[2023-06-13 04:36:30,201] [INFO] DFAST_QC pipeline started.
[2023-06-13 04:36:30,205] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 04:36:30,205] [INFO] DQC Reference Directory: /var/lib/cwl/stg10176401-6316-4ec9-b6c4-3ab48127f160/dqc_reference
[2023-06-13 04:36:32,623] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 04:36:32,625] [INFO] Task started: Prodigal
[2023-06-13 04:36:32,625] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6479ca8-14e7-4830-9642-d47add6a862f/GCA_022449925.1_ASM2244992v1_genomic.fna.gz | prodigal -d GCA_022449925.1_ASM2244992v1_genomic.fna/cds.fna -a GCA_022449925.1_ASM2244992v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 04:36:37,505] [INFO] Task succeeded: Prodigal
[2023-06-13 04:36:37,506] [INFO] Task started: HMMsearch
[2023-06-13 04:36:37,506] [INFO] Running command: hmmsearch --tblout GCA_022449925.1_ASM2244992v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10176401-6316-4ec9-b6c4-3ab48127f160/dqc_reference/reference_markers.hmm GCA_022449925.1_ASM2244992v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 04:36:37,737] [INFO] Task succeeded: HMMsearch
[2023-06-13 04:36:37,738] [INFO] Found 6/6 markers.
[2023-06-13 04:36:37,766] [INFO] Query marker FASTA was written to GCA_022449925.1_ASM2244992v1_genomic.fna/markers.fasta
[2023-06-13 04:36:37,766] [INFO] Task started: Blastn
[2023-06-13 04:36:37,767] [INFO] Running command: blastn -query GCA_022449925.1_ASM2244992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10176401-6316-4ec9-b6c4-3ab48127f160/dqc_reference/reference_markers.fasta -out GCA_022449925.1_ASM2244992v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:36:38,501] [INFO] Task succeeded: Blastn
[2023-06-13 04:36:38,506] [INFO] Selected 16 target genomes.
[2023-06-13 04:36:38,507] [INFO] Target genome list was writen to GCA_022449925.1_ASM2244992v1_genomic.fna/target_genomes.txt
[2023-06-13 04:36:38,509] [INFO] Task started: fastANI
[2023-06-13 04:36:38,510] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6479ca8-14e7-4830-9642-d47add6a862f/GCA_022449925.1_ASM2244992v1_genomic.fna.gz --refList GCA_022449925.1_ASM2244992v1_genomic.fna/target_genomes.txt --output GCA_022449925.1_ASM2244992v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 04:36:47,519] [INFO] Task succeeded: fastANI
[2023-06-13 04:36:47,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10176401-6316-4ec9-b6c4-3ab48127f160/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 04:36:47,520] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10176401-6316-4ec9-b6c4-3ab48127f160/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 04:36:47,534] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2023-06-13 04:36:47,535] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 04:36:47,535] [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
Idiomarina zobellii	strain=KMM 231	GCA_001294745.1	86103	86103	type	True	96.8261	583	668	95	conclusive
Idiomarina zobellii	strain=KMM 231	GCA_900100855.1	86103	86103	type	True	96.7292	582	668	95	conclusive
Idiomarina piscisalsi	strain=TPS4-2	GCA_003987095.1	1096243	1096243	type	True	94.5057	575	668	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_001294685.1	86102	86102	type	True	81.9607	334	668	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_900116625.1	86102	86102	type	True	81.8389	341	668	95	below_threshold
Idiomarina baltica	strain=OS145	GCA_000152885.1	190892	190892	type	True	81.196	109	668	95	below_threshold
Idiomarina loihiensis	strain=L2TR	GCA_000008465.1	135577	135577	type	True	80.5114	325	668	95	below_threshold
Idiomarina aquatica	strain=SN-14	GCA_003987185.1	1327752	1327752	type	True	80.3823	164	668	95	below_threshold
Idiomarina ramblicola	strain=R22	GCA_003987255.1	263724	263724	type	True	80.1872	286	668	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 04:36:47,537] [INFO] DFAST Taxonomy check result was written to GCA_022449925.1_ASM2244992v1_genomic.fna/tc_result.tsv
