[2024-01-24 12:16:08,740] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:08,742] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:08,742] [INFO] DQC Reference Directory: /var/lib/cwl/stg6396c021-ed38-42b9-9537-5dd5780b77f0/dqc_reference
[2024-01-24 12:16:09,987] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:09,988] [INFO] Task started: Prodigal
[2024-01-24 12:16:09,988] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d34bdd0-29da-41e4-b50d-f279719947d3/GCF_005886105.2_ASM588610v2_genomic.fna.gz | prodigal -d GCF_005886105.2_ASM588610v2_genomic.fna/cds.fna -a GCF_005886105.2_ASM588610v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:22,452] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:22,452] [INFO] Task started: HMMsearch
[2024-01-24 12:16:22,452] [INFO] Running command: hmmsearch --tblout GCF_005886105.2_ASM588610v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6396c021-ed38-42b9-9537-5dd5780b77f0/dqc_reference/reference_markers.hmm GCF_005886105.2_ASM588610v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:22,787] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:22,788] [INFO] Found 6/6 markers.
[2024-01-24 12:16:22,834] [INFO] Query marker FASTA was written to GCF_005886105.2_ASM588610v2_genomic.fna/markers.fasta
[2024-01-24 12:16:22,835] [INFO] Task started: Blastn
[2024-01-24 12:16:22,835] [INFO] Running command: blastn -query GCF_005886105.2_ASM588610v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6396c021-ed38-42b9-9537-5dd5780b77f0/dqc_reference/reference_markers.fasta -out GCF_005886105.2_ASM588610v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:23,600] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:23,603] [INFO] Selected 9 target genomes.
[2024-01-24 12:16:23,604] [INFO] Target genome list was writen to GCF_005886105.2_ASM588610v2_genomic.fna/target_genomes.txt
[2024-01-24 12:16:23,607] [INFO] Task started: fastANI
[2024-01-24 12:16:23,607] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d34bdd0-29da-41e4-b50d-f279719947d3/GCF_005886105.2_ASM588610v2_genomic.fna.gz --refList GCF_005886105.2_ASM588610v2_genomic.fna/target_genomes.txt --output GCF_005886105.2_ASM588610v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:34,800] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:34,801] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6396c021-ed38-42b9-9537-5dd5780b77f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:34,801] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6396c021-ed38-42b9-9537-5dd5780b77f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:34,809] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:16:34,809] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:34,809] [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 galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	100.0	1785	1785	95	conclusive
Pseudoalteromonas flavipulchra	strain=LMG 20361	GCA_014596995.1	137779	137779	suspected-type	True	92.777	1442	1785	95	below_threshold
Pseudoalteromonas flavipulchra	strain=NCIMB 2033	GCA_014858715.1	137779	137779	suspected-type	True	92.7452	1450	1785	95	below_threshold
Pseudoalteromonas piscicida	strain=JCM 20779	GCA_000238315.4	43662	43662	type	True	92.5693	1431	1785	95	below_threshold
Pseudoalteromonas piscicida	strain=ATCC 15057	GCA_000382005.1	43662	43662	type	True	92.556	1394	1785	95	below_threshold
Vibrio tarriae	strain=2521-89	GCA_002216685.1	2014742	2014742	type	True	79.1681	56	1785	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	78.2668	211	1785	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:34,811] [INFO] DFAST Taxonomy check result was written to GCF_005886105.2_ASM588610v2_genomic.fna/tc_result.tsv
[2024-01-24 12:16:34,811] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:34,812] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:34,812] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6396c021-ed38-42b9-9537-5dd5780b77f0/dqc_reference/checkm_data
[2024-01-24 12:16:34,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:34,868] [INFO] Task started: CheckM
[2024-01-24 12:16:34,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005886105.2_ASM588610v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005886105.2_ASM588610v2_genomic.fna/checkm_input GCF_005886105.2_ASM588610v2_genomic.fna/checkm_result
[2024-01-24 12:17:14,849] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:14,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:14,874] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:14,874] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:14,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005886105.2_ASM588610v2_genomic.fna/markers.fasta)
[2024-01-24 12:17:14,875] [INFO] Task started: Blastn
[2024-01-24 12:17:14,875] [INFO] Running command: blastn -query GCF_005886105.2_ASM588610v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6396c021-ed38-42b9-9537-5dd5780b77f0/dqc_reference/reference_markers_gtdb.fasta -out GCF_005886105.2_ASM588610v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:16,063] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:16,067] [INFO] Selected 8 target genomes.
[2024-01-24 12:17:16,067] [INFO] Target genome list was writen to GCF_005886105.2_ASM588610v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:16,073] [INFO] Task started: fastANI
[2024-01-24 12:17:16,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d34bdd0-29da-41e4-b50d-f279719947d3/GCF_005886105.2_ASM588610v2_genomic.fna.gz --refList GCF_005886105.2_ASM588610v2_genomic.fna/target_genomes_gtdb.txt --output GCF_005886105.2_ASM588610v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:28,289] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:28,300] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:28,300] [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_004103285.1	s__Pseudoalteromonas sp004103285	99.2068	1633	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.27	99.27	0.97	0.97	2	conclusive
GCF_005886535.1	s__Pseudoalteromonas sp005886535	94.4164	1349	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000814665.1	s__Pseudoalteromonas elyakovii	92.8569	1440	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0982	98.47	97.40	0.94	0.89	9	-
GCF_002289345.1	s__Pseudoalteromonas sp002289345	92.8049	1365	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.3013	N/A	N/A	N/A	N/A	1	-
GCF_002850255.1	s__Pseudoalteromonas sp002850255	92.7063	1445	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.4968	98.33	98.31	0.92	0.91	5	-
GCF_000238315.3	s__Pseudoalteromonas piscicida	92.5731	1432	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0982	97.60	97.35	0.90	0.88	13	-
GCF_016695175.1	s__Pseudoalteromonas sp002591815	92.5567	1431	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.6666	100.00	100.00	1.00	1.00	2	-
GCF_002208135.1	s__Pseudoalteromonas piscicida_A	91.3208	1437	1785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.45	98.90	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:28,302] [INFO] GTDB search result was written to GCF_005886105.2_ASM588610v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:28,302] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:28,306] [INFO] DFAST_QC result json was written to GCF_005886105.2_ASM588610v2_genomic.fna/dqc_result.json
[2024-01-24 12:17:28,306] [INFO] DFAST_QC completed!
[2024-01-24 12:17:28,306] [INFO] Total running time: 0h1m20s