[2024-01-25 19:24:50,848] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:24:50,849] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:24:50,850] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bdd26ee-ddf6-4058-991b-3ab5c1956600/dqc_reference
[2024-01-25 19:24:52,042] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:24:52,043] [INFO] Task started: Prodigal
[2024-01-25 19:24:52,043] [INFO] Running command: gunzip -c /var/lib/cwl/stg558c6303-e3b4-4eaf-aa87-9810451b0971/GCF_003025515.1_ASM302551v1_genomic.fna.gz | prodigal -d GCF_003025515.1_ASM302551v1_genomic.fna/cds.fna -a GCF_003025515.1_ASM302551v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:25:06,764] [INFO] Task succeeded: Prodigal
[2024-01-25 19:25:06,765] [INFO] Task started: HMMsearch
[2024-01-25 19:25:06,765] [INFO] Running command: hmmsearch --tblout GCF_003025515.1_ASM302551v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bdd26ee-ddf6-4058-991b-3ab5c1956600/dqc_reference/reference_markers.hmm GCF_003025515.1_ASM302551v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:25:07,047] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:25:07,048] [INFO] Found 6/6 markers.
[2024-01-25 19:25:07,101] [INFO] Query marker FASTA was written to GCF_003025515.1_ASM302551v1_genomic.fna/markers.fasta
[2024-01-25 19:25:07,102] [INFO] Task started: Blastn
[2024-01-25 19:25:07,102] [INFO] Running command: blastn -query GCF_003025515.1_ASM302551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bdd26ee-ddf6-4058-991b-3ab5c1956600/dqc_reference/reference_markers.fasta -out GCF_003025515.1_ASM302551v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:25:07,900] [INFO] Task succeeded: Blastn
[2024-01-25 19:25:07,903] [INFO] Selected 13 target genomes.
[2024-01-25 19:25:07,903] [INFO] Target genome list was writen to GCF_003025515.1_ASM302551v1_genomic.fna/target_genomes.txt
[2024-01-25 19:25:07,943] [INFO] Task started: fastANI
[2024-01-25 19:25:07,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg558c6303-e3b4-4eaf-aa87-9810451b0971/GCF_003025515.1_ASM302551v1_genomic.fna.gz --refList GCF_003025515.1_ASM302551v1_genomic.fna/target_genomes.txt --output GCF_003025515.1_ASM302551v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:25:22,659] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:22,660] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bdd26ee-ddf6-4058-991b-3ab5c1956600/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:25:22,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bdd26ee-ddf6-4058-991b-3ab5c1956600/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:25:22,669] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:25:22,669] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:25:22,669] [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 gaetbulicola	strain=DSM 26887	GCA_003025515.1	1295392	1295392	type	True	100.0	1919	1922	95	conclusive
Photobacterium gaetbulicola	strain=Gung47	GCA_000940995.1	1295392	1295392	type	True	99.9967	1908	1922	95	conclusive
Photobacterium rosenbergii	strain=DSM 19138	GCA_003026455.1	294936	294936	type	True	84.84	1329	1922	95	below_threshold
Photobacterium lutimaris	strain=JCM 13586	GCA_003025555.1	388278	388278	type	True	83.7887	1364	1922	95	below_threshold
Photobacterium sanctipauli	strain=A-394	GCA_000730475.1	1342794	1342794	type	True	81.2522	531	1922	95	below_threshold
Photobacterium sanctipauli	strain=DSM 100436	GCA_003026495.1	1342794	1342794	type	True	80.9309	747	1922	95	below_threshold
Photobacterium aquae	strain=CGMCC 1.12159	GCA_001029445.1	1195763	1195763	type	True	80.2684	600	1922	95	below_threshold
Photobacterium ganghwense	strain=JCM 12487	GCA_003025595.1	320778	320778	type	True	80.1109	613	1922	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	79.2354	367	1922	95	below_threshold
Photobacterium galatheae	strain=DSM 100496	GCA_023653475.1	1654360	1654360	type	True	78.5392	327	1922	95	below_threshold
Photobacterium salinisoli	strain=LAM9072	GCA_003614885.1	1616783	1616783	type	True	78.4139	321	1922	95	below_threshold
Vibrio rhizosphaerae	strain=LMG 23790	GCA_024347095.1	398736	398736	type	True	77.9069	83	1922	95	below_threshold
