[2024-01-24 15:19:52,621] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:52,623] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:52,624] [INFO] DQC Reference Directory: /var/lib/cwl/stg599cb3f3-3487-414c-93fd-7dfd586a0b7c/dqc_reference
[2024-01-24 15:19:53,875] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:53,876] [INFO] Task started: Prodigal
[2024-01-24 15:19:53,876] [INFO] Running command: gunzip -c /var/lib/cwl/stg52a93654-1d11-4bab-8d7c-57fcaa89c685/GCF_903819445.1_CIP110025_genomic.fna.gz | prodigal -d GCF_903819445.1_CIP110025_genomic.fna/cds.fna -a GCF_903819445.1_CIP110025_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:20:11,364] [INFO] Task succeeded: Prodigal
[2024-01-24 15:20:11,365] [INFO] Task started: HMMsearch
[2024-01-24 15:20:11,365] [INFO] Running command: hmmsearch --tblout GCF_903819445.1_CIP110025_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg599cb3f3-3487-414c-93fd-7dfd586a0b7c/dqc_reference/reference_markers.hmm GCF_903819445.1_CIP110025_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:20:11,752] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:20:11,753] [INFO] Found 6/6 markers.
[2024-01-24 15:20:11,803] [INFO] Query marker FASTA was written to GCF_903819445.1_CIP110025_genomic.fna/markers.fasta
[2024-01-24 15:20:11,803] [INFO] Task started: Blastn
[2024-01-24 15:20:11,803] [INFO] Running command: blastn -query GCF_903819445.1_CIP110025_genomic.fna/markers.fasta -db /var/lib/cwl/stg599cb3f3-3487-414c-93fd-7dfd586a0b7c/dqc_reference/reference_markers.fasta -out GCF_903819445.1_CIP110025_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:12,512] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:12,516] [INFO] Selected 22 target genomes.
[2024-01-24 15:20:12,516] [INFO] Target genome list was writen to GCF_903819445.1_CIP110025_genomic.fna/target_genomes.txt
[2024-01-24 15:20:12,526] [INFO] Task started: fastANI
[2024-01-24 15:20:12,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg52a93654-1d11-4bab-8d7c-57fcaa89c685/GCF_903819445.1_CIP110025_genomic.fna.gz --refList GCF_903819445.1_CIP110025_genomic.fna/target_genomes.txt --output GCF_903819445.1_CIP110025_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:20:37,684] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:37,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg599cb3f3-3487-414c-93fd-7dfd586a0b7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:20:37,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg599cb3f3-3487-414c-93fd-7dfd586a0b7c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:20:37,704] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:20:37,704] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:20:37,704] [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 salmonis	strain=CIP 111411	GCA_903819435.1	2654844	2654844	type	True	95.2488	1409	1662	95	conclusive
Flavobacterium hydrophilum	strain=IMCC34758	GCA_003202405.1	2211445	2211445	type	True	87.5662	1165	1662	95	below_threshold
Flavobacterium cheongpyeongense	strain=IMCC34759	GCA_003202435.1	2212651	2212651	type	True	85.6828	1107	1662	95	below_threshold
Flavobacterium hibisci	strain=THG-HG1.4	GCA_020026925.1	1914462	1914462	type	True	85.4504	1090	1662	95	below_threshold
Flavobacterium limi	strain=THG-AG6.4	GCA_010645075.1	2045105	2045105	type	True	85.1418	1197	1662	95	below_threshold
Flavobacterium limi	strain=CGMCC 1.16060	GCA_014644395.1	2045105	2045105	type	True	85.0918	1197	1662	95	below_threshold
Flavobacterium fluviatile	strain=TAPY14	GCA_010645065.1	1862387	1862387	type	True	84.9379	991	1662	95	below_threshold
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	82.4245	979	1662	95	below_threshold
Flavobacterium pectinovorum	strain=ATCC 19366	GCA_002217365.1	29533	29533	type	True	82.4127	972	1662	95	below_threshold
Flavobacterium chilense	strain=LMG 26360	GCA_001602525.1	946677	946677	type	True	82.2616	869	1662	95	below_threshold
Flavobacterium frigidimaris	strain=DSM 15937	GCA_002217275.1	262320	262320	type	True	82.2112	872	1662	95	below_threshold
Flavobacterium chilense	strain=DSM 24724	GCA_900142685.1	946677	946677	type	True	82.1633	883	1662	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	82.0257	907	1662	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_902804475.1	2704140	2704140	type	True	81.9925	869	1662	95	below_threshold
Flavobacterium bizetiae	strain=CIP 105534	GCA_904425415.1	2704140	2704140	type	True	81.9828	883	1662	95	below_threshold
Flavobacterium plurextorum	strain=CCUG 60112	GCA_002217395.1	1114867	1114867	type	True	81.9743	793	1662	95	below_threshold
Flavobacterium aquidurense	strain=DSM 18293	GCA_002217195.1	362413	362413	type	True	81.8694	887	1662	95	below_threshold
