[2024-01-24 13:17:34,083] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:34,090] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:34,091] [INFO] DQC Reference Directory: /var/lib/cwl/stg48a43ea6-76b7-4e48-9b7a-53bbd453be73/dqc_reference
[2024-01-24 13:17:35,507] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:35,508] [INFO] Task started: Prodigal
[2024-01-24 13:17:35,508] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3fd09f9-cac8-4803-89cb-3e794a091a5f/GCF_014636195.1_ASM1463619v1_genomic.fna.gz | prodigal -d GCF_014636195.1_ASM1463619v1_genomic.fna/cds.fna -a GCF_014636195.1_ASM1463619v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:47,568] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:47,569] [INFO] Task started: HMMsearch
[2024-01-24 13:17:47,569] [INFO] Running command: hmmsearch --tblout GCF_014636195.1_ASM1463619v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48a43ea6-76b7-4e48-9b7a-53bbd453be73/dqc_reference/reference_markers.hmm GCF_014636195.1_ASM1463619v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:47,870] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:47,871] [INFO] Found 6/6 markers.
[2024-01-24 13:17:47,908] [INFO] Query marker FASTA was written to GCF_014636195.1_ASM1463619v1_genomic.fna/markers.fasta
[2024-01-24 13:17:47,909] [INFO] Task started: Blastn
[2024-01-24 13:17:47,909] [INFO] Running command: blastn -query GCF_014636195.1_ASM1463619v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48a43ea6-76b7-4e48-9b7a-53bbd453be73/dqc_reference/reference_markers.fasta -out GCF_014636195.1_ASM1463619v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:48,802] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:48,806] [INFO] Selected 23 target genomes.
[2024-01-24 13:17:48,806] [INFO] Target genome list was writen to GCF_014636195.1_ASM1463619v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:48,814] [INFO] Task started: fastANI
[2024-01-24 13:17:48,814] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3fd09f9-cac8-4803-89cb-3e794a091a5f/GCF_014636195.1_ASM1463619v1_genomic.fna.gz --refList GCF_014636195.1_ASM1463619v1_genomic.fna/target_genomes.txt --output GCF_014636195.1_ASM1463619v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:05,258] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:05,259] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg48a43ea6-76b7-4e48-9b7a-53bbd453be73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:05,259] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg48a43ea6-76b7-4e48-9b7a-53bbd453be73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:05,268] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:05,269] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:05,269] [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
Neiella marina	strain=CGMCC 1.10130	GCA_014636195.1	508461	508461	type	True	100.0	1403	1406	95	conclusive
Neiella marina	strain=J221	GCA_002165625.1	508461	508461	type	True	99.996	1389	1406	95	conclusive
Yersinia alsatica	strain=IP38850	GCA_902170305.1	2890317	2890317	type	True	83.1035	61	1406	95	below_threshold
Shewanella decolorationis	strain=S12	GCA_000485795.1	256839	256839	type	True	81.8877	61	1406	95	below_threshold
Neiella holothuriorum	strain=126	GCA_019457915.1	2870530	2870530	type	True	80.2826	464	1406	95	below_threshold
Echinimonas agarilytica	strain=KMM 6351	GCA_023703465.1	1215918	1215918	type	True	77.8991	183	1406	95	below_threshold
Vibrio fluvialis	strain=ATCC 33809	GCA_001558415.2	676	676	type	True	76.7471	52	1406	95	below_threshold
Vibrio fluvialis	strain=NCTC11327	GCA_900460245.1	676	676	type	True	76.7433	53	1406	95	below_threshold
Photobacterium sanctipauli	strain=DSM 100436	GCA_003026495.1	1342794	1342794	type	True	76.4643	55	1406	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:05,274] [INFO] DFAST Taxonomy check result was written to GCF_014636195.1_ASM1463619v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:05,275] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:05,275] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:05,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48a43ea6-76b7-4e48-9b7a-53bbd453be73/dqc_reference/checkm_data
[2024-01-24 13:18:05,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:05,322] [INFO] Task started: CheckM
[2024-01-24 13:18:05,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014636195.1_ASM1463619v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014636195.1_ASM1463619v1_genomic.fna/checkm_input GCF_014636195.1_ASM1463619v1_genomic.fna/checkm_result
[2024-01-24 13:18:47,496] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:47,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:47,513] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:47,513] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:47,514] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014636195.1_ASM1463619v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:47,514] [INFO] Task started: Blastn
[2024-01-24 13:18:47,514] [INFO] Running command: blastn -query GCF_014636195.1_ASM1463619v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg48a43ea6-76b7-4e48-9b7a-53bbd453be73/dqc_reference/reference_markers_gtdb.fasta -out GCF_014636195.1_ASM1463619v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:48,759] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:48,763] [INFO] Selected 24 target genomes.
[2024-01-24 13:18:48,764] [INFO] Target genome list was writen to GCF_014636195.1_ASM1463619v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:48,801] [INFO] Task started: fastANI
[2024-01-24 13:18:48,802] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3fd09f9-cac8-4803-89cb-3e794a091a5f/GCF_014636195.1_ASM1463619v1_genomic.fna.gz --refList GCF_014636195.1_ASM1463619v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014636195.1_ASM1463619v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:04,859] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:04,873] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:04,874] [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_002165625.1	s__Neiella marina	99.996	1389	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Neiellaceae;g__Neiella	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_014773395.1	s__Neiella sp014773395	84.8099	962	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Neiellaceae;g__Neiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000485795.1	s__Shewanella decolorationis	81.8877	61	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.60	97.51	0.93	0.92	3	-
GCF_002282855.1	s__Paraferrimonas sedimenticola	76.9077	51	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Paraferrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900460245.1	s__Vibrio fluvialis	76.7777	52	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.04	97.07	0.93	0.86	63	-
GCF_000176175.1	s__Vibrio furnissii	76.5471	57	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.58	97.97	0.95	0.91	12	-
GCF_003026495.1	s__Photobacterium sanctipauli	76.4267	56	1406	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:04,876] [INFO] GTDB search result was written to GCF_014636195.1_ASM1463619v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:04,877] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:04,880] [INFO] DFAST_QC result json was written to GCF_014636195.1_ASM1463619v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:04,880] [INFO] DFAST_QC completed!
[2024-01-24 13:19:04,880] [INFO] Total running time: 0h1m31s