[2024-01-24 13:49:33,597] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:33,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:33,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ad4deb4-da3f-49ec-b0e5-2307a013970e/dqc_reference
[2024-01-24 13:49:35,012] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:35,013] [INFO] Task started: Prodigal
[2024-01-24 13:49:35,013] [INFO] Running command: gunzip -c /var/lib/cwl/stg43f01850-590e-46e4-aa90-9e0d97b5372f/GCF_011045095.1_ASM1104509v1_genomic.fna.gz | prodigal -d GCF_011045095.1_ASM1104509v1_genomic.fna/cds.fna -a GCF_011045095.1_ASM1104509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:50,164] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:50,164] [INFO] Task started: HMMsearch
[2024-01-24 13:49:50,164] [INFO] Running command: hmmsearch --tblout GCF_011045095.1_ASM1104509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ad4deb4-da3f-49ec-b0e5-2307a013970e/dqc_reference/reference_markers.hmm GCF_011045095.1_ASM1104509v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:50,455] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:50,457] [INFO] Found 6/6 markers.
[2024-01-24 13:49:50,513] [INFO] Query marker FASTA was written to GCF_011045095.1_ASM1104509v1_genomic.fna/markers.fasta
[2024-01-24 13:49:50,514] [INFO] Task started: Blastn
[2024-01-24 13:49:50,514] [INFO] Running command: blastn -query GCF_011045095.1_ASM1104509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ad4deb4-da3f-49ec-b0e5-2307a013970e/dqc_reference/reference_markers.fasta -out GCF_011045095.1_ASM1104509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:51,404] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:51,407] [INFO] Selected 10 target genomes.
[2024-01-24 13:49:51,408] [INFO] Target genome list was writen to GCF_011045095.1_ASM1104509v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:51,411] [INFO] Task started: fastANI
[2024-01-24 13:49:51,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg43f01850-590e-46e4-aa90-9e0d97b5372f/GCF_011045095.1_ASM1104509v1_genomic.fna.gz --refList GCF_011045095.1_ASM1104509v1_genomic.fna/target_genomes.txt --output GCF_011045095.1_ASM1104509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:03,081] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:03,082] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ad4deb4-da3f-49ec-b0e5-2307a013970e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:03,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ad4deb4-da3f-49ec-b0e5-2307a013970e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:03,092] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:03,093] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:03,093] [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
Grimontia sedimenti	strain=S25	GCA_011045095.1	2711294	2711294	type	True	100.0	1682	1684	95	conclusive
Grimontia indica	strain=AK16	GCA_000333895.2	1056512	1056512	type	True	94.5781	1491	1684	95	below_threshold
Grimontia celer	strain=CECT 9029	GCA_900055185.1	1796497	1796497	type	True	91.2656	1467	1684	95	below_threshold
Grimontia marina	strain=CECT 8713	GCA_900060185.1	646534	646534	type	True	89.7292	1275	1684	95	below_threshold
Grimontia hollisae	strain=CIP 101886	GCA_000176515.1	673	673	type	True	81.9667	763	1684	95	below_threshold
Photobacterium galatheae	strain=DSM 100496	GCA_023653475.1	1654360	1654360	type	True	77.9143	209	1684	95	below_threshold
Vibrio stylophorae	strain=CECT 7929	GCA_921293875.1	659351	659351	type	True	77.8308	141	1684	95	below_threshold
Vibrio pomeroyi	strain=LMG 20537	GCA_024347595.1	198832	198832	type	True	77.6884	170	1684	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	77.0192	91	1684	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	76.2515	65	1684	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:03,102] [INFO] DFAST Taxonomy check result was written to GCF_011045095.1_ASM1104509v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:03,104] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:03,104] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:03,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ad4deb4-da3f-49ec-b0e5-2307a013970e/dqc_reference/checkm_data
[2024-01-24 13:50:03,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:03,162] [INFO] Task started: CheckM
[2024-01-24 13:50:03,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011045095.1_ASM1104509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011045095.1_ASM1104509v1_genomic.fna/checkm_input GCF_011045095.1_ASM1104509v1_genomic.fna/checkm_result
[2024-01-24 13:50:51,649] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:51,650] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:51,668] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:51,668] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:51,668] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011045095.1_ASM1104509v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:51,669] [INFO] Task started: Blastn
[2024-01-24 13:50:51,669] [INFO] Running command: blastn -query GCF_011045095.1_ASM1104509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ad4deb4-da3f-49ec-b0e5-2307a013970e/dqc_reference/reference_markers_gtdb.fasta -out GCF_011045095.1_ASM1104509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:52,978] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:52,982] [INFO] Selected 6 target genomes.
[2024-01-24 13:50:52,982] [INFO] Target genome list was writen to GCF_011045095.1_ASM1104509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:52,988] [INFO] Task started: fastANI
[2024-01-24 13:50:52,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg43f01850-590e-46e4-aa90-9e0d97b5372f/GCF_011045095.1_ASM1104509v1_genomic.fna.gz --refList GCF_011045095.1_ASM1104509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011045095.1_ASM1104509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:01,492] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:01,504] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:01,504] [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_011045095.1	s__Enterovibrio sedimenti	100.0	1682	1684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000333895.2	s__Enterovibrio indicus	94.5748	1492	1684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	96.52	96.52	0.90	0.90	2	-
GCF_900055185.1	s__Enterovibrio celer	91.258	1468	1684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900060185.1	s__Enterovibrio marinus	89.7359	1274	1684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176515.1	s__Enterovibrio hollisae	81.9667	763	1684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	99.40	99.22	0.97	0.96	10	-
GCA_001310415.1	s__Enterovibrio sp001310415	81.5975	820	1684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	96.68	96.68	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:01,513] [INFO] GTDB search result was written to GCF_011045095.1_ASM1104509v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:01,513] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:01,517] [INFO] DFAST_QC result json was written to GCF_011045095.1_ASM1104509v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:01,517] [INFO] DFAST_QC completed!
[2024-01-24 13:51:01,518] [INFO] Total running time: 0h1m28s