[2024-01-24 12:42:08,649] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:08,653] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:08,653] [INFO] DQC Reference Directory: /var/lib/cwl/stg445d4236-5f86-4cc5-af8e-4cb6954cf269/dqc_reference
[2024-01-24 12:42:10,012] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:10,013] [INFO] Task started: Prodigal
[2024-01-24 12:42:10,014] [INFO] Running command: gunzip -c /var/lib/cwl/stgce1514f1-a2db-42ed-96ce-dc3cf8ad6017/GCF_003007715.1_ASM300771v1_genomic.fna.gz | prodigal -d GCF_003007715.1_ASM300771v1_genomic.fna/cds.fna -a GCF_003007715.1_ASM300771v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:22,586] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:22,587] [INFO] Task started: HMMsearch
[2024-01-24 12:42:22,587] [INFO] Running command: hmmsearch --tblout GCF_003007715.1_ASM300771v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg445d4236-5f86-4cc5-af8e-4cb6954cf269/dqc_reference/reference_markers.hmm GCF_003007715.1_ASM300771v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:22,870] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:22,872] [INFO] Found 6/6 markers.
[2024-01-24 12:42:22,913] [INFO] Query marker FASTA was written to GCF_003007715.1_ASM300771v1_genomic.fna/markers.fasta
[2024-01-24 12:42:22,914] [INFO] Task started: Blastn
[2024-01-24 12:42:22,914] [INFO] Running command: blastn -query GCF_003007715.1_ASM300771v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg445d4236-5f86-4cc5-af8e-4cb6954cf269/dqc_reference/reference_markers.fasta -out GCF_003007715.1_ASM300771v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:23,748] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:23,753] [INFO] Selected 15 target genomes.
[2024-01-24 12:42:23,753] [INFO] Target genome list was writen to GCF_003007715.1_ASM300771v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:23,760] [INFO] Task started: fastANI
[2024-01-24 12:42:23,761] [INFO] Running command: fastANI --query /var/lib/cwl/stgce1514f1-a2db-42ed-96ce-dc3cf8ad6017/GCF_003007715.1_ASM300771v1_genomic.fna.gz --refList GCF_003007715.1_ASM300771v1_genomic.fna/target_genomes.txt --output GCF_003007715.1_ASM300771v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:36,554] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:36,554] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg445d4236-5f86-4cc5-af8e-4cb6954cf269/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:36,555] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg445d4236-5f86-4cc5-af8e-4cb6954cf269/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:36,579] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:42:36,580] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:36,580] [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 shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	100.0	1371	1374	95	conclusive
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	96.5612	1194	1374	95	conclusive
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	82.9677	755	1374	95	below_threshold
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	81.9949	866	1374	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	81.8936	750	1374	95	below_threshold
Marinobacter halophilus	strain=CGMCC 1.12481	GCA_014637865.1	1323740	1323740	type	True	81.8827	863	1374	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.7047	616	1374	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	80.4974	610	1374	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	80.0785	623	1374	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	79.9608	538	1374	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	79.5663	523	1374	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	79.4361	555	1374	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	79.3262	562	1374	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	79.0699	390	1374	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.7661	453	1374	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:36,581] [INFO] DFAST Taxonomy check result was written to GCF_003007715.1_ASM300771v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:36,582] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:36,582] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:36,583] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg445d4236-5f86-4cc5-af8e-4cb6954cf269/dqc_reference/checkm_data
[2024-01-24 12:42:36,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:36,625] [INFO] Task started: CheckM
[2024-01-24 12:42:36,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003007715.1_ASM300771v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003007715.1_ASM300771v1_genomic.fna/checkm_input GCF_003007715.1_ASM300771v1_genomic.fna/checkm_result
[2024-01-24 12:43:16,433] [INFO] Task succeeded: CheckM
[2024-01-24 12:43:16,434] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:43:16,459] [INFO] ===== Completeness check finished =====
[2024-01-24 12:43:16,460] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:43:16,460] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003007715.1_ASM300771v1_genomic.fna/markers.fasta)
[2024-01-24 12:43:16,461] [INFO] Task started: Blastn
[2024-01-24 12:43:16,461] [INFO] Running command: blastn -query GCF_003007715.1_ASM300771v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg445d4236-5f86-4cc5-af8e-4cb6954cf269/dqc_reference/reference_markers_gtdb.fasta -out GCF_003007715.1_ASM300771v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:43:17,892] [INFO] Task succeeded: Blastn
[2024-01-24 12:43:17,896] [INFO] Selected 12 target genomes.
[2024-01-24 12:43:17,897] [INFO] Target genome list was writen to GCF_003007715.1_ASM300771v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:43:17,906] [INFO] Task started: fastANI
[2024-01-24 12:43:17,906] [INFO] Running command: fastANI --query /var/lib/cwl/stgce1514f1-a2db-42ed-96ce-dc3cf8ad6017/GCF_003007715.1_ASM300771v1_genomic.fna.gz --refList GCF_003007715.1_ASM300771v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003007715.1_ASM300771v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:28,344] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:28,364] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:43:28,365] [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_003007715.1	s__Marinobacter shengliensis	100.0	1372	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.96	95.10	0.86	0.82	7	conclusive
GCF_001447155.2	s__Marinobacter sp001447155	94.4308	1157	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002258215.1	s__Marinobacter vinifirmus	82.9725	753	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_000934705.1	s__Marinobacter excellens	82.5793	886	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018402255.1	s__Marinobacter sp018402255	82.4999	817	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.33	99.33	0.88	0.88	2	-
GCA_014859525.1	s__Marinobacter sp014859525	82.4269	736	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007685.1	s__Marinobacter halophilus	81.9996	867	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000284615.1	s__Marinobacter hydrocarbonoclasticus	81.8133	786	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.10	96.48	0.88	0.81	26	-
GCF_003315345.1	s__Marinobacter pelagius_A	80.613	616	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744735.1	s__Marinobacter guineae	80.0694	624	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820575.1	s__Marinobacter sediminum	79.5507	524	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643965.1	s__Marinobacter sp017643965	79.5276	464	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:43:28,367] [INFO] GTDB search result was written to GCF_003007715.1_ASM300771v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:28,367] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:28,371] [INFO] DFAST_QC result json was written to GCF_003007715.1_ASM300771v1_genomic.fna/dqc_result.json
[2024-01-24 12:43:28,371] [INFO] DFAST_QC completed!
[2024-01-24 12:43:28,372] [INFO] Total running time: 0h1m20s