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	77.8674	171	1922	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:25:22,671] [INFO] DFAST Taxonomy check result was written to GCF_003025515.1_ASM302551v1_genomic.fna/tc_result.tsv
[2024-01-25 19:25:22,672] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:25:22,672] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:25:22,672] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bdd26ee-ddf6-4058-991b-3ab5c1956600/dqc_reference/checkm_data
[2024-01-25 19:25:22,673] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:25:22,731] [INFO] Task started: CheckM
[2024-01-25 19:25:22,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003025515.1_ASM302551v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003025515.1_ASM302551v1_genomic.fna/checkm_input GCF_003025515.1_ASM302551v1_genomic.fna/checkm_result
[2024-01-25 19:26:07,462] [INFO] Task succeeded: CheckM
[2024-01-25 19:26:07,463] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:26:07,501] [INFO] ===== Completeness check finished =====
[2024-01-25 19:26:07,501] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:26:07,502] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003025515.1_ASM302551v1_genomic.fna/markers.fasta)
[2024-01-25 19:26:07,502] [INFO] Task started: Blastn
[2024-01-25 19:26:07,503] [INFO] Running command: blastn -query GCF_003025515.1_ASM302551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bdd26ee-ddf6-4058-991b-3ab5c1956600/dqc_reference/reference_markers_gtdb.fasta -out GCF_003025515.1_ASM302551v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:26:08,763] [INFO] Task succeeded: Blastn
[2024-01-25 19:26:08,765] [INFO] Selected 11 target genomes.
[2024-01-25 19:26:08,765] [INFO] Target genome list was writen to GCF_003025515.1_ASM302551v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:26:08,773] [INFO] Task started: fastANI
[2024-01-25 19:26:08,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg558c6303-e3b4-4eaf-aa87-9810451b0971/GCF_003025515.1_ASM302551v1_genomic.fna.gz --refList GCF_003025515.1_ASM302551v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003025515.1_ASM302551v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:26:22,782] [INFO] Task succeeded: fastANI
[2024-01-25 19:26:22,789] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:26:22,789] [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_000940995.1	s__Photobacterium gaetbulicola	99.9967	1908	1922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.90	95.81	0.93	0.87	3	conclusive
GCF_003026455.1	s__Photobacterium rosenbergii	84.8417	1330	1922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.32	95.32	0.83	0.83	2	-
GCF_003025555.1	s__Photobacterium lutimaris	83.7926	1363	1922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003026495.1	s__Photobacterium sanctipauli	80.9348	746	1922	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	80.275	598	1922	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	80.273	637	1922	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	80.1298	622	1922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001939735.1	s__Photobacterium proteolyticum	80.1142	625	1922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003025595.1	s__Photobacterium ganghwense	80.0979	614	1922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.50	98.82	0.97	0.96	4	-
GCF_000331515.1	s__Photobacterium marinum	79.9744	532	1922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	96.66	96.66	0.88	0.88	2	-
GCF_001650345.1	s__Photobacterium jeanii	79.7738	405	1922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:26:22,791] [INFO] GTDB search result was written to GCF_003025515.1_ASM302551v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:26:22,791] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:26:22,794] [INFO] DFAST_QC result json was written to GCF_003025515.1_ASM302551v1_genomic.fna/dqc_result.json
[2024-01-25 19:26:22,794] [INFO] DFAST_QC completed!
[2024-01-25 19:26:22,794] [INFO] Total running time: 0h1m32s