[2024-01-24 12:13:23,544] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:23,713] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:23,713] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcd80a6b-cb37-482f-a680-4b74d5966352/dqc_reference
[2024-01-24 12:13:24,929] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:24,930] [INFO] Task started: Prodigal
[2024-01-24 12:13:24,930] [INFO] Running command: gunzip -c /var/lib/cwl/stgd01b2a36-0ad0-4bc0-8753-b93b2644d9ad/GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/cds.fna -a GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:31,720] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:31,721] [INFO] Task started: HMMsearch
[2024-01-24 12:13:31,721] [INFO] Running command: hmmsearch --tblout GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcd80a6b-cb37-482f-a680-4b74d5966352/dqc_reference/reference_markers.hmm GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:32,011] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:32,013] [INFO] Found 6/6 markers.
[2024-01-24 12:13:32,042] [INFO] Query marker FASTA was written to GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:13:32,043] [INFO] Task started: Blastn
[2024-01-24 12:13:32,043] [INFO] Running command: blastn -query GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcd80a6b-cb37-482f-a680-4b74d5966352/dqc_reference/reference_markers.fasta -out GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:32,880] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:32,883] [INFO] Selected 15 target genomes.
[2024-01-24 12:13:32,883] [INFO] Target genome list was writen to GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:13:32,915] [INFO] Task started: fastANI
[2024-01-24 12:13:32,916] [INFO] Running command: fastANI --query /var/lib/cwl/stgd01b2a36-0ad0-4bc0-8753-b93b2644d9ad/GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna.gz --refList GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:42,068] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:42,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcd80a6b-cb37-482f-a680-4b74d5966352/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:42,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcd80a6b-cb37-482f-a680-4b74d5966352/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:42,075] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:13:42,076] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:13:42,076] [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
Pseudidiomarina maritima	strain=CGMCC 1.7285	GCA_900115255.1	519453	519453	type	True	100.0	809	809	95	inconclusive
Pseudidiomarina tainanensis	strain=PIN1	GCA_004214835.1	502365	502365	type	True	97.6366	746	809	95	inconclusive
Pseudidiomarina marina	strain=PIM1	GCA_003987045.1	502366	502366	type	True	83.8002	621	809	95	below_threshold
Pseudidiomarina donghaiensis	strain=908033	GCA_003987405.1	519452	519452	type	True	81.353	400	809	95	below_threshold
Pseudidiomarina donghaiensis	strain=CGMCC 1.7284	GCA_900116895.1	519452	519452	type	True	81.2934	404	809	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001418345.1	1381080	1381080	type	True	81.2654	389	809	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001517265.1	1381080	1381080	type	True	81.2654	389	809	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:42,078] [INFO] DFAST Taxonomy check result was written to GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:13:42,079] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:42,079] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:42,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcd80a6b-cb37-482f-a680-4b74d5966352/dqc_reference/checkm_data
[2024-01-24 12:13:42,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:42,116] [INFO] Task started: CheckM
[2024-01-24 12:13:42,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/checkm_input GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:14:08,290] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:08,292] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:08,312] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:08,312] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:08,312] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:14:08,313] [INFO] Task started: Blastn
[2024-01-24 12:14:08,313] [INFO] Running command: blastn -query GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgbcd80a6b-cb37-482f-a680-4b74d5966352/dqc_reference/reference_markers_gtdb.fasta -out GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:09,503] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:09,513] [INFO] Selected 10 target genomes.
[2024-01-24 12:14:09,514] [INFO] Target genome list was writen to GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:09,522] [INFO] Task started: fastANI
[2024-01-24 12:14:09,523] [INFO] Running command: fastANI --query /var/lib/cwl/stgd01b2a36-0ad0-4bc0-8753-b93b2644d9ad/GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna.gz --refList GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:15,189] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:15,196] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:15,196] [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_004214835.1	s__Pseudidiomarina tainanensis	97.6366	746	809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.72	97.72	0.94	0.94	2	conclusive
GCA_002279005.1	s__Pseudidiomarina sp002279005	84.3025	448	809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009734345.1	s__Pseudidiomarina andamanensis	84.2894	611	809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987045.1	s__Pseudidiomarina marina	83.8002	621	809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.46	97.46	0.94	0.94	2	-
GCF_900116895.1	s__Pseudidiomarina donghaiensis	81.2934	404	809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001418345.1	s__Pseudidiomarina woesei	81.2654	389	809	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018222985.1	s__Pseudidiomarina sp018222985	80.7515	395	809	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 12:14:15,199] [INFO] GTDB search result was written to GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:15,199] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:15,203] [INFO] DFAST_QC result json was written to GCF_900115255.1_IMG-taxon_2617270903_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:14:15,204] [INFO] DFAST_QC completed!
[2024-01-24 12:14:15,204] [INFO] Total running time: 0h0m52s