Flavobacterium oncorhynchi	strain=CCUG 59446	GCA_002217355.1	728056	728056	type	True	81.8187	791	1662	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	81.6107	836	1662	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	81.4189	871	1662	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	81.1394	914	1662	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.1774	169	1662	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:20:37,706] [INFO] DFAST Taxonomy check result was written to GCF_903819445.1_CIP110025_genomic.fna/tc_result.tsv
[2024-01-24 15:20:37,707] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:20:37,707] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:20:37,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg599cb3f3-3487-414c-93fd-7dfd586a0b7c/dqc_reference/checkm_data
[2024-01-24 15:20:37,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:20:37,763] [INFO] Task started: CheckM
[2024-01-24 15:20:37,763] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_903819445.1_CIP110025_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_903819445.1_CIP110025_genomic.fna/checkm_input GCF_903819445.1_CIP110025_genomic.fna/checkm_result
[2024-01-24 15:21:31,056] [INFO] Task succeeded: CheckM
[2024-01-24 15:21:31,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:21:31,084] [INFO] ===== Completeness check finished =====
[2024-01-24 15:21:31,084] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:21:31,085] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_903819445.1_CIP110025_genomic.fna/markers.fasta)
[2024-01-24 15:21:31,085] [INFO] Task started: Blastn
[2024-01-24 15:21:31,085] [INFO] Running command: blastn -query GCF_903819445.1_CIP110025_genomic.fna/markers.fasta -db /var/lib/cwl/stg599cb3f3-3487-414c-93fd-7dfd586a0b7c/dqc_reference/reference_markers_gtdb.fasta -out GCF_903819445.1_CIP110025_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:21:32,038] [INFO] Task succeeded: Blastn
[2024-01-24 15:21:32,042] [INFO] Selected 18 target genomes.
[2024-01-24 15:21:32,043] [INFO] Target genome list was writen to GCF_903819445.1_CIP110025_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:21:32,055] [INFO] Task started: fastANI
[2024-01-24 15:21:32,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg52a93654-1d11-4bab-8d7c-57fcaa89c685/GCF_903819445.1_CIP110025_genomic.fna.gz --refList GCF_903819445.1_CIP110025_genomic.fna/target_genomes_gtdb.txt --output GCF_903819445.1_CIP110025_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:52,923] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:52,940] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:52,941] [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_000735715.2	s__Flavobacterium chungangense	99.9799	1646	1662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.81	95.16	0.89	0.84	4	conclusive
GCF_003202405.1	s__Flavobacterium hydrophilum	87.5796	1164	1662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202435.1	s__Flavobacterium cheongpyeongense	85.6936	1106	1662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010645075.1	s__Flavobacterium limi	85.1595	1195	1662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010645065.1	s__Flavobacterium fluviatile	84.9431	990	1662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282055.1	s__Flavobacterium sp000282055	83.4433	1035	1662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707955.1	s__Flavobacterium sp009707955	82.5458	959	1662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003688345.1	s__Flavobacterium sp003688345	82.3328	942	1662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001602525.1	s__Flavobacterium chilense	82.2485	871	1662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	96.61	0.93	0.86	3	-
GCF_900129795.1	s__Flavobacterium sp900129795	82.0905	931	1662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_018383905.1	s__Flavobacterium branchiicola	82.0667	833	1662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902804475.1	s__Flavobacterium bizetiae	81.9898	870	1662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.96	99.94	0.99	0.99	3	-
GCF_000708595.2	s__Flavobacterium sp000708595	81.9744	878	1662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	98.27	0.95	0.93	3	-
GCF_002217395.1	s__Flavobacterium plurextorum	81.9743	793	1662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.27	98.27	0.92	0.92	2	-
GCA_002482975.1	s__Flavobacterium sp002482975	81.9256	886	1662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004368785.1	s__Flavobacterium sp004368785	81.8884	881	1662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900129595.1	s__Flavobacterium frigidimaris	81.8385	897	1662	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015182285.1	s__Flavobacterium sp015182285	81.3959	859	1662	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 15:21:52,942] [INFO] GTDB search result was written to GCF_903819445.1_CIP110025_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:52,943] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:52,950] [INFO] DFAST_QC result json was written to GCF_903819445.1_CIP110025_genomic.fna/dqc_result.json
[2024-01-24 15:21:52,950] [INFO] DFAST_QC completed!
[2024-01-24 15:21:52,950] [INFO] Total running time: 0h2m0s