[2024-01-24 13:57:01,124] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:01,130] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:01,131] [INFO] DQC Reference Directory: /var/lib/cwl/stgca9dc84d-c894-40dc-b259-6d3cbf75473c/dqc_reference
[2024-01-24 13:57:02,541] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:02,542] [INFO] Task started: Prodigal
[2024-01-24 13:57:02,542] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbdd65c8-7c7c-40cd-87de-a5be7cf5d0ad/GCF_003634635.1_ASM363463v1_genomic.fna.gz | prodigal -d GCF_003634635.1_ASM363463v1_genomic.fna/cds.fna -a GCF_003634635.1_ASM363463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:14,689] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:14,689] [INFO] Task started: HMMsearch
[2024-01-24 13:57:14,689] [INFO] Running command: hmmsearch --tblout GCF_003634635.1_ASM363463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca9dc84d-c894-40dc-b259-6d3cbf75473c/dqc_reference/reference_markers.hmm GCF_003634635.1_ASM363463v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:15,062] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:15,064] [INFO] Found 6/6 markers.
[2024-01-24 13:57:15,102] [INFO] Query marker FASTA was written to GCF_003634635.1_ASM363463v1_genomic.fna/markers.fasta
[2024-01-24 13:57:15,103] [INFO] Task started: Blastn
[2024-01-24 13:57:15,103] [INFO] Running command: blastn -query GCF_003634635.1_ASM363463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca9dc84d-c894-40dc-b259-6d3cbf75473c/dqc_reference/reference_markers.fasta -out GCF_003634635.1_ASM363463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:15,947] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:15,951] [INFO] Selected 17 target genomes.
[2024-01-24 13:57:15,951] [INFO] Target genome list was writen to GCF_003634635.1_ASM363463v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:15,964] [INFO] Task started: fastANI
[2024-01-24 13:57:15,964] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbdd65c8-7c7c-40cd-87de-a5be7cf5d0ad/GCF_003634635.1_ASM363463v1_genomic.fna.gz --refList GCF_003634635.1_ASM363463v1_genomic.fna/target_genomes.txt --output GCF_003634635.1_ASM363463v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:29,372] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:29,373] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca9dc84d-c894-40dc-b259-6d3cbf75473c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:29,373] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca9dc84d-c894-40dc-b259-6d3cbf75473c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:29,387] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:29,388] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:29,388] [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
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	100.0	1321	1321	95	conclusive
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	82.7862	739	1321	95	below_threshold
Marinobacter daepoensis	strain=DSM 16072	GCA_000421165.1	262077	262077	type	True	81.9419	789	1321	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	81.6744	782	1321	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	81.6689	782	1321	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	81.2121	661	1321	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.5624	603	1321	95	below_threshold
Marinobacter halophilus	strain=CGMCC 1.12481	GCA_014637865.1	1323740	1323740	type	True	80.4942	694	1321	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	80.4913	523	1321	95	below_threshold
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	80.4141	707	1321	95	below_threshold
Marinobacter persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	80.4131	525	1321	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	80.0459	603	1321	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	79.9327	506	1321	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	79.7221	571	1321	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	79.7138	513	1321	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	79.1398	520	1321	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	79.0611	460	1321	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:29,390] [INFO] DFAST Taxonomy check result was written to GCF_003634635.1_ASM363463v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:29,390] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:29,390] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:29,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca9dc84d-c894-40dc-b259-6d3cbf75473c/dqc_reference/checkm_data
[2024-01-24 13:57:29,392] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:29,431] [INFO] Task started: CheckM
[2024-01-24 13:57:29,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003634635.1_ASM363463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003634635.1_ASM363463v1_genomic.fna/checkm_input GCF_003634635.1_ASM363463v1_genomic.fna/checkm_result
[2024-01-24 13:58:08,876] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:08,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:08,896] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:08,896] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:08,896] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003634635.1_ASM363463v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:08,897] [INFO] Task started: Blastn
[2024-01-24 13:58:08,897] [INFO] Running command: blastn -query GCF_003634635.1_ASM363463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca9dc84d-c894-40dc-b259-6d3cbf75473c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003634635.1_ASM363463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:10,229] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:10,233] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:10,233] [INFO] Target genome list was writen to GCF_003634635.1_ASM363463v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:10,253] [INFO] Task started: fastANI
[2024-01-24 13:58:10,253] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbdd65c8-7c7c-40cd-87de-a5be7cf5d0ad/GCF_003634635.1_ASM363463v1_genomic.fna.gz --refList GCF_003634635.1_ASM363463v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003634635.1_ASM363463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:21,802] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:21,814] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:21,814] [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_000284615.1	s__Marinobacter hydrocarbonoclasticus	97.5334	1208	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.10	96.48	0.88	0.81	26	conclusive
GCF_002258215.1	s__Marinobacter vinifirmus	82.8084	737	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_000421165.1	s__Marinobacter daepoensis	81.9419	789	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.99	98.99	0.93	0.93	2	-
GCF_001447155.2	s__Marinobacter sp001447155	81.9329	780	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007715.1	s__Marinobacter shengliensis	81.6744	782	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.96	95.10	0.86	0.82	7	-
GCF_003007675.1	s__Marinobacter fuscus	81.2121	661	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315345.1	s__Marinobacter pelagius_A	80.6487	593	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934325.1	s__Marinobacter persicus_A	80.6	523	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900114925.1	s__Marinobacter pelagius	80.5624	603	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114155.1	s__Marinobacter persicus	80.4806	524	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003007685.1	s__Marinobacter halophilus	80.409	708	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001650915.1	s__Marinobacter sp001650915	80.0406	620	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.33	97.47	0.91	0.86	4	-
GCF_008107725.1	s__Marinobacter sp008107725	79.8766	614	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686085.1	s__Marinobacter sp000686085	79.1992	567	1321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:21,816] [INFO] GTDB search result was written to GCF_003634635.1_ASM363463v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:21,816] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:21,821] [INFO] DFAST_QC result json was written to GCF_003634635.1_ASM363463v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:21,821] [INFO] DFAST_QC completed!
[2024-01-24 13:58:21,821] [INFO] Total running time: 0h1m21s