95	below_threshold
Flavobacterium nitrogenifigens	strain=NXU-44	GCA_003254565.1	1617283	1617283	type	True	85.3772	1257	1959	95	below_threshold
Flavobacterium nitrogenifigens	strain=DSM 29982	GCA_900182675.1	1617283	1617283	type	True	85.3312	1261	1959	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	85.1918	1281	1959	95	below_threshold
Flavobacterium foetidum	strain=JCM 32085	GCA_004634245.1	2026681	2026681	type	True	84.3852	1193	1959	95	below_threshold
Flavobacterium johnsoniae	strain=UW101; ATCC 17061	GCA_000016645.1	986	986	type	True	84.2531	1242	1959	95	below_threshold
Flavobacterium johnsoniae	strain=DSM 2064	GCA_900142355.1	986	986	type	True	84.2306	1234	1959	95	below_threshold
Flavobacterium johnsoniae	strain=ATCC 17061	GCA_002221975.1	986	986	type	True	84.2133	1224	1959	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	83.5815	1080	1959	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	83.2772	1174	1959	95	below_threshold
Flavobacterium denitrificans	strain=DSM 15936	GCA_000425445.1	281361	281361	type	True	83.2457	1077	1959	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.6594	228	1959	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:45,174] [INFO] DFAST Taxonomy check result was written to GCF_003122385.1_ASM312238v1_genomic.fna/tc_result.tsv
[2024-01-25 18:58:45,175] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:45,175] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:45,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fe837fc-842e-4700-a801-25303e25dd27/dqc_reference/checkm_data
[2024-01-25 18:58:45,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:45,233] [INFO] Task started: CheckM
[2024-01-25 18:58:45,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003122385.1_ASM312238v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003122385.1_ASM312238v1_genomic.fna/checkm_input GCF_003122385.1_ASM312238v1_genomic.fna/checkm_result
[2024-01-25 18:59:34,653] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:34,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:34,677] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:34,678] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:34,678] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003122385.1_ASM312238v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:34,678] [INFO] Task started: Blastn
[2024-01-25 18:59:34,678] [INFO] Running command: blastn -query GCF_003122385.1_ASM312238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fe837fc-842e-4700-a801-25303e25dd27/dqc_reference/reference_markers_gtdb.fasta -out GCF_003122385.1_ASM312238v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:35,680] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:35,683] [INFO] Selected 15 target genomes.
[2024-01-25 18:59:35,683] [INFO] Target genome list was writen to GCF_003122385.1_ASM312238v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:35,702] [INFO] Task started: fastANI
[2024-01-25 18:59:35,703] [INFO] Running command: fastANI --query /var/lib/cwl/stgab56a24c-3003-4d22-a983-b8b024fb93d3/GCF_003122385.1_ASM312238v1_genomic.fna.gz --refList GCF_003122385.1_ASM312238v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003122385.1_ASM312238v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:56,840] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:56,850] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:59:56,850] [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_003122385.1	s__Flavobacterium crocinum	100.0	1957	1959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013393195.1	s__Flavobacterium collinsii_A	90.093	1562	1959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112575.1	s__Flavobacterium phragmitis	89.6959	1545	1959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207905.1	s__Flavobacterium notoginsengisoli	86.244	1366	1959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902167265.1	s__Flavobacterium anhuiense_B	85.7723	1498	1959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	4	-
GCF_013388355.1	s__Flavobacterium sp013388355	85.7616	951	1959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254625.1	s__Flavobacterium ginsenosidimutans	85.7463	1356	1959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735615.1	s__Flavobacterium sp016735615	85.6695	1291	1959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254545.1	s__Flavobacterium tistrianum	85.4737	1215	1959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254565.1	s__Flavobacterium nitrogenifigens	85.3981	1254	1959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002303885.1	s__Flavobacterium sp002303885	85.2042	1289	1959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429295.1	s__Flavobacterium sp001429295	85.0387	1274	1959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.90	97.90	0.95	0.95	2	-
GCF_004634245.1	s__Flavobacterium foetidum	84.3952	1193	1959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016645.1	s__Flavobacterium johnsoniae	84.2472	1242	1959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.23	96.72	0.94	0.86	7	-
GCF_000425445.1	s__Flavobacterium denitrificans	83.2542	1076	1959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:59:56,852] [INFO] GTDB search result was written to GCF_003122385.1_ASM312238v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:56,852] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:56,855] [INFO] DFAST_QC result json was written to GCF_003122385.1_ASM312238v1_genomic.fna/dqc_result.json
[2024-01-25 18:59:56,855] [INFO] DFAST_QC completed!
[2024-01-25 18:59:56,855] [INFO] Total running time: 0h1m51s