[2024-01-24 11:20:49,921] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:49,924] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:49,924] [INFO] DQC Reference Directory: /var/lib/cwl/stg990c04dd-cb57-49a0-95df-2a2a5a31c38c/dqc_reference
[2024-01-24 11:20:51,130] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:51,131] [INFO] Task started: Prodigal
[2024-01-24 11:20:51,132] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c3d2e1b-0997-42b1-96a2-1b93782acb4b/GCF_027111255.2_ASM2711125v2_genomic.fna.gz | prodigal -d GCF_027111255.2_ASM2711125v2_genomic.fna/cds.fna -a GCF_027111255.2_ASM2711125v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:09,795] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:09,795] [INFO] Task started: HMMsearch
[2024-01-24 11:21:09,796] [INFO] Running command: hmmsearch --tblout GCF_027111255.2_ASM2711125v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg990c04dd-cb57-49a0-95df-2a2a5a31c38c/dqc_reference/reference_markers.hmm GCF_027111255.2_ASM2711125v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:10,101] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:10,102] [INFO] Found 6/6 markers.
[2024-01-24 11:21:10,145] [INFO] Query marker FASTA was written to GCF_027111255.2_ASM2711125v2_genomic.fna/markers.fasta
[2024-01-24 11:21:10,146] [INFO] Task started: Blastn
[2024-01-24 11:21:10,146] [INFO] Running command: blastn -query GCF_027111255.2_ASM2711125v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg990c04dd-cb57-49a0-95df-2a2a5a31c38c/dqc_reference/reference_markers.fasta -out GCF_027111255.2_ASM2711125v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:10,826] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:10,830] [INFO] Selected 14 target genomes.
[2024-01-24 11:21:10,830] [INFO] Target genome list was writen to GCF_027111255.2_ASM2711125v2_genomic.fna/target_genomes.txt
[2024-01-24 11:21:10,845] [INFO] Task started: fastANI
[2024-01-24 11:21:10,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c3d2e1b-0997-42b1-96a2-1b93782acb4b/GCF_027111255.2_ASM2711125v2_genomic.fna.gz --refList GCF_027111255.2_ASM2711125v2_genomic.fna/target_genomes.txt --output GCF_027111255.2_ASM2711125v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:27,193] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:27,194] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg990c04dd-cb57-49a0-95df-2a2a5a31c38c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:27,195] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg990c04dd-cb57-49a0-95df-2a2a5a31c38c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:27,209] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:21:27,209] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:21:27,209] [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 hibisci	strain=THG-HG1.4	GCA_020026925.1	1914462	1914462	type	True	93.1735	1325	1809	95	below_threshold
Flavobacterium limi	strain=CGMCC 1.16060	GCA_014644395.1	2045105	2045105	type	True	87.039	1282	1809	95	below_threshold
Flavobacterium limi	strain=THG-AG6.4	GCA_010645075.1	2045105	2045105	type	True	87.0352	1295	1809	95	below_threshold
Flavobacterium hydrophilum	strain=IMCC34758	GCA_003202405.1	2211445	2211445	type	True	85.8801	1307	1809	95	below_threshold
Flavobacterium fluviatile	strain=TAPY14	GCA_010645065.1	1862387	1862387	type	True	85.7673	1102	1809	95	below_threshold
Flavobacterium salmonis	strain=CIP 111411	GCA_903819435.1	2654844	2654844	type	True	84.9639	1278	1809	95	below_threshold
Flavobacterium ajazii	strain=SSM4.2	GCA_010614725.1	2692318	2692318	type	True	84.6627	1175	1809	95	below_threshold
Flavobacterium cutihirudinis	strain=DSM 25795	GCA_003385895.1	1265740	1265740	type	True	81.878	839	1809	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	81.8351	905	1809	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	81.7402	900	1809	95	below_threshold
Flavobacterium denitrificans	strain=DSM 15936	GCA_000425445.1	281361	281361	type	True	81.7109	842	1809	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	81.6881	852	1809	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	81.4797	890	1809	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.5289	170	1809	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:27,211] [INFO] DFAST Taxonomy check result was written to GCF_027111255.2_ASM2711125v2_genomic.fna/tc_result.tsv
[2024-01-24 11:21:27,211] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:27,212] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:27,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg990c04dd-cb57-49a0-95df-2a2a5a31c38c/dqc_reference/checkm_data
[2024-01-24 11:21:27,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:27,263] [INFO] Task started: CheckM
[2024-01-24 11:21:27,263] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027111255.2_ASM2711125v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027111255.2_ASM2711125v2_genomic.fna/checkm_input GCF_027111255.2_ASM2711125v2_genomic.fna/checkm_result
[2024-01-24 11:22:22,041] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:22,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:22,064] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:22,064] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:22,065] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027111255.2_ASM2711125v2_genomic.fna/markers.fasta)
[2024-01-24 11:22:22,065] [INFO] Task started: Blastn
[2024-01-24 11:22:22,065] [INFO] Running command: blastn -query GCF_027111255.2_ASM2711125v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg990c04dd-cb57-49a0-95df-2a2a5a31c38c/dqc_reference/reference_markers_gtdb.fasta -out GCF_027111255.2_ASM2711125v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:23,024] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:23,028] [INFO] Selected 14 target genomes.
[2024-01-24 11:22:23,029] [INFO] Target genome list was writen to GCF_027111255.2_ASM2711125v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:23,039] [INFO] Task started: fastANI
[2024-01-24 11:22:23,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c3d2e1b-0997-42b1-96a2-1b93782acb4b/GCF_027111255.2_ASM2711125v2_genomic.fna.gz --refList GCF_027111255.2_ASM2711125v2_genomic.fna/target_genomes_gtdb.txt --output GCF_027111255.2_ASM2711125v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:39,439] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:39,462] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:22:39,462] [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_010645075.1	s__Flavobacterium limi	87.038	1294	1809	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003202405.1	s__Flavobacterium hydrophilum	85.8801	1307	1809	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010645065.1	s__Flavobacterium fluviatile	85.7673	1102	1809	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735715.2	s__Flavobacterium chungangense	85.0182	1255	1809	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.81	95.16	0.89	0.84	4	-
GCF_010614725.1	s__Flavobacterium ajazii	84.6966	1169	1809	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	84.317	1159	1809	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385895.1	s__Flavobacterium cutihirudinis	81.8824	837	1809	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745775.1	s__Flavobacterium sp000745775	81.8397	878	1809	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142715.1	s__Flavobacterium pectinovorum	81.802	974	1809	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.30	96.60	0.94	0.89	3	-
GCF_003688345.1	s__Flavobacterium sp003688345	81.7713	960	1809	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000425445.1	s__Flavobacterium denitrificans	81.7319	838	1809	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362055.1	s__Flavobacterium sp004362055	81.7272	850	1809	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946915.1	s__Flavobacterium sp003946915	81.5525	831	1809	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016405855.1	s__Flavobacterium sp002399805	81.2494	887	1809	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.61	96.61	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:22:39,464] [INFO] GTDB search result was written to GCF_027111255.2_ASM2711125v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:39,465] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:39,468] [INFO] DFAST_QC result json was written to GCF_027111255.2_ASM2711125v2_genomic.fna/dqc_result.json
[2024-01-24 11:22:39,468] [INFO] DFAST_QC completed!
[2024-01-24 11:22:39,468] [INFO] Total running time: 0h1m50s