[2024-01-24 13:41:41,049] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:41,052] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:41,052] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3395c73-31f1-455f-b06f-11a1bf958bf3/dqc_reference
[2024-01-24 13:41:42,306] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:42,307] [INFO] Task started: Prodigal
[2024-01-24 13:41:42,307] [INFO] Running command: gunzip -c /var/lib/cwl/stgdacb04ad-796d-43bf-98fe-b7aab9a5c238/GCF_000950265.1_CFSAN029431_01.0_genomic.fna.gz | prodigal -d GCF_000950265.1_CFSAN029431_01.0_genomic.fna/cds.fna -a GCF_000950265.1_CFSAN029431_01.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:50,891] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:50,891] [INFO] Task started: HMMsearch
[2024-01-24 13:41:50,892] [INFO] Running command: hmmsearch --tblout GCF_000950265.1_CFSAN029431_01.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3395c73-31f1-455f-b06f-11a1bf958bf3/dqc_reference/reference_markers.hmm GCF_000950265.1_CFSAN029431_01.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:51,232] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:51,233] [INFO] Found 6/6 markers.
[2024-01-24 13:41:51,270] [INFO] Query marker FASTA was written to GCF_000950265.1_CFSAN029431_01.0_genomic.fna/markers.fasta
[2024-01-24 13:41:51,270] [INFO] Task started: Blastn
[2024-01-24 13:41:51,270] [INFO] Running command: blastn -query GCF_000950265.1_CFSAN029431_01.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3395c73-31f1-455f-b06f-11a1bf958bf3/dqc_reference/reference_markers.fasta -out GCF_000950265.1_CFSAN029431_01.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:52,087] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:52,092] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:52,092] [INFO] Target genome list was writen to GCF_000950265.1_CFSAN029431_01.0_genomic.fna/target_genomes.txt
[2024-01-24 13:41:52,097] [INFO] Task started: fastANI
[2024-01-24 13:41:52,097] [INFO] Running command: fastANI --query /var/lib/cwl/stgdacb04ad-796d-43bf-98fe-b7aab9a5c238/GCF_000950265.1_CFSAN029431_01.0_genomic.fna.gz --refList GCF_000950265.1_CFSAN029431_01.0_genomic.fna/target_genomes.txt --output GCF_000950265.1_CFSAN029431_01.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:03,617] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:03,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3395c73-31f1-455f-b06f-11a1bf958bf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:03,619] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3395c73-31f1-455f-b06f-11a1bf958bf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:03,639] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:42:03,639] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:03,640] [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 iliopiscarium	strain=ATCC 51760	GCA_000950265.1	56192	56192	type	True	100.0	1368	1374	95	conclusive
Photobacterium iliopiscarium	strain=ATCC 51760	GCA_003026395.1	56192	56192	type	True	99.9489	1367	1374	95	conclusive
Photobacterium carnosum	strain=TMW 2.2021	GCA_002849605.1	2023717	2023717	type	True	92.8326	1168	1374	95	below_threshold
Photobacterium piscicola	strain=type strain: NCCB 100098	GCA_900166965.1	1378299	1378299	type	True	90.8236	1252	1374	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_900166975.1	1935446	1935446	type	True	87.32	1122	1374	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	87.2424	1140	1374	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_003026275.1	659	659	type	True	87.1394	1135	1374	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	87.0903	1142	1374	95	below_threshold
Photobacterium phosphoreum	strain=JCM 21184	GCA_002954725.1	659	659	type	True	87.0714	1143	1374	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	78.9544	334	1374	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	78.6535	357	1374	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	77.3671	172	1374	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:03,642] [INFO] DFAST Taxonomy check result was written to GCF_000950265.1_CFSAN029431_01.0_genomic.fna/tc_result.tsv
[2024-01-24 13:42:03,642] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:03,643] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:03,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3395c73-31f1-455f-b06f-11a1bf958bf3/dqc_reference/checkm_data
[2024-01-24 13:42:03,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:03,692] [INFO] Task started: CheckM
[2024-01-24 13:42:03,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000950265.1_CFSAN029431_01.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000950265.1_CFSAN029431_01.0_genomic.fna/checkm_input GCF_000950265.1_CFSAN029431_01.0_genomic.fna/checkm_result
[2024-01-24 13:42:34,898] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:34,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:34,919] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:34,920] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:34,920] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000950265.1_CFSAN029431_01.0_genomic.fna/markers.fasta)
[2024-01-24 13:42:34,921] [INFO] Task started: Blastn
[2024-01-24 13:42:34,921] [INFO] Running command: blastn -query GCF_000950265.1_CFSAN029431_01.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3395c73-31f1-455f-b06f-11a1bf958bf3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000950265.1_CFSAN029431_01.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:36,150] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:36,153] [INFO] Selected 7 target genomes.
[2024-01-24 13:42:36,153] [INFO] Target genome list was writen to GCF_000950265.1_CFSAN029431_01.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:36,177] [INFO] Task started: fastANI
[2024-01-24 13:42:36,177] [INFO] Running command: fastANI --query /var/lib/cwl/stgdacb04ad-796d-43bf-98fe-b7aab9a5c238/GCF_000950265.1_CFSAN029431_01.0_genomic.fna.gz --refList GCF_000950265.1_CFSAN029431_01.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000950265.1_CFSAN029431_01.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:44,533] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:44,543] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:44,544] [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_003026395.1	s__Photobacterium iliopiscarium	99.9489	1367	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.31	98.95	0.95	0.91	7	conclusive
GCF_002849605.1	s__Photobacterium carnosum	92.8172	1169	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.77	98.77	0.93	0.93	2	-
GCF_900166965.1	s__Photobacterium piscicola	90.8236	1252	1374	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	87.3131	1124	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954725.1	s__Photobacterium phosphoreum	87.0652	1143	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.41	96.65	0.93	0.88	23	-
GCF_003026355.1	s__Photobacterium kishitanii	85.393	1104	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.67	97.61	0.95	0.91	24	-
GCF_002954455.1	s__Photobacterium aquimaris	84.958	1064	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.51	95.34	0.95	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:44,546] [INFO] GTDB search result was written to GCF_000950265.1_CFSAN029431_01.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:44,546] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:44,549] [INFO] DFAST_QC result json was written to GCF_000950265.1_CFSAN029431_01.0_genomic.fna/dqc_result.json
[2024-01-24 13:42:44,550] [INFO] DFAST_QC completed!
[2024-01-24 13:42:44,550] [INFO] Total running time: 0h1m4s