[2024-01-24 10:57:37,964] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:37,967] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:37,967] [INFO] DQC Reference Directory: /var/lib/cwl/stg517eef1d-820b-4c85-a61c-73d1ad410712/dqc_reference
[2024-01-24 10:57:39,307] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:39,308] [INFO] Task started: Prodigal
[2024-01-24 10:57:39,308] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf451f53-bf78-4ea4-83a9-543c14b40521/GCF_030410025.1_ASM3041002v1_genomic.fna.gz | prodigal -d GCF_030410025.1_ASM3041002v1_genomic.fna/cds.fna -a GCF_030410025.1_ASM3041002v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:48,940] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:48,940] [INFO] Task started: HMMsearch
[2024-01-24 10:57:48,941] [INFO] Running command: hmmsearch --tblout GCF_030410025.1_ASM3041002v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg517eef1d-820b-4c85-a61c-73d1ad410712/dqc_reference/reference_markers.hmm GCF_030410025.1_ASM3041002v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:49,258] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:49,263] [INFO] Found 6/6 markers.
[2024-01-24 10:57:49,298] [INFO] Query marker FASTA was written to GCF_030410025.1_ASM3041002v1_genomic.fna/markers.fasta
[2024-01-24 10:57:49,298] [INFO] Task started: Blastn
[2024-01-24 10:57:49,298] [INFO] Running command: blastn -query GCF_030410025.1_ASM3041002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg517eef1d-820b-4c85-a61c-73d1ad410712/dqc_reference/reference_markers.fasta -out GCF_030410025.1_ASM3041002v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:50,107] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:50,111] [INFO] Selected 10 target genomes.
[2024-01-24 10:57:50,112] [INFO] Target genome list was writen to GCF_030410025.1_ASM3041002v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:50,129] [INFO] Task started: fastANI
[2024-01-24 10:57:50,130] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf451f53-bf78-4ea4-83a9-543c14b40521/GCF_030410025.1_ASM3041002v1_genomic.fna.gz --refList GCF_030410025.1_ASM3041002v1_genomic.fna/target_genomes.txt --output GCF_030410025.1_ASM3041002v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:59,103] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:59,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg517eef1d-820b-4c85-a61c-73d1ad410712/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:59,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg517eef1d-820b-4c85-a61c-73d1ad410712/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:59,116] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:59,116] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:59,117] [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
Vibrio superstes	strain=NBRC 103154	GCA_007990955.1	198815	198815	type	True	92.5386	1114	1354	95	below_threshold
Vibrio superstes	strain=G3-29	GCA_003569005.1	198815	198815	type	True	92.452	1132	1354	95	below_threshold
Vibrio comitans	strain=LMG 23416	GCA_024346835.1	413401	413401	type	True	87.8093	1088	1354	95	below_threshold
Vibrio comitans	strain=NBRC 102076	GCA_006538565.1	413401	413401	type	True	87.7832	1072	1354	95	below_threshold
Vibrio inusitatus	strain=NBRC 102082	GCA_006538525.1	413402	413402	type	True	86.8774	1021	1354	95	below_threshold
Vibrio inusitatus	strain=LMG 23434	GCA_024346935.1	413402	413402	type	True	86.8449	1045	1354	95	below_threshold
Vibrio gallicus	strain=CIP 107863	GCA_024346875.1	190897	190897	type	True	81.2658	349	1354	95	below_threshold
Vibrio ezurae	strain=HDS1-1	GCA_003568985.1	252583	252583	type	True	81.2038	536	1354	95	below_threshold
Vibrio neonatus	strain=JCM 21521	GCA_024346975.1	278860	278860	type	True	81.1568	576	1354	95	below_threshold
Vibrio ishigakensis	strain=JCM 19231	GCA_024347675.1	1481914	1481914	type	True	79.9625	439	1354	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:59,119] [INFO] DFAST Taxonomy check result was written to GCF_030410025.1_ASM3041002v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:59,120] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:59,120] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:59,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg517eef1d-820b-4c85-a61c-73d1ad410712/dqc_reference/checkm_data
[2024-01-24 10:57:59,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:59,168] [INFO] Task started: CheckM
[2024-01-24 10:57:59,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030410025.1_ASM3041002v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030410025.1_ASM3041002v1_genomic.fna/checkm_input GCF_030410025.1_ASM3041002v1_genomic.fna/checkm_result
[2024-01-24 10:58:33,522] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:33,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.85%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:33,548] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:33,548] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:33,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030410025.1_ASM3041002v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:33,549] [INFO] Task started: Blastn
[2024-01-24 10:58:33,549] [INFO] Running command: blastn -query GCF_030410025.1_ASM3041002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg517eef1d-820b-4c85-a61c-73d1ad410712/dqc_reference/reference_markers_gtdb.fasta -out GCF_030410025.1_ASM3041002v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:34,778] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:34,783] [INFO] Selected 6 target genomes.
[2024-01-24 10:58:34,783] [INFO] Target genome list was writen to GCF_030410025.1_ASM3041002v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:34,812] [INFO] Task started: fastANI
[2024-01-24 10:58:34,812] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf451f53-bf78-4ea4-83a9-543c14b40521/GCF_030410025.1_ASM3041002v1_genomic.fna.gz --refList GCF_030410025.1_ASM3041002v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030410025.1_ASM3041002v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:41,111] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:41,120] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:41,120] [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_001677275.1	s__Vibrio breoganii	97.5001	1224	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.22	96.88	0.90	0.86	59	conclusive
GCF_003569005.1	s__Vibrio superstes	92.4675	1131	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006538565.1	s__Vibrio comitans	87.7832	1072	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538525.1	s__Vibrio inusitatus	86.8774	1021	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000467185.1	s__Vibrio ezurae	81.1801	520	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001676025.1	s__Vibrio sp001676025	80.9152	580	1354	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:41,122] [INFO] GTDB search result was written to GCF_030410025.1_ASM3041002v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:41,122] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:41,125] [INFO] DFAST_QC result json was written to GCF_030410025.1_ASM3041002v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:41,126] [INFO] DFAST_QC completed!
[2024-01-24 10:58:41,126] [INFO] Total running time: 0h1m3s