[2024-01-25 18:04:20,349] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:04:20,351] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:04:20,351] [INFO] DQC Reference Directory: /var/lib/cwl/stg193159dd-db6d-42f9-a6b7-8f2b34af4e3f/dqc_reference
[2024-01-25 18:04:21,539] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:04:21,539] [INFO] Task started: Prodigal
[2024-01-25 18:04:21,540] [INFO] Running command: gunzip -c /var/lib/cwl/stgfdcfbbb0-830c-4c11-a12a-ec1db7c4ff40/GCF_013140855.1_ASM1314085v1_genomic.fna.gz | prodigal -d GCF_013140855.1_ASM1314085v1_genomic.fna/cds.fna -a GCF_013140855.1_ASM1314085v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:04:32,194] [INFO] Task succeeded: Prodigal
[2024-01-25 18:04:32,194] [INFO] Task started: HMMsearch
[2024-01-25 18:04:32,194] [INFO] Running command: hmmsearch --tblout GCF_013140855.1_ASM1314085v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg193159dd-db6d-42f9-a6b7-8f2b34af4e3f/dqc_reference/reference_markers.hmm GCF_013140855.1_ASM1314085v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:04:32,457] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:04:32,458] [INFO] Found 6/6 markers.
[2024-01-25 18:04:32,497] [INFO] Query marker FASTA was written to GCF_013140855.1_ASM1314085v1_genomic.fna/markers.fasta
[2024-01-25 18:04:32,498] [INFO] Task started: Blastn
[2024-01-25 18:04:32,498] [INFO] Running command: blastn -query GCF_013140855.1_ASM1314085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg193159dd-db6d-42f9-a6b7-8f2b34af4e3f/dqc_reference/reference_markers.fasta -out GCF_013140855.1_ASM1314085v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:33,201] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:33,205] [INFO] Selected 16 target genomes.
[2024-01-25 18:04:33,206] [INFO] Target genome list was writen to GCF_013140855.1_ASM1314085v1_genomic.fna/target_genomes.txt
[2024-01-25 18:04:33,216] [INFO] Task started: fastANI
[2024-01-25 18:04:33,217] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdcfbbb0-830c-4c11-a12a-ec1db7c4ff40/GCF_013140855.1_ASM1314085v1_genomic.fna.gz --refList GCF_013140855.1_ASM1314085v1_genomic.fna/target_genomes.txt --output GCF_013140855.1_ASM1314085v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:04:46,689] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:46,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg193159dd-db6d-42f9-a6b7-8f2b34af4e3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:04:46,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg193159dd-db6d-42f9-a6b7-8f2b34af4e3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:04:46,699] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:04:46,699] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:04:46,699] [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 caenipelagi	strain=JBTF-M23	GCA_013140855.1	2726988	2726988	type	True	100.0	1678	1679	95	conclusive
Pseudoalteromonas byunsanensis	strain=JCM 12483	GCA_001854475.1	327939	327939	type	True	80.863	724	1679	95	below_threshold
Pseudoalteromonas amylolytica	strain=JW1	GCA_001854605.1	1859457	1859457	type	True	80.8154	707	1679	95	below_threshold
Pseudoalteromonas aurantia	strain=208	GCA_014858725.1	43654	43654	type	True	79.4749	367	1679	95	below_threshold
Pseudoalteromonas citrea	strain=DSM 8771	GCA_000238375.4	43655	43655	type	True	79.4243	390	1679	95	below_threshold
Pseudoalteromonas phenolica	strain=O-BC30	GCA_014925335.1	161398	161398	suspected-type	True	79.1744	330	1679	95	below_threshold
Pseudoalteromonas lipolytica	strain=LMEB 39	GCA_014925285.1	570156	570156	suspected-type	True	78.7534	259	1679	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	78.6243	257	1679	95	below_threshold
Pseudoalteromonas lipolytica	strain=CGMCC 1.8499	GCA_900116435.1	570156	570156	suspected-type	True	78.6211	261	1679	95	below_threshold
Pseudoalteromonas spongiae	strain=UST010723-006	GCA_000238255.4	298657	298657	type	True	78.3713	192	1679	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	78.333	230	1679	95	below_threshold
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	78.1642	233	1679	95	below_threshold
Motilimonas cestriensis	strain=MKS20	GCA_021295315.1	2742685	2742685	type	True	76.5711	67	1679	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	75.627	57	1679	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:04:46,700] [INFO] DFAST Taxonomy check result was written to GCF_013140855.1_ASM1314085v1_genomic.fna/tc_result.tsv
[2024-01-25 18:04:46,701] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:04:46,701] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:04:46,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg193159dd-db6d-42f9-a6b7-8f2b34af4e3f/dqc_reference/checkm_data
[2024-01-25 18:04:46,702] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:04:46,749] [INFO] Task started: CheckM
[2024-01-25 18:04:46,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013140855.1_ASM1314085v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013140855.1_ASM1314085v1_genomic.fna/checkm_input GCF_013140855.1_ASM1314085v1_genomic.fna/checkm_result
[2024-01-25 18:05:23,070] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:23,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:23,101] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:23,101] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:23,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013140855.1_ASM1314085v1_genomic.fna/markers.fasta)
[2024-01-25 18:05:23,102] [INFO] Task started: Blastn
[2024-01-25 18:05:23,102] [INFO] Running command: blastn -query GCF_013140855.1_ASM1314085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg193159dd-db6d-42f9-a6b7-8f2b34af4e3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013140855.1_ASM1314085v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:24,207] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:24,210] [INFO] Selected 8 target genomes.
[2024-01-25 18:05:24,211] [INFO] Target genome list was writen to GCF_013140855.1_ASM1314085v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:24,224] [INFO] Task started: fastANI
[2024-01-25 18:05:24,224] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdcfbbb0-830c-4c11-a12a-ec1db7c4ff40/GCF_013140855.1_ASM1314085v1_genomic.fna.gz --refList GCF_013140855.1_ASM1314085v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013140855.1_ASM1314085v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:05:33,232] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:33,238] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:05:33,239] [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_013140855.1	s__Pseudoalteromonas caenipelagi	100.0	1678	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014694405.1	s__Pseudoalteromonas sp014694405	87.5769	1272	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176705.1	s__Pseudoalteromonas sp009176705	83.0441	1070	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002964665.1	s__Pseudoalteromonas sp002964665	80.974	678	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001854475.1	s__Pseudoalteromonas byunsanensis	80.8654	724	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854605.1	s__Pseudoalteromonas amylolytica	80.8148	707	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003590335.1	s__Pseudoalteromonas sp003590335	79.1268	394	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.57	97.56	0.90	0.89	3	-
GCF_900116435.1	s__Pseudoalteromonas lipolytica	78.6062	262	1679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.07	98.83	0.92	0.86	12	-
--------------------------------------------------------------------------------
[2024-01-25 18:05:33,240] [INFO] GTDB search result was written to GCF_013140855.1_ASM1314085v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:05:33,241] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:05:33,246] [INFO] DFAST_QC result json was written to GCF_013140855.1_ASM1314085v1_genomic.fna/dqc_result.json
[2024-01-25 18:05:33,246] [INFO] DFAST_QC completed!
[2024-01-25 18:05:33,246] [INFO] Total running time: 0h1m13s