[2024-01-25 17:51:50,720] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:50,722] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:50,722] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7592be0-4a61-40d7-a91c-d9358e6170e3/dqc_reference
[2024-01-25 17:51:51,852] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:51,853] [INFO] Task started: Prodigal
[2024-01-25 17:51:51,853] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d36efd7-2c95-48fc-833a-a09d14a17e2a/GCF_000238255.3_ASM23825v4_genomic.fna.gz | prodigal -d GCF_000238255.3_ASM23825v4_genomic.fna/cds.fna -a GCF_000238255.3_ASM23825v4_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:52:00,872] [INFO] Task succeeded: Prodigal
[2024-01-25 17:52:00,872] [INFO] Task started: HMMsearch
[2024-01-25 17:52:00,872] [INFO] Running command: hmmsearch --tblout GCF_000238255.3_ASM23825v4_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7592be0-4a61-40d7-a91c-d9358e6170e3/dqc_reference/reference_markers.hmm GCF_000238255.3_ASM23825v4_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:52:01,145] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:52:01,146] [INFO] Found 6/6 markers.
[2024-01-25 17:52:01,193] [INFO] Query marker FASTA was written to GCF_000238255.3_ASM23825v4_genomic.fna/markers.fasta
[2024-01-25 17:52:01,193] [INFO] Task started: Blastn
[2024-01-25 17:52:01,193] [INFO] Running command: blastn -query GCF_000238255.3_ASM23825v4_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7592be0-4a61-40d7-a91c-d9358e6170e3/dqc_reference/reference_markers.fasta -out GCF_000238255.3_ASM23825v4_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:01,929] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:01,932] [INFO] Selected 19 target genomes.
[2024-01-25 17:52:01,932] [INFO] Target genome list was writen to GCF_000238255.3_ASM23825v4_genomic.fna/target_genomes.txt
[2024-01-25 17:52:01,955] [INFO] Task started: fastANI
[2024-01-25 17:52:01,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d36efd7-2c95-48fc-833a-a09d14a17e2a/GCF_000238255.3_ASM23825v4_genomic.fna.gz --refList GCF_000238255.3_ASM23825v4_genomic.fna/target_genomes.txt --output GCF_000238255.3_ASM23825v4_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:18,976] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:18,976] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7592be0-4a61-40d7-a91c-d9358e6170e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:18,976] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7592be0-4a61-40d7-a91c-d9358e6170e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:18,988] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:52:18,988] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:52:18,988] [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 spongiae	strain=UST010723-006	GCA_000238255.4	298657	298657	type	True	100.0	1583	1583	95	conclusive
Pseudoalteromonas piratica	strain=OCN003	GCA_000788395.1	1348114	1348114	type	True	85.1054	998	1583	95	below_threshold
Vibrio splendidus	strain=LMG 19031	GCA_024347615.1	29497	29497	type	True	79.9039	67	1583	95	below_threshold
Pseudoalteromonas phenolica	strain=KCTC 12086	GCA_001444405.1	161398	161398	suspected-type	True	79.6377	258	1583	95	below_threshold
Pseudoalteromonas phenolica	strain=O-BC30	GCA_014925335.1	161398	161398	suspected-type	True	79.6358	260	1583	95	below_threshold
Pseudoalteromonas phenolica	strain=O-BC30	GCA_004103265.1	161398	161398	suspected-type	True	79.1303	229	1583	95	below_threshold
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	79.0612	209	1583	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	78.8939	76	1583	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	78.5746	245	1583	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	78.4012	244	1583	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KCTC 12958	GCA_001455325.1	152297	152297	suspected-type	True	78.3723	243	1583	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	78.299	243	1583	95	below_threshold
Pseudoalteromonas prydzensis	strain=ACAM 620	GCA_014925355.1	182141	182141	type	True	78.1769	257	1583	95	below_threshold
Pseudoalteromonas ulvae	strain=UL12	GCA_014925405.1	107327	107327	type	True	78.1179	210	1583	95	below_threshold
Pseudoalteromonas prydzensis	strain=DSM 14232	GCA_001661495.1	182141	182141	type	True	77.7657	251	1583	95	below_threshold
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	77.7554	231	1583	95	below_threshold
