[2024-01-25 19:46:06,082] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:06,083] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:06,084] [INFO] DQC Reference Directory: /var/lib/cwl/stga5a704e4-3754-4c3c-a142-96ac490decbc/dqc_reference
[2024-01-25 19:46:07,209] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:07,211] [INFO] Task started: Prodigal
[2024-01-25 19:46:07,211] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a3373f5-8071-46e2-a11e-3b332ad259dd/GCF_000753735.1_ASM75373v1_genomic.fna.gz | prodigal -d GCF_000753735.1_ASM75373v1_genomic.fna/cds.fna -a GCF_000753735.1_ASM75373v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:13,996] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:13,996] [INFO] Task started: HMMsearch
[2024-01-25 19:46:13,997] [INFO] Running command: hmmsearch --tblout GCF_000753735.1_ASM75373v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5a704e4-3754-4c3c-a142-96ac490decbc/dqc_reference/reference_markers.hmm GCF_000753735.1_ASM75373v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:14,180] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:14,181] [INFO] Found 6/6 markers.
[2024-01-25 19:46:14,202] [INFO] Query marker FASTA was written to GCF_000753735.1_ASM75373v1_genomic.fna/markers.fasta
[2024-01-25 19:46:14,202] [INFO] Task started: Blastn
[2024-01-25 19:46:14,202] [INFO] Running command: blastn -query GCF_000753735.1_ASM75373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5a704e4-3754-4c3c-a142-96ac490decbc/dqc_reference/reference_markers.fasta -out GCF_000753735.1_ASM75373v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:14,909] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:14,912] [INFO] Selected 27 target genomes.
[2024-01-25 19:46:14,912] [INFO] Target genome list was writen to GCF_000753735.1_ASM75373v1_genomic.fna/target_genomes.txt
[2024-01-25 19:46:14,929] [INFO] Task started: fastANI
[2024-01-25 19:46:14,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a3373f5-8071-46e2-a11e-3b332ad259dd/GCF_000753735.1_ASM75373v1_genomic.fna.gz --refList GCF_000753735.1_ASM75373v1_genomic.fna/target_genomes.txt --output GCF_000753735.1_ASM75373v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:31,046] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:31,046] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5a704e4-3754-4c3c-a142-96ac490decbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:31,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5a704e4-3754-4c3c-a142-96ac490decbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:31,057] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:46:31,057] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:46:31,057] [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 atlantica	strain=MCCC 1A10513	GCA_000753735.1	1517416	1517416	type	True	100.0	878	880	95	conclusive
Pseudidiomarina gelatinasegens	strain=R04H25	GCA_004025325.1	2487740	2487740	type	True	80.5364	178	880	95	below_threshold
Pseudidiomarina homiensis	strain=PO-M2	GCA_003987225.1	364198	364198	type	True	80.144	316	880	95	below_threshold
Pseudidiomarina aquimaris	strain=SW15	GCA_003987395.1	641841	641841	type	True	79.9859	335	880	95	below_threshold
Pseudidiomarina tainanensis	strain=PIN1	GCA_004214835.1	502365	502365	type	True	79.9563	189	880	95	below_threshold
Pseudidiomarina donghaiensis	strain=CGMCC 1.7284	GCA_900116895.1	519452	519452	type	True	79.4898	210	880	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001418345.1	1381080	1381080	type	True	79.4776	197	880	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001517265.1	1381080	1381080	type	True	79.4734	196	880	95	below_threshold
Pseudidiomarina piscicola	strain=CECT 9734	GCA_902806985.1	2614830	2614830	type	True	79.4541	260	880	95	below_threshold
Pseudidiomarina donghaiensis	strain=908033	GCA_003987405.1	519452	519452	type	True	79.4219	212	880	95	below_threshold
Pseudidiomarina sediminum	strain=c121	GCA_003987265.1	431675	431675	type	True	78.9062	275	880	95	below_threshold
Pseudidiomarina sediminum	strain=DSM 21906	GCA_000423165.1	431675	431675	type	True	78.9003	271	880	95	below_threshold
Pseudidiomarina halophila	strain=BH195	GCA_003987215.1	1449799	1449799	type	True	78.89	291	880	95	below_threshold
Pseudidiomarina insulisalsae	strain=CVS-6	GCA_003987065.1	575789	575789	type	True	78.7317	281	880	95	below_threshold
Aliidiomarina indica	strain=SW123	GCA_015354615.1	2749147	2749147	type	True	77.911	50	880	95	below_threshold