[2023-06-13 04:36:47,537] [INFO] ===== Taxonomy check completed =====
[2023-06-13 04:36:47,537] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 04:36:47,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10176401-6316-4ec9-b6c4-3ab48127f160/dqc_reference/checkm_data
[2023-06-13 04:36:47,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 04:36:47,563] [INFO] Task started: CheckM
[2023-06-13 04:36:47,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022449925.1_ASM2244992v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022449925.1_ASM2244992v1_genomic.fna/checkm_input GCA_022449925.1_ASM2244992v1_genomic.fna/checkm_result
[2023-06-13 04:37:09,248] [INFO] Task succeeded: CheckM
[2023-06-13 04:37:09,250] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.02%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 04:37:09,277] [INFO] ===== Completeness check finished =====
[2023-06-13 04:37:09,277] [INFO] ===== Start GTDB Search =====
[2023-06-13 04:37:09,278] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022449925.1_ASM2244992v1_genomic.fna/markers.fasta)
[2023-06-13 04:37:09,278] [INFO] Task started: Blastn
[2023-06-13 04:37:09,279] [INFO] Running command: blastn -query GCA_022449925.1_ASM2244992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10176401-6316-4ec9-b6c4-3ab48127f160/dqc_reference/reference_markers_gtdb.fasta -out GCA_022449925.1_ASM2244992v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:37:10,403] [INFO] Task succeeded: Blastn
[2023-06-13 04:37:10,408] [INFO] Selected 11 target genomes.
[2023-06-13 04:37:10,409] [INFO] Target genome list was writen to GCA_022449925.1_ASM2244992v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 04:37:10,415] [INFO] Task started: fastANI
[2023-06-13 04:37:10,415] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6479ca8-14e7-4830-9642-d47add6a862f/GCA_022449925.1_ASM2244992v1_genomic.fna.gz --refList GCA_022449925.1_ASM2244992v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022449925.1_ASM2244992v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 04:37:17,402] [INFO] Task succeeded: fastANI
[2023-06-13 04:37:17,413] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 04:37:17,413] [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_900100855.1	s__Idiomarina zobellii	96.7292	582	668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.93	96.27	0.89	0.85	9	conclusive
GCF_003987095.1	s__Idiomarina piscisalsi	94.5057	575	668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002808045.1	s__Idiomarina sp002808045	87.9168	568	668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.72	96.72	0.95	0.95	2	-
GCF_002211765.1	s__Idiomarina piscisalsi_A	87.9138	557	668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.69	97.69	0.90	0.90	2	-
GCF_004362895.1	s__Idiomarina sp002729675	82.0017	172	668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.61	97.37	0.88	0.80	5	-
GCF_900116625.1	s__Idiomarina abyssalis	81.8389	341	668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.70	97.34	0.91	0.79	25	-
GCF_000008465.1	s__Idiomarina loihiensis	80.5214	324	668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.95	95.80	0.91	0.86	17	-
GCF_003987065.1	s__Pseudidiomarina insulisalsae	77.6001	67	668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 04:37:17,415] [INFO] GTDB search result was written to GCA_022449925.1_ASM2244992v1_genomic.fna/result_gtdb.tsv
[2023-06-13 04:37:17,416] [INFO] ===== GTDB Search completed =====
[2023-06-13 04:37:17,420] [INFO] DFAST_QC result json was written to GCA_022449925.1_ASM2244992v1_genomic.fna/dqc_result.json
[2023-06-13 04:37:17,420] [INFO] DFAST_QC completed!
[2023-06-13 04:37:17,420] [INFO] Total running time: 0h0m47s