[2024-01-24 13:13:51,570] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:51,581] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:51,581] [INFO] DQC Reference Directory: /var/lib/cwl/stg38e4ad2f-ccc3-430b-8eff-00666bab2c49/dqc_reference
[2024-01-24 13:13:52,890] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:52,891] [INFO] Task started: Prodigal
[2024-01-24 13:13:52,891] [INFO] Running command: gunzip -c /var/lib/cwl/stg44663d28-066e-4083-b9b2-3fd62751ffb6/GCF_900638245.1_56772_F02_genomic.fna.gz | prodigal -d GCF_900638245.1_56772_F02_genomic.fna/cds.fna -a GCF_900638245.1_56772_F02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:14:05,417] [INFO] Task succeeded: Prodigal
[2024-01-24 13:14:05,418] [INFO] Task started: HMMsearch
[2024-01-24 13:14:05,418] [INFO] Running command: hmmsearch --tblout GCF_900638245.1_56772_F02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38e4ad2f-ccc3-430b-8eff-00666bab2c49/dqc_reference/reference_markers.hmm GCF_900638245.1_56772_F02_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:14:05,726] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:14:05,727] [INFO] Found 6/6 markers.
[2024-01-24 13:14:05,767] [INFO] Query marker FASTA was written to GCF_900638245.1_56772_F02_genomic.fna/markers.fasta
[2024-01-24 13:14:05,767] [INFO] Task started: Blastn
[2024-01-24 13:14:05,767] [INFO] Running command: blastn -query GCF_900638245.1_56772_F02_genomic.fna/markers.fasta -db /var/lib/cwl/stg38e4ad2f-ccc3-430b-8eff-00666bab2c49/dqc_reference/reference_markers.fasta -out GCF_900638245.1_56772_F02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:06,458] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:06,462] [INFO] Selected 11 target genomes.
[2024-01-24 13:14:06,462] [INFO] Target genome list was writen to GCF_900638245.1_56772_F02_genomic.fna/target_genomes.txt
[2024-01-24 13:14:06,474] [INFO] Task started: fastANI
[2024-01-24 13:14:06,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg44663d28-066e-4083-b9b2-3fd62751ffb6/GCF_900638245.1_56772_F02_genomic.fna.gz --refList GCF_900638245.1_56772_F02_genomic.fna/target_genomes.txt --output GCF_900638245.1_56772_F02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:15,388] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:15,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38e4ad2f-ccc3-430b-8eff-00666bab2c49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:15,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38e4ad2f-ccc3-430b-8eff-00666bab2c49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:15,399] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:14:15,400] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:15,400] [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
Kaistella jeonii	strain=NCTC13459	GCA_900638245.1	266749	266749	type	True	100.0	1095	1096	95	conclusive
Kaistella jeonii	strain=DSM 17048	GCA_900112115.1	266749	266749	type	True	99.9651	1063	1096	95	conclusive
Kaistella jeonii	strain=DSM 17048	GCA_000812865.1	266749	266749	type	True	99.9616	1072	1096	95	conclusive
Kaistella gelatinilytica	strain=G5-32	GCA_015679325.1	2787636	2787636	type	True	90.9094	921	1096	95	below_threshold
Kaistella chaponensis	strain=DSM 23145	GCA_900156725.1	713588	713588	type	True	82.8376	716	1096	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	80.0227	524	1096	95	below_threshold
Kaistella daneshvariae	strain=H3001	GCA_003860505.1	2487074	2487074	type	True	78.4153	340	1096	95	below_threshold
Kaistella palustris	strain=DSM 21579	GCA_000422265.1	493376	493376	type	True	78.4029	353	1096	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	78.3475	329	1096	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_020985365.1	2852098	2852098	type	True	78.3453	331	1096	95	below_threshold
Chryseobacterium vrystaatense	strain=LMG 22846	GCA_000737765.1	307480	307480	type	True	76.8108	174	1096	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:15,402] [INFO] DFAST Taxonomy check result was written to GCF_900638245.1_56772_F02_genomic.fna/tc_result.tsv
[2024-01-24 13:14:15,403] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:15,403] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:15,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38e4ad2f-ccc3-430b-8eff-00666bab2c49/dqc_reference/checkm_data
[2024-01-24 13:14:15,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:15,439] [INFO] Task started: CheckM
[2024-01-24 13:14:15,440] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900638245.1_56772_F02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900638245.1_56772_F02_genomic.fna/checkm_input GCF_900638245.1_56772_F02_genomic.fna/checkm_result
[2024-01-24 13:14:56,438] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:56,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:56,476] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:56,476] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:56,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900638245.1_56772_F02_genomic.fna/markers.fasta)
[2024-01-24 13:14:56,477] [INFO] Task started: Blastn
[2024-01-24 13:14:56,478] [INFO] Running command: blastn -query GCF_900638245.1_56772_F02_genomic.fna/markers.fasta -db /var/lib/cwl/stg38e4ad2f-ccc3-430b-8eff-00666bab2c49/dqc_reference/reference_markers_gtdb.fasta -out GCF_900638245.1_56772_F02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:58,165] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:58,170] [INFO] Selected 13 target genomes.
[2024-01-24 13:14:58,171] [INFO] Target genome list was writen to GCF_900638245.1_56772_F02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:58,189] [INFO] Task started: fastANI
[2024-01-24 13:14:58,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg44663d28-066e-4083-b9b2-3fd62751ffb6/GCF_900638245.1_56772_F02_genomic.fna.gz --refList GCF_900638245.1_56772_F02_genomic.fna/target_genomes_gtdb.txt --output GCF_900638245.1_56772_F02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:07,301] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:07,317] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:07,317] [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_000812865.1	s__Kaistella jeonii	99.9616	1072	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	99.99	1.00	1.00	3	conclusive
GCF_015679325.1	s__Kaistella gelatinilytica	90.9075	921	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156725.1	s__Kaistella chaponensis	82.8261	717	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015191005.1	s__Kaistella flava	80.6917	592	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003860585.1	s__Kaistella carnis	79.9817	523	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	96.86	96.44	0.91	0.90	4	-
GCF_900109615.1	s__Kaistella antarctica	79.7948	525	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	1.00	1.00	3	-
GCF_007362475.1	s__Kaistella sp007362475	79.7202	432	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002415135.1	s__Kaistella sp002415135	79.5594	568	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004359195.1	s__Kaistella sp004359195	79.5443	516	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002426785.1	s__Kaistella sp002426785	78.3092	362	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	98.19	97.96	0.88	0.84	4	-
GCA_015999765.1	s__Kaistella sp015999765	78.3064	325	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	100.00	100.00	0.96	0.96	2	-
GCF_000735695.2	s__Kaistella haifensis	78.1707	350	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Kaistella	95.0	96.72	96.43	0.83	0.82	4	-
GCF_001424145.1	s__Chryseobacterium sp001424145	76.948	218	1096	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:07,319] [INFO] GTDB search result was written to GCF_900638245.1_56772_F02_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:07,319] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:07,322] [INFO] DFAST_QC result json was written to GCF_900638245.1_56772_F02_genomic.fna/dqc_result.json
[2024-01-24 13:15:07,323] [INFO] DFAST_QC completed!
[2024-01-24 13:15:07,323] [INFO] Total running time: 0h1m16s