[2024-01-24 13:31:33,479] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,481] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg397b007d-834b-4223-a83c-75d14d5eef97/dqc_reference
[2024-01-24 13:31:34,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,787] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,788] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ebc6d57-3f09-4aa9-b834-4a65e77b5e18/GCF_007097145.1_ASM709714v1_genomic.fna.gz | prodigal -d GCF_007097145.1_ASM709714v1_genomic.fna/cds.fna -a GCF_007097145.1_ASM709714v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:54,706] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:54,706] [INFO] Task started: HMMsearch
[2024-01-24 13:31:54,707] [INFO] Running command: hmmsearch --tblout GCF_007097145.1_ASM709714v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg397b007d-834b-4223-a83c-75d14d5eef97/dqc_reference/reference_markers.hmm GCF_007097145.1_ASM709714v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:55,047] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:55,048] [INFO] Found 6/6 markers.
[2024-01-24 13:31:55,094] [INFO] Query marker FASTA was written to GCF_007097145.1_ASM709714v1_genomic.fna/markers.fasta
[2024-01-24 13:31:55,094] [INFO] Task started: Blastn
[2024-01-24 13:31:55,094] [INFO] Running command: blastn -query GCF_007097145.1_ASM709714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg397b007d-834b-4223-a83c-75d14d5eef97/dqc_reference/reference_markers.fasta -out GCF_007097145.1_ASM709714v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:55,793] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:55,797] [INFO] Selected 13 target genomes.
[2024-01-24 13:31:55,798] [INFO] Target genome list was writen to GCF_007097145.1_ASM709714v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:55,808] [INFO] Task started: fastANI
[2024-01-24 13:31:55,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ebc6d57-3f09-4aa9-b834-4a65e77b5e18/GCF_007097145.1_ASM709714v1_genomic.fna.gz --refList GCF_007097145.1_ASM709714v1_genomic.fna/target_genomes.txt --output GCF_007097145.1_ASM709714v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:06,080] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:06,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg397b007d-834b-4223-a83c-75d14d5eef97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:06,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg397b007d-834b-4223-a83c-75d14d5eef97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:06,092] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:06,092] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:06,092] [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 zepuense	strain=ZT4R6	GCA_007097145.1	2593302	2593302	type	True	100.0	1563	1566	95	conclusive
Flavobacterium subsaxonicum	strain=WB 4.1-42	GCA_000769935.1	426226	426226	type	True	83.4409	949	1566	95	below_threshold
Flavobacterium subsaxonicum	strain=DSM 21790	GCA_000422725.1	426226	426226	type	True	83.4129	958	1566	95	below_threshold
Flavobacterium rivuli	strain=WB 3.3-2	GCA_000769825.1	498301	498301	type	True	79.6223	667	1566	95	below_threshold
Flavobacterium rivuli	strain=DSM 21788	GCA_000378485.1	498301	498301	type	True	79.6083	679	1566	95	below_threshold
Flavobacterium akiainvivens	strain=IK-1	GCA_001278115.1	1202724	1202724	type	True	78.5174	534	1566	95	below_threshold
Flavobacterium akiainvivens	strain=DSM 25510	GCA_900115875.1	1202724	1202724	type	True	78.5082	526	1566	95	below_threshold
Flavobacterium coralii	strain=D11R37	GCA_019891545.1	2838017	2838017	type	True	78.1997	312	1566	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	78.0664	336	1566	95	below_threshold
Flavobacterium album	strain=HYN0059	GCA_003096035.1	2175091	2175091	type	True	77.9692	341	1566	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	77.6373	205	1566	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	77.3512	63	1566	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:06,094] [INFO] DFAST Taxonomy check result was written to GCF_007097145.1_ASM709714v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:06,095] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:06,095] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:06,095] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg397b007d-834b-4223-a83c-75d14d5eef97/dqc_reference/checkm_data
[2024-01-24 13:32:06,096] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:06,157] [INFO] Task started: CheckM
[2024-01-24 13:32:06,157] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007097145.1_ASM709714v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007097145.1_ASM709714v1_genomic.fna/checkm_input GCF_007097145.1_ASM709714v1_genomic.fna/checkm_result
[2024-01-24 13:33:01,760] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:01,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:01,793] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:01,794] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:01,794] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007097145.1_ASM709714v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:01,795] [INFO] Task started: Blastn
[2024-01-24 13:33:01,795] [INFO] Running command: blastn -query GCF_007097145.1_ASM709714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg397b007d-834b-4223-a83c-75d14d5eef97/dqc_reference/reference_markers_gtdb.fasta -out GCF_007097145.1_ASM709714v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:02,856] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:02,861] [INFO] Selected 10 target genomes.
[2024-01-24 13:33:02,862] [INFO] Target genome list was writen to GCF_007097145.1_ASM709714v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:02,882] [INFO] Task started: fastANI
[2024-01-24 13:33:02,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ebc6d57-3f09-4aa9-b834-4a65e77b5e18/GCF_007097145.1_ASM709714v1_genomic.fna.gz --refList GCF_007097145.1_ASM709714v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007097145.1_ASM709714v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:12,326] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:12,336] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:12,336] [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_007097145.1	s__Flavobacterium sp007097145	100.0	1563	1566	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_000422725.1	s__Flavobacterium subsaxonicum	83.426	957	1566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000378485.1	s__Flavobacterium rivuli	79.6011	680	1566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003403075.1	s__Flavobacterium sp003403075	78.956	526	1566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826935.1	s__Flavobacterium sp009826935	78.6367	534	1566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278115.1	s__Flavobacterium akiainvivens	78.5357	531	1566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001708385.1	s__Flavobacterium psychrophilum_A	78.2844	424	1566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004028155.1	s__Flavobacterium cerinum	78.2624	339	1566	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	78.0118	334	1566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096035.1	s__Flavobacterium album	77.9692	341	1566	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:12,338] [INFO] GTDB search result was written to GCF_007097145.1_ASM709714v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:12,338] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:12,343] [INFO] DFAST_QC result json was written to GCF_007097145.1_ASM709714v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:12,343] [INFO] DFAST_QC completed!
[2024-01-24 13:33:12,343] [INFO] Total running time: 0h1m39s