[2024-01-25 19:53:35,495] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:35,496] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:35,496] [INFO] DQC Reference Directory: /var/lib/cwl/stgfaf359d0-1489-4a22-8a27-c3c977de1fa3/dqc_reference
[2024-01-25 19:53:36,606] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:36,606] [INFO] Task started: Prodigal
[2024-01-25 19:53:36,607] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd4636cf-41f6-46a3-8ad6-205b42cdfe58/GCF_014925355.1_ASM1492535v1_genomic.fna.gz | prodigal -d GCF_014925355.1_ASM1492535v1_genomic.fna/cds.fna -a GCF_014925355.1_ASM1492535v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:53:46,314] [INFO] Task succeeded: Prodigal
[2024-01-25 19:53:46,314] [INFO] Task started: HMMsearch
[2024-01-25 19:53:46,314] [INFO] Running command: hmmsearch --tblout GCF_014925355.1_ASM1492535v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfaf359d0-1489-4a22-8a27-c3c977de1fa3/dqc_reference/reference_markers.hmm GCF_014925355.1_ASM1492535v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:53:46,617] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:53:46,618] [INFO] Found 6/6 markers.
[2024-01-25 19:53:46,657] [INFO] Query marker FASTA was written to GCF_014925355.1_ASM1492535v1_genomic.fna/markers.fasta
[2024-01-25 19:53:46,657] [INFO] Task started: Blastn
[2024-01-25 19:53:46,657] [INFO] Running command: blastn -query GCF_014925355.1_ASM1492535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfaf359d0-1489-4a22-8a27-c3c977de1fa3/dqc_reference/reference_markers.fasta -out GCF_014925355.1_ASM1492535v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:47,348] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:47,351] [INFO] Selected 11 target genomes.
[2024-01-25 19:53:47,351] [INFO] Target genome list was writen to GCF_014925355.1_ASM1492535v1_genomic.fna/target_genomes.txt
[2024-01-25 19:53:47,355] [INFO] Task started: fastANI
[2024-01-25 19:53:47,355] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd4636cf-41f6-46a3-8ad6-205b42cdfe58/GCF_014925355.1_ASM1492535v1_genomic.fna.gz --refList GCF_014925355.1_ASM1492535v1_genomic.fna/target_genomes.txt --output GCF_014925355.1_ASM1492535v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:53:58,039] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:58,039] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfaf359d0-1489-4a22-8a27-c3c977de1fa3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:53:58,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfaf359d0-1489-4a22-8a27-c3c977de1fa3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:53:58,047] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:53:58,047] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:53:58,047] [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 prydzensis	strain=ACAM 620	GCA_014925355.1	182141	182141	type	True	100.0	1723	1725	95	conclusive
Pseudoalteromonas prydzensis	strain=DSM 14232	GCA_001661495.1	182141	182141	type	True	99.977	1694	1725	95	conclusive
Pseudoalteromonas ostreae	strain=hOe-66	GCA_018069805.1	2774154	2774154	type	True	86.0819	1096	1725	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	85.8894	1230	1725	95	below_threshold
Pseudoalteromonas neustonica	strain=PAMC 28425	GCA_001653135.1	1840331	1840331	type	True	82.2287	916	1725	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	80.5482	647	1725	95	below_threshold
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	80.3886	616	1725	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	80.3083	623	1725	95	below_threshold
Vibrio tasmaniensis	strain=LMG 20012	GCA_024347635.1	212663	212663	suspected-type	True	78.3416	66	1725	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	77.9698	69	1725	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:53:58,049] [INFO] DFAST Taxonomy check result was written to GCF_014925355.1_ASM1492535v1_genomic.fna/tc_result.tsv
[2024-01-25 19:53:58,049] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:53:58,049] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:53:58,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfaf359d0-1489-4a22-8a27-c3c977de1fa3/dqc_reference/checkm_data
[2024-01-25 19:53:58,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:53:58,099] [INFO] Task started: CheckM
[2024-01-25 19:53:58,099] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014925355.1_ASM1492535v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014925355.1_ASM1492535v1_genomic.fna/checkm_input GCF_014925355.1_ASM1492535v1_genomic.fna/checkm_result
[2024-01-25 19:54:29,339] [INFO] Task succeeded: CheckM
[2024-01-25 19:54:29,340] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:54:29,364] [INFO] ===== Completeness check finished =====
[2024-01-25 19:54:29,365] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:54:29,365] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014925355.1_ASM1492535v1_genomic.fna/markers.fasta)
[2024-01-25 19:54:29,366] [INFO] Task started: Blastn
[2024-01-25 19:54:29,366] [INFO] Running command: blastn -query GCF_014925355.1_ASM1492535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfaf359d0-1489-4a22-8a27-c3c977de1fa3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014925355.1_ASM1492535v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:30,441] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:30,447] [INFO] Selected 8 target genomes.
[2024-01-25 19:54:30,448] [INFO] Target genome list was writen to GCF_014925355.1_ASM1492535v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:54:30,452] [INFO] Task started: fastANI
[2024-01-25 19:54:30,452] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd4636cf-41f6-46a3-8ad6-205b42cdfe58/GCF_014925355.1_ASM1492535v1_genomic.fna.gz --refList GCF_014925355.1_ASM1492535v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014925355.1_ASM1492535v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:54:39,910] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:39,916] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:54:39,917] [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_001661495.1	s__Pseudoalteromonas prydzensis	99.977	1694	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.53	97.08	0.91	0.82	3	conclusive
GCA_011050055.1	s__Pseudoalteromonas prydzensis_A	90.4838	1232	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238355.1	s__Pseudoalteromonas haloplanktis	86.6196	1284	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.55	99.12	0.96	0.93	3	-
GCF_018069805.1	s__Pseudoalteromonas sp018069805	86.0977	1094	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498845.1	s__Pseudoalteromonas rhizosphaerae	85.8847	1230	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.81	97.24	0.86	0.81	17	-
GCF_012927645.1	s__Pseudoalteromonas arctica_A	85.5317	1023	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002310835.1	s__Pseudoalteromonas tetraodonis	80.5592	645	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	96.28	0.91	0.84	28	-
GCF_000238275.3	s__Pseudoalteromonas undina	80.5271	644	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.09	0.91	0.86	14	-
--------------------------------------------------------------------------------
[2024-01-25 19:54:39,918] [INFO] GTDB search result was written to GCF_014925355.1_ASM1492535v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:54:39,918] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:54:39,921] [INFO] DFAST_QC result json was written to GCF_014925355.1_ASM1492535v1_genomic.fna/dqc_result.json
[2024-01-25 19:54:39,921] [INFO] DFAST_QC completed!
[2024-01-25 19:54:39,921] [INFO] Total running time: 0h1m4s