[2024-01-24 11:20:03,172] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:03,173] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:03,174] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6dc00a8-f9b5-4ffd-a50a-5aca231e6c0b/dqc_reference
[2024-01-24 11:20:04,371] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:04,372] [INFO] Task started: Prodigal
[2024-01-24 11:20:04,372] [INFO] Running command: gunzip -c /var/lib/cwl/stgfffc7d65-d64f-4af4-ae76-57dfd9770b42/GCF_000238335.3_ASM23833v4_genomic.fna.gz | prodigal -d GCF_000238335.3_ASM23833v4_genomic.fna/cds.fna -a GCF_000238335.3_ASM23833v4_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:12,380] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:12,381] [INFO] Task started: HMMsearch
[2024-01-24 11:20:12,381] [INFO] Running command: hmmsearch --tblout GCF_000238335.3_ASM23833v4_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6dc00a8-f9b5-4ffd-a50a-5aca231e6c0b/dqc_reference/reference_markers.hmm GCF_000238335.3_ASM23833v4_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:12,632] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:12,633] [INFO] Found 6/6 markers.
[2024-01-24 11:20:12,665] [INFO] Query marker FASTA was written to GCF_000238335.3_ASM23833v4_genomic.fna/markers.fasta
[2024-01-24 11:20:12,665] [INFO] Task started: Blastn
[2024-01-24 11:20:12,665] [INFO] Running command: blastn -query GCF_000238335.3_ASM23833v4_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6dc00a8-f9b5-4ffd-a50a-5aca231e6c0b/dqc_reference/reference_markers.fasta -out GCF_000238335.3_ASM23833v4_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:13,362] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:13,365] [INFO] Selected 15 target genomes.
[2024-01-24 11:20:13,365] [INFO] Target genome list was writen to GCF_000238335.3_ASM23833v4_genomic.fna/target_genomes.txt
[2024-01-24 11:20:13,390] [INFO] Task started: fastANI
[2024-01-24 11:20:13,390] [INFO] Running command: fastANI --query /var/lib/cwl/stgfffc7d65-d64f-4af4-ae76-57dfd9770b42/GCF_000238335.3_ASM23833v4_genomic.fna.gz --refList GCF_000238335.3_ASM23833v4_genomic.fna/target_genomes.txt --output GCF_000238335.3_ASM23833v4_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:25,325] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:25,325] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6dc00a8-f9b5-4ffd-a50a-5aca231e6c0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:25,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6dc00a8-f9b5-4ffd-a50a-5aca231e6c0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:25,337] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:25,337] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:25,338] [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 marina	strain=DSM 17587	GCA_000238335.4	267375	267375	type	True	100.0	1391	1391	95	conclusive
Pseudoalteromonas carrageenovora	strain=ATCC 43555	GCA_900239935.1	227	227	type	True	84.3563	975	1391	95	below_threshold
Pseudoalteromonas carrageenovora	strain=IAM 12662	GCA_014925295.1	227	227	type	True	84.2544	973	1391	95	below_threshold
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	84.1831	944	1391	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	83.2973	899	1391	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	83.0971	967	1391	95	below_threshold
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	82.6479	917	1391	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	81.769	760	1391	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	81.7135	772	1391	95	below_threshold
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	81.6573	735	1391	95	below_threshold
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	81.6406	741	1391	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	78.5051	60	1391	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	76.4021	59	1391	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	76.1649	75	1391	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:25,339] [INFO] DFAST Taxonomy check result was written to GCF_000238335.3_ASM23833v4_genomic.fna/tc_result.tsv
[2024-01-24 11:20:25,340] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:25,340] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:25,340] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6dc00a8-f9b5-4ffd-a50a-5aca231e6c0b/dqc_reference/checkm_data
[2024-01-24 11:20:25,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:25,380] [INFO] Task started: CheckM
[2024-01-24 11:20:25,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000238335.3_ASM23833v4_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000238335.3_ASM23833v4_genomic.fna/checkm_input GCF_000238335.3_ASM23833v4_genomic.fna/checkm_result
[2024-01-24 11:20:52,868] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:52,870] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:20:52,885] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:52,886] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:52,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000238335.3_ASM23833v4_genomic.fna/markers.fasta)
[2024-01-24 11:20:52,886] [INFO] Task started: Blastn
[2024-01-24 11:20:52,886] [INFO] Running command: blastn -query GCF_000238335.3_ASM23833v4_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6dc00a8-f9b5-4ffd-a50a-5aca231e6c0b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000238335.3_ASM23833v4_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:53,972] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:53,975] [INFO] Selected 13 target genomes.
[2024-01-24 11:20:53,975] [INFO] Target genome list was writen to GCF_000238335.3_ASM23833v4_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:20:54,005] [INFO] Task started: fastANI
[2024-01-24 11:20:54,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgfffc7d65-d64f-4af4-ae76-57dfd9770b42/GCF_000238335.3_ASM23833v4_genomic.fna.gz --refList GCF_000238335.3_ASM23833v4_genomic.fna/target_genomes_gtdb.txt --output GCF_000238335.3_ASM23833v4_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:05,879] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:05,891] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:05,891] [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_000238335.3	s__Pseudoalteromonas marina	100.0	1391	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	97.57	0.91	0.88	12	conclusive
GCF_001468485.1	s__Pseudoalteromonas sp001468485	91.4829	1219	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.31	96.95	0.95	0.92	8	-
GCF_900239935.1	s__Pseudoalteromonas carrageenovora	84.3576	974	1391	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	83.5664	879	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.38	98.38	0.93	0.93	2	-
GCF_002221525.1	s__Pseudoalteromonas espejiana	83.4856	925	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001974875.1	s__Pseudoalteromonas sp001974875	82.7705	974	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.73	97.18	0.90	0.86	5	-
GCF_008370255.1	s__Pseudoalteromonas sp008370255	82.7565	934	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238395.3	s__Pseudoalteromonas arctica	82.6623	939	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCF_000690055.1	s__Pseudoalteromonas fuliginea	82.6557	915	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	97.88	0.92	0.87	9	-
GCF_002310835.1	s__Pseudoalteromonas tetraodonis	81.7243	769	1391	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	81.6405	741	1391	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	81.4957	723	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.16	95.35	0.86	0.83	5	-
GCA_018402495.1	s__Pseudoalteromonas sp018402495	81.2057	721	1391	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:05,892] [INFO] GTDB search result was written to GCF_000238335.3_ASM23833v4_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:05,893] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:05,896] [INFO] DFAST_QC result json was written to GCF_000238335.3_ASM23833v4_genomic.fna/dqc_result.json
[2024-01-24 11:21:05,896] [INFO] DFAST_QC completed!
[2024-01-24 11:21:05,896] [INFO] Total running time: 0h1m3s