[2024-01-24 14:23:04,136] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:04,142] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:04,142] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3bac123-dfbf-4ec3-bde9-08c0b00ec9d3/dqc_reference
[2024-01-24 14:23:05,439] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:05,440] [INFO] Task started: Prodigal
[2024-01-24 14:23:05,440] [INFO] Running command: gunzip -c /var/lib/cwl/stg59a7934b-ff1a-4ed4-9f64-78ae588ef6fa/GCF_003987425.1_ASM398742v1_genomic.fna.gz | prodigal -d GCF_003987425.1_ASM398742v1_genomic.fna/cds.fna -a GCF_003987425.1_ASM398742v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:12,220] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:12,221] [INFO] Task started: HMMsearch
[2024-01-24 14:23:12,221] [INFO] Running command: hmmsearch --tblout GCF_003987425.1_ASM398742v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3bac123-dfbf-4ec3-bde9-08c0b00ec9d3/dqc_reference/reference_markers.hmm GCF_003987425.1_ASM398742v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:12,506] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:12,507] [INFO] Found 6/6 markers.
[2024-01-24 14:23:12,532] [INFO] Query marker FASTA was written to GCF_003987425.1_ASM398742v1_genomic.fna/markers.fasta
[2024-01-24 14:23:12,532] [INFO] Task started: Blastn
[2024-01-24 14:23:12,532] [INFO] Running command: blastn -query GCF_003987425.1_ASM398742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3bac123-dfbf-4ec3-bde9-08c0b00ec9d3/dqc_reference/reference_markers.fasta -out GCF_003987425.1_ASM398742v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:13,310] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:13,312] [INFO] Selected 23 target genomes.
[2024-01-24 14:23:13,313] [INFO] Target genome list was writen to GCF_003987425.1_ASM398742v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:13,322] [INFO] Task started: fastANI
[2024-01-24 14:23:13,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg59a7934b-ff1a-4ed4-9f64-78ae588ef6fa/GCF_003987425.1_ASM398742v1_genomic.fna.gz --refList GCF_003987425.1_ASM398742v1_genomic.fna/target_genomes.txt --output GCF_003987425.1_ASM398742v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:25,305] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:25,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3bac123-dfbf-4ec3-bde9-08c0b00ec9d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:25,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3bac123-dfbf-4ec3-bde9-08c0b00ec9d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:25,331] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:23:25,331] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:25,332] [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 planktonica	strain=TS-T11	GCA_003987425.1	1323738	1323738	type	True	100.0	856	856	95	conclusive
Pseudidiomarina planktonica	strain=CGMCC 1.12458	GCA_900177775.1	1323738	1323738	type	True	99.9996	855	856	95	conclusive
Pseudidiomarina salinarum	strain=ISL-52	GCA_003987105.1	435908	435908	type	True	78.4064	119	856	95	below_threshold
Pseudidiomarina insulisalsae	strain=CVS-6	GCA_003987065.1	575789	575789	type	True	78.391	125	856	95	below_threshold
Pseudidiomarina salinarum	strain=ISL-52	GCA_000753715.1	435908	435908	type	True	78.32	119	856	95	below_threshold
Pseudidiomarina tainanensis	strain=PIN1	GCA_004214835.1	502365	502365	type	True	78.2668	125	856	95	below_threshold
Pseudidiomarina halophila	strain=BH195	GCA_003987215.1	1449799	1449799	type	True	77.9741	131	856	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001517265.1	1381080	1381080	type	True	77.8753	147	856	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001418345.1	1381080	1381080	type	True	77.8753	147	856	95	below_threshold
Pseudidiomarina donghaiensis	strain=908033	GCA_003987405.1	519452	519452	type	True	77.867	152	856	95	below_threshold
Pseudidiomarina donghaiensis	strain=CGMCC 1.7284	GCA_900116895.1	519452	519452	type	True	77.8044	153	856	95	below_threshold
Idiomarina tyrosinivorans	strain=CC-PW-9	GCA_003987475.1	1445662	1445662	type	True	77.7994	85	856	95	below_threshold
Pseudidiomarina maritima	strain=CGMCC 1.7285	GCA_900115255.1	519453	519453	type	True	77.7903	135	856	95	below_threshold
Pseudidiomarina gelatinasegens	strain=R04H25	GCA_004025325.1	2487740	2487740	type	True	77.6339	136	856	95	below_threshold
