[2024-01-24 13:57:00,947] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:00,949] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:00,949] [INFO] DQC Reference Directory: /var/lib/cwl/stg3eda6f52-5ac8-49ad-af49-8ee9b56300dd/dqc_reference
[2024-01-24 13:57:02,342] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:02,343] [INFO] Task started: Prodigal
[2024-01-24 13:57:02,343] [INFO] Running command: gunzip -c /var/lib/cwl/stgb67825cd-833d-44af-a703-bb0b197999e1/GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/cds.fna -a GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:09,096] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:09,097] [INFO] Task started: HMMsearch
[2024-01-24 13:57:09,097] [INFO] Running command: hmmsearch --tblout GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3eda6f52-5ac8-49ad-af49-8ee9b56300dd/dqc_reference/reference_markers.hmm GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:09,388] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:09,389] [INFO] Found 6/6 markers.
[2024-01-24 13:57:09,425] [INFO] Query marker FASTA was written to GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:57:09,426] [INFO] Task started: Blastn
[2024-01-24 13:57:09,426] [INFO] Running command: blastn -query GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3eda6f52-5ac8-49ad-af49-8ee9b56300dd/dqc_reference/reference_markers.fasta -out GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:10,162] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:10,165] [INFO] Selected 18 target genomes.
[2024-01-24 13:57:10,166] [INFO] Target genome list was writen to GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:57:10,179] [INFO] Task started: fastANI
[2024-01-24 13:57:10,179] [INFO] Running command: fastANI --query /var/lib/cwl/stgb67825cd-833d-44af-a703-bb0b197999e1/GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna.gz --refList GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:22,189] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:22,190] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3eda6f52-5ac8-49ad-af49-8ee9b56300dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:22,190] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3eda6f52-5ac8-49ad-af49-8ee9b56300dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:22,200] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:57:22,201] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:22,201] [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 abyssalis	strain=KMM 227	GCA_900116625.1	86102	86102	type	True	100.0	887	887	95	conclusive
Idiomarina abyssalis	strain=KMM 227	GCA_001294685.1	86102	86102	type	True	99.9853	876	887	95	conclusive
Idiomarina ramblicola	strain=R22	GCA_003987255.1	263724	263724	type	True	85.8844	689	887	95	below_threshold
Idiomarina loihiensis	strain=L2TR	GCA_000008465.1	135577	135577	type	True	85.0075	655	887	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_001294745.1	86103	86103	type	True	82.4314	408	887	95	below_threshold
Idiomarina piscisalsi	strain=TPS4-2	GCA_003987095.1	1096243	1096243	type	True	81.4644	403	887	95	below_threshold
Idiomarina fontislapidosi	strain=F23	GCA_003987025.1	263723	263723	type	True	78.1986	129	887	95	below_threshold
Aliidiomarina halalkaliphila	strain=IM 1326	GCA_007096385.1	2593535	2593535	type	True	77.2948	53	887	95	below_threshold
Pseudidiomarina aestuarii	strain=KYW314	GCA_003987355.1	624146	624146	suspected-type	True	76.9474	78	887	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:22,202] [INFO] DFAST Taxonomy check result was written to GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:57:22,203] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:22,203] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:22,204] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3eda6f52-5ac8-49ad-af49-8ee9b56300dd/dqc_reference/checkm_data
[2024-01-24 13:57:22,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:22,243] [INFO] Task started: CheckM
[2024-01-24 13:57:22,243] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/checkm_input GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:57:48,214] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:48,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:48,240] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:48,240] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:48,240] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:57:48,241] [INFO] Task started: Blastn
[2024-01-24 13:57:48,241] [INFO] Running command: blastn -query GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3eda6f52-5ac8-49ad-af49-8ee9b56300dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:49,328] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:49,332] [INFO] Selected 17 target genomes.
[2024-01-24 13:57:49,332] [INFO] Target genome list was writen to GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:49,341] [INFO] Task started: fastANI
[2024-01-24 13:57:49,341] [INFO] Running command: fastANI --query /var/lib/cwl/stgb67825cd-833d-44af-a703-bb0b197999e1/GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna.gz --refList GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:59,792] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:59,801] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:59,801] [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_900116625.1	s__Idiomarina abyssalis	100.0	887	887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.70	97.34	0.91	0.79	25	conclusive
GCF_003987255.1	s__Idiomarina ramblicola	85.8844	689	887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000008465.1	s__Idiomarina loihiensis	84.9954	655	887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.95	95.80	0.91	0.86	17	-
GCF_900100855.1	s__Idiomarina zobellii	82.4901	406	887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.93	96.27	0.89	0.85	9	-
GCF_003987095.1	s__Idiomarina piscisalsi	81.4644	403	887	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	81.4437	417	887	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	80.7998	401	887	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	80.6318	212	887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.61	97.37	0.88	0.80	5	-
GCF_003226255.1	s__Idiomarina fontislapidosi	78.2334	128	887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003987355.1	s__Pseudidiomarina aestuarii	76.9839	79	887	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:59,803] [INFO] GTDB search result was written to GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:59,804] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:59,807] [INFO] DFAST_QC result json was written to GCF_900116625.1_IMG-taxon_2642422567_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:57:59,807] [INFO] DFAST_QC completed!
[2024-01-24 13:57:59,807] [INFO] Total running time: 0h0m59s