[2024-01-24 12:23:03,784] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,786] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,786] [INFO] DQC Reference Directory: /var/lib/cwl/stg267f4922-90ec-42db-ad3b-c4a7e53eac6a/dqc_reference
[2024-01-24 12:23:05,099] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,100] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,100] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d8a2329-9bb6-48b3-b1e4-573ef111ae86/GCF_004363665.1_ASM436366v1_genomic.fna.gz | prodigal -d GCF_004363665.1_ASM436366v1_genomic.fna/cds.fna -a GCF_004363665.1_ASM436366v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:21,653] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:21,653] [INFO] Task started: HMMsearch
[2024-01-24 12:23:21,653] [INFO] Running command: hmmsearch --tblout GCF_004363665.1_ASM436366v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg267f4922-90ec-42db-ad3b-c4a7e53eac6a/dqc_reference/reference_markers.hmm GCF_004363665.1_ASM436366v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:21,912] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:21,913] [INFO] Found 6/6 markers.
[2024-01-24 12:23:21,958] [INFO] Query marker FASTA was written to GCF_004363665.1_ASM436366v1_genomic.fna/markers.fasta
[2024-01-24 12:23:21,959] [INFO] Task started: Blastn
[2024-01-24 12:23:21,959] [INFO] Running command: blastn -query GCF_004363665.1_ASM436366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg267f4922-90ec-42db-ad3b-c4a7e53eac6a/dqc_reference/reference_markers.fasta -out GCF_004363665.1_ASM436366v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:22,836] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:22,840] [INFO] Selected 15 target genomes.
[2024-01-24 12:23:22,840] [INFO] Target genome list was writen to GCF_004363665.1_ASM436366v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:22,850] [INFO] Task started: fastANI
[2024-01-24 12:23:22,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d8a2329-9bb6-48b3-b1e4-573ef111ae86/GCF_004363665.1_ASM436366v1_genomic.fna.gz --refList GCF_004363665.1_ASM436366v1_genomic.fna/target_genomes.txt --output GCF_004363665.1_ASM436366v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:36,117] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:36,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg267f4922-90ec-42db-ad3b-c4a7e53eac6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:36,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg267f4922-90ec-42db-ad3b-c4a7e53eac6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:36,129] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:36,129] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:36,129] [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 lutimaris	strain=JCM 13586	GCA_003025555.1	388278	388278	type	True	99.9959	1956	1962	95	conclusive
Photobacterium gaetbulicola	strain=Gung47	GCA_000940995.1	1295392	1295392	type	True	83.7412	1390	1962	95	below_threshold
Photobacterium gaetbulicola	strain=DSM 26887	GCA_003025515.1	1295392	1295392	type	True	83.7256	1376	1962	95	below_threshold
Photobacterium rosenbergii	strain=DSM 19138	GCA_003026455.1	294936	294936	type	True	83.4125	1219	1962	95	below_threshold
Photobacterium sanctipauli	strain=A-394	GCA_000730475.1	1342794	1342794	type	True	80.9638	522	1962	95	below_threshold
Photobacterium sanctipauli	strain=DSM 100436	GCA_003026495.1	1342794	1342794	type	True	80.6277	747	1962	95	below_threshold
Photobacterium aphoticum	strain=KCTC 23057	GCA_014652075.1	754436	754436	type	True	80.3496	602	1962	95	below_threshold
Photobacterium aphoticum	strain=DSM 25995	GCA_003025575.1	754436	754436	type	True	80.3292	557	1962	95	below_threshold
Photobacterium aphoticum	strain=DSM 25995	GCA_001029435.1	754436	754436	type	True	80.2317	607	1962	95	below_threshold
Photobacterium marinum	strain=AK15	GCA_000331515.1	1056511	1056511	type	True	79.8768	504	1962	95	below_threshold
Vibrio panuliri	strain=LBS 2	GCA_008830195.1	1381081	1381081	type	True	78.5162	167	1962	95	below_threshold
Vibrio panuliri	strain=JCM 19500	GCA_009938205.1	1381081	1381081	type	True	78.4617	162	1962	95	below_threshold
Vibrio stylophorae	strain=CECT 7929	GCA_921293875.1	659351	659351	type	True	78.249	128	1962	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:36,131] [INFO] DFAST Taxonomy check result was written to GCF_004363665.1_ASM436366v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:36,131] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:36,132] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:36,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg267f4922-90ec-42db-ad3b-c4a7e53eac6a/dqc_reference/checkm_data
[2024-01-24 12:23:36,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:36,189] [INFO] Task started: CheckM
[2024-01-24 12:23:36,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004363665.1_ASM436366v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004363665.1_ASM436366v1_genomic.fna/checkm_input GCF_004363665.1_ASM436366v1_genomic.fna/checkm_result
[2024-01-24 12:24:24,391] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:24,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:24,410] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:24,410] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:24,411] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004363665.1_ASM436366v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:24,411] [INFO] Task started: Blastn
[2024-01-24 12:24:24,411] [INFO] Running command: blastn -query GCF_004363665.1_ASM436366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg267f4922-90ec-42db-ad3b-c4a7e53eac6a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004363665.1_ASM436366v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:25,646] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:25,649] [INFO] Selected 8 target genomes.
[2024-01-24 12:24:25,650] [INFO] Target genome list was writen to GCF_004363665.1_ASM436366v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:25,654] [INFO] Task started: fastANI
[2024-01-24 12:24:25,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d8a2329-9bb6-48b3-b1e4-573ef111ae86/GCF_004363665.1_ASM436366v1_genomic.fna.gz --refList GCF_004363665.1_ASM436366v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004363665.1_ASM436366v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:34,821] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:34,829] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:34,829] [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_003025555.1	s__Photobacterium lutimaris	99.9959	1956	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000940995.1	s__Photobacterium gaetbulicola	83.7345	1391	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.90	95.81	0.93	0.87	3	-
GCF_003026455.1	s__Photobacterium rosenbergii	83.4125	1219	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.32	95.32	0.83	0.83	2	-
GCF_003026495.1	s__Photobacterium sanctipauli	80.6453	746	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001029435.1	s__Photobacterium aphoticum	80.2317	607	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.09	97.29	0.97	0.93	4	-
GCF_009910675.1	s__Photobacterium alginatilyticum	80.0924	586	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001029445.1	s__Photobacterium aquae	80.0509	559	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331515.1	s__Photobacterium marinum	79.8629	505	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	96.66	96.66	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:34,831] [INFO] GTDB search result was written to GCF_004363665.1_ASM436366v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:34,831] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:34,835] [INFO] DFAST_QC result json was written to GCF_004363665.1_ASM436366v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:34,835] [INFO] DFAST_QC completed!
[2024-01-24 12:24:34,835] [INFO] Total running time: 0h1m31s