[2024-01-24 13:57:00,468] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:00,470] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:00,470] [INFO] DQC Reference Directory: /var/lib/cwl/stgf10d3bae-88c1-4428-9b9b-aeeb15a6fac4/dqc_reference
[2024-01-24 13:57:01,823] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:01,824] [INFO] Task started: Prodigal
[2024-01-24 13:57:01,824] [INFO] Running command: gunzip -c /var/lib/cwl/stga94586e6-f018-46b0-9042-e1b6c7f8e593/GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/cds.fna -a GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:08,238] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:08,239] [INFO] Task started: HMMsearch
[2024-01-24 13:57:08,239] [INFO] Running command: hmmsearch --tblout GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf10d3bae-88c1-4428-9b9b-aeeb15a6fac4/dqc_reference/reference_markers.hmm GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:08,516] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:08,517] [INFO] Found 6/6 markers.
[2024-01-24 13:57:08,542] [INFO] Query marker FASTA was written to GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:57:08,542] [INFO] Task started: Blastn
[2024-01-24 13:57:08,542] [INFO] Running command: blastn -query GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf10d3bae-88c1-4428-9b9b-aeeb15a6fac4/dqc_reference/reference_markers.fasta -out GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:09,264] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:09,268] [INFO] Selected 28 target genomes.
[2024-01-24 13:57:09,268] [INFO] Target genome list was writen to GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:57:09,303] [INFO] Task started: fastANI
[2024-01-24 13:57:09,303] [INFO] Running command: fastANI --query /var/lib/cwl/stga94586e6-f018-46b0-9042-e1b6c7f8e593/GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna.gz --refList GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:22,656] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:22,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf10d3bae-88c1-4428-9b9b-aeeb15a6fac4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:22,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf10d3bae-88c1-4428-9b9b-aeeb15a6fac4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:22,676] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:22,676] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:22,676] [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 indica	strain=CGMCC 1.10824	GCA_900104245.1	1159017	1159017	type	True	100.0	718	719	95	conclusive
Pseudidiomarina woesei	strain=DSM 27808	GCA_001418345.1	1381080	1381080	type	True	79.5498	208	719	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001517265.1	1381080	1381080	type	True	79.5379	209	719	95	below_threshold
Pseudidiomarina donghaiensis	strain=908033	GCA_003987405.1	519452	519452	type	True	79.5338	224	719	95	below_threshold
Pseudidiomarina donghaiensis	strain=CGMCC 1.7284	GCA_900116895.1	519452	519452	type	True	79.4018	227	719	95	below_threshold
Pseudidiomarina marina	strain=PIM1	GCA_003987045.1	502366	502366	type	True	79.2675	224	719	95	below_threshold
Pseudidiomarina tainanensis	strain=PIN1	GCA_004214835.1	502365	502365	type	True	79.2605	213	719	95	below_threshold
Pseudidiomarina maritima	strain=CGMCC 1.7285	GCA_900115255.1	519453	519453	type	True	78.9957	217	719	95	below_threshold
Pseudidiomarina aquimaris	strain=SW15	GCA_003987395.1	641841	641841	type	True	78.8874	124	719	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_900116625.1	86102	86102	type	True	78.86	55	719	95	below_threshold
Pseudidiomarina taiwanensis	strain=PIT1	GCA_003987435.1	337250	337250	type	True	78.7209	120	719	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_001294685.1	86102	86102	type	True	78.6185	52	719	95	below_threshold
Pseudidiomarina planktonica	strain=CGMCC 1.12458	GCA_900177775.1	1323738	1323738	type	True	77.9157	92	719	95	below_threshold
Pseudidiomarina planktonica	strain=TS-T11	GCA_003987425.1	1323738	1323738	type	True	77.8937	92	719	95	below_threshold
Idiomarina ramblicola	strain=R22	GCA_003987255.1	263724	263724	type	True	77.764	59	719	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:22,678] [INFO] DFAST Taxonomy check result was written to GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:57:22,679] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:22,679] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:22,679] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf10d3bae-88c1-4428-9b9b-aeeb15a6fac4/dqc_reference/checkm_data
[2024-01-24 13:57:22,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:22,704] [INFO] Task started: CheckM
[2024-01-24 13:57:22,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/checkm_input GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:57:48,066] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:48,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:48,087] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:48,088] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:48,088] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:57:48,089] [INFO] Task started: Blastn
[2024-01-24 13:57:48,089] [INFO] Running command: blastn -query GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf10d3bae-88c1-4428-9b9b-aeeb15a6fac4/dqc_reference/reference_markers_gtdb.fasta -out GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:49,182] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:49,185] [INFO] Selected 24 target genomes.
[2024-01-24 13:57:49,185] [INFO] Target genome list was writen to GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:49,202] [INFO] Task started: fastANI
[2024-01-24 13:57:49,202] [INFO] Running command: fastANI --query /var/lib/cwl/stga94586e6-f018-46b0-9042-e1b6c7f8e593/GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna.gz --refList GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:03,274] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:03,289] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:03,290] [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_900104245.1	s__Pseudidiomarina indica	100.0	718	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003182315.1	s__Pseudidiomarina maritima_A	79.8609	167	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	98.70	97.84	0.93	0.89	6	-
GCF_001418345.1	s__Pseudidiomarina woesei	79.5547	210	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900116895.1	s__Pseudidiomarina donghaiensis	79.4191	227	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009734345.1	s__Pseudidiomarina andamanensis	79.4014	235	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214835.1	s__Pseudidiomarina tainanensis	79.271	212	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.72	97.72	0.94	0.94	2	-
GCF_003987045.1	s__Pseudidiomarina marina	79.2525	224	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.46	97.46	0.94	0.94	2	-
GCA_002279005.1	s__Pseudidiomarina sp002279005	79.2449	174	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116625.1	s__Idiomarina abyssalis	78.8935	54	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.70	97.34	0.91	0.79	25	-
GCF_003987395.1	s__Pseudidiomarina aquimaris	78.8681	125	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.26	97.14	0.86	0.77	3	-
GCF_003987435.1	s__Pseudidiomarina taiwanensis	78.7745	118	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987225.1	s__Pseudidiomarina homiensis	78.682	130	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987355.1	s__Pseudidiomarina aestuarii	78.6593	108	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177775.1	s__Pseudidiomarina planktonica	77.9252	91	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003987255.1	s__Idiomarina ramblicola	77.764	59	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299895.1	s__Idiomarina xiamenensis	77.4192	73	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:03,292] [INFO] GTDB search result was written to GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:03,292] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:03,297] [INFO] DFAST_QC result json was written to GCF_900104245.1_IMG-taxon_2596583643_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:58:03,297] [INFO] DFAST_QC completed!
[2024-01-24 13:58:03,297] [INFO] Total running time: 0h1m3s