Shewanella electrodiphila	strain=DSM 24955	GCA_023283985.1	934143	934143	type	True	76.8951	83	1583	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	76.2664	57	1583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:52:18,990] [INFO] DFAST Taxonomy check result was written to GCF_000238255.3_ASM23825v4_genomic.fna/tc_result.tsv
[2024-01-25 17:52:18,990] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:18,990] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:18,991] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7592be0-4a61-40d7-a91c-d9358e6170e3/dqc_reference/checkm_data
[2024-01-25 17:52:18,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:19,039] [INFO] Task started: CheckM
[2024-01-25 17:52:19,039] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000238255.3_ASM23825v4_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000238255.3_ASM23825v4_genomic.fna/checkm_input GCF_000238255.3_ASM23825v4_genomic.fna/checkm_result
[2024-01-25 17:52:49,226] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:49,227] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:49,243] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:49,243] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:49,244] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000238255.3_ASM23825v4_genomic.fna/markers.fasta)
[2024-01-25 17:52:49,244] [INFO] Task started: Blastn
[2024-01-25 17:52:49,244] [INFO] Running command: blastn -query GCF_000238255.3_ASM23825v4_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7592be0-4a61-40d7-a91c-d9358e6170e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000238255.3_ASM23825v4_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:50,424] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:50,428] [INFO] Selected 13 target genomes.
[2024-01-25 17:52:50,428] [INFO] Target genome list was writen to GCF_000238255.3_ASM23825v4_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:50,443] [INFO] Task started: fastANI
[2024-01-25 17:52:50,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d36efd7-2c95-48fc-833a-a09d14a17e2a/GCF_000238255.3_ASM23825v4_genomic.fna.gz --refList GCF_000238255.3_ASM23825v4_genomic.fna/target_genomes_gtdb.txt --output GCF_000238255.3_ASM23825v4_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:53:02,372] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:02,380] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:53:02,381] [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_000238255.3	s__Pseudoalteromonas spongiae	100.0	1583	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.31	96.27	0.89	0.86	4	conclusive
GCF_001399975.1	s__Pseudoalteromonas sp001399975	94.53	1330	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000788395.1	s__Pseudoalteromonas piratica	85.1056	998	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001444405.1	s__Pseudoalteromonas phenolica	79.6386	255	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.52	98.61	0.97	0.92	4	-
GCF_005876835.1	s__Pseudoalteromonas phenolica_B	79.0528	242	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005886345.1	s__Pseudoalteromonas phenolica_A	79.0107	247	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.97	0.91	0.89	3	-
GCF_900239935.1	s__Pseudoalteromonas carrageenovora	78.64	229	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.00	96.44	0.97	0.91	6	-
GCF_001306915.1	s__Pseudoalteromonas lipolytica_A	78.3561	271	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.22	97.66	0.91	0.90	9	-
GCA_018402495.1	s__Pseudoalteromonas sp018402495	78.3547	209	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100985.1	s__Pseudoalteromonas sp018100985	78.108	197	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.38	98.38	0.93	0.93	2	-
GCF_002165575.1	s__Pseudoalteromonas sp002165575	77.7687	214	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661495.1	s__Pseudoalteromonas prydzensis	77.741	253	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.53	97.08	0.91	0.82	3	-
GCA_011050055.1	s__Pseudoalteromonas prydzensis_A	76.7678	207	1583	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:53:02,382] [INFO] GTDB search result was written to GCF_000238255.3_ASM23825v4_genomic.fna/result_gtdb.tsv
[2024-01-25 17:53:02,382] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:53:02,385] [INFO] DFAST_QC result json was written to GCF_000238255.3_ASM23825v4_genomic.fna/dqc_result.json
[2024-01-25 17:53:02,386] [INFO] DFAST_QC completed!
[2024-01-25 17:53:02,386] [INFO] Total running time: 0h1m12s