Idiomarina tyrosinivorans	strain=CC-PW-9	GCA_003987475.1	1445662	1445662	type	True	77.8972	85	880	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:31,058] [INFO] DFAST Taxonomy check result was written to GCF_000753735.1_ASM75373v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:31,059] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:31,059] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:31,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5a704e4-3754-4c3c-a142-96ac490decbc/dqc_reference/checkm_data
[2024-01-25 19:46:31,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:31,090] [INFO] Task started: CheckM
[2024-01-25 19:46:31,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000753735.1_ASM75373v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000753735.1_ASM75373v1_genomic.fna/checkm_input GCF_000753735.1_ASM75373v1_genomic.fna/checkm_result
[2024-01-25 19:46:55,954] [INFO] Task succeeded: CheckM
[2024-01-25 19:46:55,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:46:56,008] [INFO] ===== Completeness check finished =====
[2024-01-25 19:46:56,008] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:46:56,009] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000753735.1_ASM75373v1_genomic.fna/markers.fasta)
[2024-01-25 19:46:56,009] [INFO] Task started: Blastn
[2024-01-25 19:46:56,009] [INFO] Running command: blastn -query GCF_000753735.1_ASM75373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5a704e4-3754-4c3c-a142-96ac490decbc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000753735.1_ASM75373v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:57,171] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:57,174] [INFO] Selected 23 target genomes.
[2024-01-25 19:46:57,174] [INFO] Target genome list was writen to GCF_000753735.1_ASM75373v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:46:57,201] [INFO] Task started: fastANI
[2024-01-25 19:46:57,201] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a3373f5-8071-46e2-a11e-3b332ad259dd/GCF_000753735.1_ASM75373v1_genomic.fna.gz --refList GCF_000753735.1_ASM75373v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000753735.1_ASM75373v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:10,501] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:10,511] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:10,512] [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_000753735.1	s__Pseudidiomarina atlantica	100.0	878	880	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_004025325.1	s__Pseudidiomarina gelatinasegens	80.5704	177	880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182315.1	s__Pseudidiomarina maritima_A	80.2562	193	880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	98.70	97.84	0.93	0.89	6	-
GCF_003987225.1	s__Pseudidiomarina homiensis	80.1617	315	880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987395.1	s__Pseudidiomarina aquimaris	80.0024	334	880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.26	97.14	0.86	0.77	3	-
GCF_004214835.1	s__Pseudidiomarina tainanensis	79.9563	189	880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.72	97.72	0.94	0.94	2	-
GCF_900116895.1	s__Pseudidiomarina donghaiensis	79.502	209	880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	0.99	0.99	2	-
GCF_902806985.1	s__Pseudidiomarina piscicola	79.4837	261	880	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	79.1221	206	880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423165.1	s__Pseudidiomarina sediminum	78.9166	270	880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003987215.1	s__Pseudidiomarina halophila	78.896	290	880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987065.1	s__Pseudidiomarina insulisalsae	78.7317	281	880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001870515.1	s__Idiomarina sp001870515	78.7163	82	880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000753715.1	s__Pseudidiomarina salinarum	78.6103	124	880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003987355.1	s__Pseudidiomarina aestuarii	78.2893	155	880	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	77.8884	84	880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685255.1	s__Idiomarina sp002685255	77.7554	74	880	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.23	98.54	0.93	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:10,513] [INFO] GTDB search result was written to GCF_000753735.1_ASM75373v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:10,514] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:10,517] [INFO] DFAST_QC result json was written to GCF_000753735.1_ASM75373v1_genomic.fna/dqc_result.json
[2024-01-25 19:47:10,517] [INFO] DFAST_QC completed!
[2024-01-25 19:47:10,517] [INFO] Total running time: 0h1m4s