[2024-01-24 13:48:43,122] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:43,125] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:43,125] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ea788d4-427e-4666-811c-a478384fb02b/dqc_reference
[2024-01-24 13:48:44,481] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:44,482] [INFO] Task started: Prodigal
[2024-01-24 13:48:44,483] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b9be2eb-055f-437e-8f68-ea837d73ac73/GCF_002954725.1_ASM295472v1_genomic.fna.gz | prodigal -d GCF_002954725.1_ASM295472v1_genomic.fna/cds.fna -a GCF_002954725.1_ASM295472v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:48:54,401] [INFO] Task succeeded: Prodigal
[2024-01-24 13:48:54,401] [INFO] Task started: HMMsearch
[2024-01-24 13:48:54,401] [INFO] Running command: hmmsearch --tblout GCF_002954725.1_ASM295472v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ea788d4-427e-4666-811c-a478384fb02b/dqc_reference/reference_markers.hmm GCF_002954725.1_ASM295472v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:48:54,704] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:48:54,705] [INFO] Found 6/6 markers.
[2024-01-24 13:48:54,744] [INFO] Query marker FASTA was written to GCF_002954725.1_ASM295472v1_genomic.fna/markers.fasta
[2024-01-24 13:48:54,745] [INFO] Task started: Blastn
[2024-01-24 13:48:54,745] [INFO] Running command: blastn -query GCF_002954725.1_ASM295472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ea788d4-427e-4666-811c-a478384fb02b/dqc_reference/reference_markers.fasta -out GCF_002954725.1_ASM295472v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:55,560] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:55,565] [INFO] Selected 11 target genomes.
[2024-01-24 13:48:55,565] [INFO] Target genome list was writen to GCF_002954725.1_ASM295472v1_genomic.fna/target_genomes.txt
[2024-01-24 13:48:55,570] [INFO] Task started: fastANI
[2024-01-24 13:48:55,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b9be2eb-055f-437e-8f68-ea837d73ac73/GCF_002954725.1_ASM295472v1_genomic.fna.gz --refList GCF_002954725.1_ASM295472v1_genomic.fna/target_genomes.txt --output GCF_002954725.1_ASM295472v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:06,813] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:06,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ea788d4-427e-4666-811c-a478384fb02b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:06,814] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ea788d4-427e-4666-811c-a478384fb02b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:06,823] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:49:06,823] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:06,823] [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
Photobacterium phosphoreum	strain=JCM 21184	GCA_002954725.1	659	659	type	True	99.9884	1494	1514	95	conclusive
Photobacterium phosphoreum	strain=ATCC 11040	GCA_003026275.1	659	659	type	True	99.9588	1452	1514	95	conclusive
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	99.9131	1420	1514	95	conclusive
Photobacterium iliopiscarium	strain=ATCC 51760	GCA_003026395.1	56192	56192	type	True	87.1379	1163	1514	95	below_threshold
Photobacterium carnosum	strain=TMW 2.2021	GCA_002849605.1	2023717	2023717	type	True	87.1197	1137	1514	95	below_threshold
Photobacterium iliopiscarium	strain=ATCC 51760	GCA_000950265.1	56192	56192	type	True	87.088	1164	1514	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	86.0689	1119	1514	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_900166975.1	1935446	1935446	type	True	86.044	1117	1514	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	79.1924	348	1514	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	78.0396	135	1514	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	77.9495	183	1514	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:06,825] [INFO] DFAST Taxonomy check result was written to GCF_002954725.1_ASM295472v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:06,826] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:06,826] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:06,826] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ea788d4-427e-4666-811c-a478384fb02b/dqc_reference/checkm_data
[2024-01-24 13:49:06,828] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:06,874] [INFO] Task started: CheckM
[2024-01-24 13:49:06,875] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002954725.1_ASM295472v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002954725.1_ASM295472v1_genomic.fna/checkm_input GCF_002954725.1_ASM295472v1_genomic.fna/checkm_result
[2024-01-24 13:49:41,442] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:41,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:41,461] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:41,462] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:41,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002954725.1_ASM295472v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:41,462] [INFO] Task started: Blastn
[2024-01-24 13:49:41,463] [INFO] Running command: blastn -query GCF_002954725.1_ASM295472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ea788d4-427e-4666-811c-a478384fb02b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002954725.1_ASM295472v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:42,779] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:42,784] [INFO] Selected 6 target genomes.
[2024-01-24 13:49:42,785] [INFO] Target genome list was writen to GCF_002954725.1_ASM295472v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:42,791] [INFO] Task started: fastANI
[2024-01-24 13:49:42,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b9be2eb-055f-437e-8f68-ea837d73ac73/GCF_002954725.1_ASM295472v1_genomic.fna.gz --refList GCF_002954725.1_ASM295472v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002954725.1_ASM295472v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:50,285] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:50,298] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:50,299] [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_002954725.1	s__Photobacterium phosphoreum	99.9884	1494	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.41	96.65	0.93	0.88	23	conclusive
GCF_003026395.1	s__Photobacterium iliopiscarium	87.1379	1163	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.31	98.95	0.95	0.91	7	-
GCF_002849605.1	s__Photobacterium carnosum	87.1125	1137	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.77	98.77	0.93	0.93	2	-
GCF_003026355.1	s__Photobacterium kishitanii	86.7461	1248	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.67	97.61	0.95	0.91	24	-
GCF_900166965.1	s__Photobacterium piscicola	86.5512	1220	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.92	98.92	0.94	0.94	2	-
GCF_900166975.1	s__Photobacterium toruni	86.0426	1117	1514	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 13:49:50,300] [INFO] GTDB search result was written to GCF_002954725.1_ASM295472v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:50,301] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:50,304] [INFO] DFAST_QC result json was written to GCF_002954725.1_ASM295472v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:50,304] [INFO] DFAST_QC completed!
[2024-01-24 13:49:50,304] [INFO] Total running time: 0h1m7s