[2024-01-24 13:31:12,017] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:12,019] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:12,019] [INFO] DQC Reference Directory: /var/lib/cwl/stg36e26729-1d15-4b21-8190-80d7935dcee7/dqc_reference
[2024-01-24 13:31:13,235] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:13,236] [INFO] Task started: Prodigal
[2024-01-24 13:31:13,237] [INFO] Running command: gunzip -c /var/lib/cwl/stg57cb9dce-fb29-4688-96b6-c6ea047d8269/GCF_001596795.1_ASM159679v1_genomic.fna.gz | prodigal -d GCF_001596795.1_ASM159679v1_genomic.fna/cds.fna -a GCF_001596795.1_ASM159679v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:21,493] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:21,494] [INFO] Task started: HMMsearch
[2024-01-24 13:31:21,494] [INFO] Running command: hmmsearch --tblout GCF_001596795.1_ASM159679v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36e26729-1d15-4b21-8190-80d7935dcee7/dqc_reference/reference_markers.hmm GCF_001596795.1_ASM159679v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:21,719] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:21,720] [INFO] Found 6/6 markers.
[2024-01-24 13:31:21,755] [INFO] Query marker FASTA was written to GCF_001596795.1_ASM159679v1_genomic.fna/markers.fasta
[2024-01-24 13:31:21,756] [INFO] Task started: Blastn
[2024-01-24 13:31:21,756] [INFO] Running command: blastn -query GCF_001596795.1_ASM159679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36e26729-1d15-4b21-8190-80d7935dcee7/dqc_reference/reference_markers.fasta -out GCF_001596795.1_ASM159679v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:22,407] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:22,411] [INFO] Selected 15 target genomes.
[2024-01-24 13:31:22,411] [INFO] Target genome list was writen to GCF_001596795.1_ASM159679v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:22,419] [INFO] Task started: fastANI
[2024-01-24 13:31:22,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg57cb9dce-fb29-4688-96b6-c6ea047d8269/GCF_001596795.1_ASM159679v1_genomic.fna.gz --refList GCF_001596795.1_ASM159679v1_genomic.fna/target_genomes.txt --output GCF_001596795.1_ASM159679v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:35,429] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:35,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36e26729-1d15-4b21-8190-80d7935dcee7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:35,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36e26729-1d15-4b21-8190-80d7935dcee7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:35,442] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:31:35,442] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:31:35,443] [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
Pseudoalteromonas espejiana	strain=ATCC 29659	GCA_002221525.1	28107	28107	type	True	87.6011	1205	1443	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	87.5487	1163	1443	95	below_threshold
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	86.0293	1082	1443	95	below_threshold
Pseudoalteromonas carrageenovora	strain=ATCC 43555	GCA_900239935.1	227	227	type	True	86.0008	1126	1443	95	below_threshold
Pseudoalteromonas carrageenovora	strain=IAM 12662	GCA_014925295.1	227	227	type	True	85.8961	1147	1443	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	83.042	1037	1443	95	below_threshold
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	81.6163	767	1443	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	81.4455	798	1443	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KCTC 12958	GCA_001455325.1	152297	152297	suspected-type	True	81.4082	794	1443	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	81.3901	796	1443	95	below_threshold
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	81.3874	767	1443	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	80.1854	594	1443	95	below_threshold
Vibrio nitrifigilis	strain=NFV-1	GCA_015686695.1	2789781	2789781	type	True	76.3862	50	1443	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	76.3652	67	1443	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	76.332	71	1443	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:35,444] [INFO] DFAST Taxonomy check result was written to GCF_001596795.1_ASM159679v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:35,445] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:35,445] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:35,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36e26729-1d15-4b21-8190-80d7935dcee7/dqc_reference/checkm_data
[2024-01-24 13:31:35,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:35,490] [INFO] Task started: CheckM
[2024-01-24 13:31:35,490] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001596795.1_ASM159679v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001596795.1_ASM159679v1_genomic.fna/checkm_input GCF_001596795.1_ASM159679v1_genomic.fna/checkm_result
[2024-01-24 13:32:04,406] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:04,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:04,428] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:04,429] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:04,429] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001596795.1_ASM159679v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:04,429] [INFO] Task started: Blastn
[2024-01-24 13:32:04,429] [INFO] Running command: blastn -query GCF_001596795.1_ASM159679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36e26729-1d15-4b21-8190-80d7935dcee7/dqc_reference/reference_markers_gtdb.fasta -out GCF_001596795.1_ASM159679v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:05,354] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:05,357] [INFO] Selected 8 target genomes.
[2024-01-24 13:32:05,357] [INFO] Target genome list was writen to GCF_001596795.1_ASM159679v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:05,363] [INFO] Task started: fastANI
[2024-01-24 13:32:05,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg57cb9dce-fb29-4688-96b6-c6ea047d8269/GCF_001596795.1_ASM159679v1_genomic.fna.gz --refList GCF_001596795.1_ASM159679v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001596795.1_ASM159679v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:14,201] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:14,209] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:14,210] [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
GCA_007988745.1	s__Pseudoalteromonas atlantica	97.8571	1291	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.93	97.66	0.89	0.85	29	conclusive
GCF_001401805.1	s__Pseudoalteromonas sp001401805	92.6889	1246	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.16	97.37	0.91	0.90	5	-
GCF_002221525.1	s__Pseudoalteromonas espejiana	87.5986	1205	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900239935.1	s__Pseudoalteromonas carrageenovora	86.0029	1125	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.00	96.44	0.97	0.91	6	-
GCF_018100985.1	s__Pseudoalteromonas sp018100985	85.0828	1004	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.38	98.38	0.93	0.93	2	-
GCF_000238275.3	s__Pseudoalteromonas undina	81.598	769	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.09	0.91	0.86	14	-
GCF_004328665.1	s__Pseudoalteromonas sp001974855	81.4401	743	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.16	95.35	0.86	0.83	5	-
GCF_002310835.1	s__Pseudoalteromonas tetraodonis	81.3815	797	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	96.28	0.91	0.84	28	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:14,212] [INFO] GTDB search result was written to GCF_001596795.1_ASM159679v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:14,213] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:14,217] [INFO] DFAST_QC result json was written to GCF_001596795.1_ASM159679v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:14,217] [INFO] DFAST_QC completed!
[2024-01-24 13:32:14,217] [INFO] Total running time: 0h1m2s