Aliidiomarina shirensis	strain=AIS	GCA_003987345.1	1048642	1048642	type	True	77.222	57	856	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	76.4813	58	856	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_017824735.1	2793282	2793282	type	True	76.2252	57	856	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:25,335] [INFO] DFAST Taxonomy check result was written to GCF_003987425.1_ASM398742v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:25,336] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:25,336] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:25,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3bac123-dfbf-4ec3-bde9-08c0b00ec9d3/dqc_reference/checkm_data
[2024-01-24 14:23:25,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:25,367] [INFO] Task started: CheckM
[2024-01-24 14:23:25,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987425.1_ASM398742v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987425.1_ASM398742v1_genomic.fna/checkm_input GCF_003987425.1_ASM398742v1_genomic.fna/checkm_result
[2024-01-24 14:23:52,232] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:52,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:52,252] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:52,252] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:52,253] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987425.1_ASM398742v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:52,254] [INFO] Task started: Blastn
[2024-01-24 14:23:52,254] [INFO] Running command: blastn -query GCF_003987425.1_ASM398742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3bac123-dfbf-4ec3-bde9-08c0b00ec9d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987425.1_ASM398742v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:53,371] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:53,374] [INFO] Selected 20 target genomes.
[2024-01-24 14:23:53,374] [INFO] Target genome list was writen to GCF_003987425.1_ASM398742v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:53,389] [INFO] Task started: fastANI
[2024-01-24 14:23:53,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg59a7934b-ff1a-4ed4-9f64-78ae588ef6fa/GCF_003987425.1_ASM398742v1_genomic.fna.gz --refList GCF_003987425.1_ASM398742v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987425.1_ASM398742v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:01,782] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:01,797] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:01,798] [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_900177775.1	s__Pseudidiomarina planktonica	99.9996	855	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003987045.1	s__Pseudidiomarina marina	78.5468	121	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.46	97.46	0.94	0.94	2	-
GCF_003987065.1	s__Pseudidiomarina insulisalsae	78.4029	124	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000753715.1	s__Pseudidiomarina salinarum	78.3231	120	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004214835.1	s__Pseudidiomarina tainanensis	78.258	126	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.72	97.72	0.94	0.94	2	-
GCF_003182315.1	s__Pseudidiomarina maritima_A	77.9824	110	856	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	77.8753	147	856	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	77.8044	153	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002279005.1	s__Pseudidiomarina sp002279005	77.7703	119	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987475.1	s__Idiomarina tyrosinivorans	77.76	86	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004025325.1	s__Pseudidiomarina gelatinasegens	77.6339	136	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222985.1	s__Pseudidiomarina sp018222985	77.6002	137	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100855.1	s__Idiomarina zobellii	77.4822	109	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.93	96.27	0.89	0.85	9	-
GCF_003987335.1	s__Aliidiomarina maris	77.44	63	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	99.15	98.30	0.97	0.95	3	-
GCF_003987095.1	s__Idiomarina piscisalsi	77.2628	97	856	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	77.2461	110	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987345.1	s__Aliidiomarina shirensis	77.2264	57	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	99.30	99.30	0.95	0.95	2	-
GCF_017824735.1	s__Rheinheimera sp017824735	76.2385	58	856	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Rheinheimera	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:01,799] [INFO] GTDB search result was written to GCF_003987425.1_ASM398742v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:01,800] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:01,804] [INFO] DFAST_QC result json was written to GCF_003987425.1_ASM398742v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:01,804] [INFO] DFAST_QC completed!
[2024-01-24 14:24:01,804] [INFO] Total running time: 0h0m58s