[2024-01-24 13:01:11,961] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:11,964] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:11,964] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc6507ef-407f-431c-8a4c-cca2edebff1d/dqc_reference
[2024-01-24 13:01:13,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:13,240] [INFO] Task started: Prodigal
[2024-01-24 13:01:13,240] [INFO] Running command: gunzip -c /var/lib/cwl/stg89fa186a-36c3-4e63-bf1d-c32be1a07012/GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/cds.fna -a GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:19,623] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:19,623] [INFO] Task started: HMMsearch
[2024-01-24 13:01:19,623] [INFO] Running command: hmmsearch --tblout GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc6507ef-407f-431c-8a4c-cca2edebff1d/dqc_reference/reference_markers.hmm GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:19,916] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:19,918] [INFO] Found 6/6 markers.
[2024-01-24 13:01:19,956] [INFO] Query marker FASTA was written to GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:01:19,957] [INFO] Task started: Blastn
[2024-01-24 13:01:19,957] [INFO] Running command: blastn -query GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc6507ef-407f-431c-8a4c-cca2edebff1d/dqc_reference/reference_markers.fasta -out GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:20,689] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:20,692] [INFO] Selected 16 target genomes.
[2024-01-24 13:01:20,693] [INFO] Target genome list was writen to GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:01:20,700] [INFO] Task started: fastANI
[2024-01-24 13:01:20,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg89fa186a-36c3-4e63-bf1d-c32be1a07012/GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna.gz --refList GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:29,946] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:29,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc6507ef-407f-431c-8a4c-cca2edebff1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:29,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc6507ef-407f-431c-8a4c-cca2edebff1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:29,957] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:01:29,957] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:29,957] [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_900100855.1	86103	86103	type	True	100.0	846	847	95	conclusive
Idiomarina zobellii	strain=KMM 231	GCA_001294745.1	86103	86103	type	True	99.9913	839	847	95	conclusive
Idiomarina piscisalsi	strain=TPS4-2	GCA_003987095.1	1096243	1096243	type	True	94.5901	720	847	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_001294685.1	86102	86102	type	True	82.2435	409	847	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_900116625.1	86102	86102	type	True	82.1405	408	847	95	below_threshold
Idiomarina baltica	strain=OS145	GCA_000152885.1	190892	190892	type	True	81.4379	150	847	95	below_threshold
Idiomarina loihiensis	strain=L2TR	GCA_000008465.1	135577	135577	type	True	80.7795	420	847	95	below_threshold
Idiomarina ramblicola	strain=R22	GCA_003987255.1	263724	263724	type	True	80.3711	378	847	95	below_threshold
Idiomarina aquatica	strain=SN-14	GCA_003987185.1	1327752	1327752	type	True	79.9157	220	847	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:29,960] [INFO] DFAST Taxonomy check result was written to GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:01:29,961] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:29,961] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:29,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc6507ef-407f-431c-8a4c-cca2edebff1d/dqc_reference/checkm_data
[2024-01-24 13:01:29,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:29,989] [INFO] Task started: CheckM
[2024-01-24 13:01:29,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/checkm_input GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:01:54,218] [INFO] Task succeeded: CheckM
[2024-01-24 13:01:54,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:01:54,241] [INFO] ===== Completeness check finished =====
[2024-01-24 13:01:54,241] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:01:54,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:01:54,242] [INFO] Task started: Blastn
[2024-01-24 13:01:54,242] [INFO] Running command: blastn -query GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc6507ef-407f-431c-8a4c-cca2edebff1d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:55,344] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:55,348] [INFO] Selected 11 target genomes.
[2024-01-24 13:01:55,348] [INFO] Target genome list was writen to GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:01:55,356] [INFO] Task started: fastANI
[2024-01-24 13:01:55,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg89fa186a-36c3-4e63-bf1d-c32be1a07012/GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna.gz --refList GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:02,642] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:02,650] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:02,651] [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	100.0	846	847	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	94.5901	720	847	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	88.1832	675	847	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	87.9618	681	847	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	82.879	232	847	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	82.1507	409	847	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	80.7827	421	847	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	77.6495	85	847	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 13:02:02,652] [INFO] GTDB search result was written to GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:02,653] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:02,657] [INFO] DFAST_QC result json was written to GCF_900100855.1_IMG-taxon_2643221445_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:02:02,657] [INFO] DFAST_QC completed!
[2024-01-24 13:02:02,658] [INFO] Total running time: 0h0m51s