[2024-01-24 12:16:08,723] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:08,725] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:08,725] [INFO] DQC Reference Directory: /var/lib/cwl/stg29afa32e-a27e-4c2b-aaac-9ebbe65a3611/dqc_reference
[2024-01-24 12:16:10,033] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:10,034] [INFO] Task started: Prodigal
[2024-01-24 12:16:10,034] [INFO] Running command: gunzip -c /var/lib/cwl/stg977926a6-808b-497a-9814-d8822093ce1d/GCF_000347775.1_ASM34777v1_genomic.fna.gz | prodigal -d GCF_000347775.1_ASM34777v1_genomic.fna/cds.fna -a GCF_000347775.1_ASM34777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:21,960] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:21,961] [INFO] Task started: HMMsearch
[2024-01-24 12:16:21,961] [INFO] Running command: hmmsearch --tblout GCF_000347775.1_ASM34777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29afa32e-a27e-4c2b-aaac-9ebbe65a3611/dqc_reference/reference_markers.hmm GCF_000347775.1_ASM34777v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:22,273] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:22,274] [INFO] Found 6/6 markers.
[2024-01-24 12:16:22,321] [INFO] Query marker FASTA was written to GCF_000347775.1_ASM34777v1_genomic.fna/markers.fasta
[2024-01-24 12:16:22,322] [INFO] Task started: Blastn
[2024-01-24 12:16:22,322] [INFO] Running command: blastn -query GCF_000347775.1_ASM34777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29afa32e-a27e-4c2b-aaac-9ebbe65a3611/dqc_reference/reference_markers.fasta -out GCF_000347775.1_ASM34777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:23,139] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:23,142] [INFO] Selected 16 target genomes.
[2024-01-24 12:16:23,142] [INFO] Target genome list was writen to GCF_000347775.1_ASM34777v1_genomic.fna/target_genomes.txt
[2024-01-24 12:16:23,148] [INFO] Task started: fastANI
[2024-01-24 12:16:23,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg977926a6-808b-497a-9814-d8822093ce1d/GCF_000347775.1_ASM34777v1_genomic.fna.gz --refList GCF_000347775.1_ASM34777v1_genomic.fna/target_genomes.txt --output GCF_000347775.1_ASM34777v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:35,216] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:35,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29afa32e-a27e-4c2b-aaac-9ebbe65a3611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:35,218] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29afa32e-a27e-4c2b-aaac-9ebbe65a3611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:35,235] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:16:35,235] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:35,235] [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 santoriniensis	strain=NKSG1	GCA_000347775.1	523742	523742	type	True	100.0	1323	1325	95	conclusive
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	91.9968	1124	1325	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	81.2819	672	1325	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	79.8574	486	1325	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	79.7558	569	1325	95	below_threshold
Marinobacter nitratireducens	strain=AK21	GCA_000708045.1	1137280	1137280	type	True	79.6992	513	1325	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	79.6504	491	1325	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	79.4816	377	1325	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	79.465	506	1325	95	below_threshold
Marinobacter persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	79.4638	397	1325	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	79.4495	520	1325	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	79.3637	503	1325	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	79.2075	478	1325	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	79.1962	481	1325	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.7493	417	1325	95	below_threshold
Marinobacter zhejiangensis	strain=CGMCC 1.7061	GCA_900114775.1	488535	488535	type	True	78.4955	326	1325	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:35,238] [INFO] DFAST Taxonomy check result was written to GCF_000347775.1_ASM34777v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:35,239] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:35,239] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:35,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29afa32e-a27e-4c2b-aaac-9ebbe65a3611/dqc_reference/checkm_data
[2024-01-24 12:16:35,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:35,288] [INFO] Task started: CheckM
[2024-01-24 12:16:35,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000347775.1_ASM34777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000347775.1_ASM34777v1_genomic.fna/checkm_input GCF_000347775.1_ASM34777v1_genomic.fna/checkm_result
[2024-01-24 12:17:13,532] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:13,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:13,558] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:13,559] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:13,559] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000347775.1_ASM34777v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:13,559] [INFO] Task started: Blastn
[2024-01-24 12:17:13,560] [INFO] Running command: blastn -query GCF_000347775.1_ASM34777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29afa32e-a27e-4c2b-aaac-9ebbe65a3611/dqc_reference/reference_markers_gtdb.fasta -out GCF_000347775.1_ASM34777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:14,887] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:14,892] [INFO] Selected 10 target genomes.
[2024-01-24 12:17:14,892] [INFO] Target genome list was writen to GCF_000347775.1_ASM34777v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:14,900] [INFO] Task started: fastANI
[2024-01-24 12:17:14,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg977926a6-808b-497a-9814-d8822093ce1d/GCF_000347775.1_ASM34777v1_genomic.fna.gz --refList GCF_000347775.1_ASM34777v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000347775.1_ASM34777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:22,702] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:22,718] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:22,718] [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_000347775.1	s__Marinobacter santoriniensis	100.0	1323	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900114925.1	s__Marinobacter pelagius	81.2719	673	1325	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	81.23	659	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623515.1	s__Marinobacter sp018623515	80.7854	565	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762755.1	s__Marinobacter sp014762755	80.4919	500	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166295.1	s__Marinobacter adhaerens	79.9272	590	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCF_002934325.1	s__Marinobacter persicus_A	79.7469	418	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	0.99	0.99	3	-
GCF_001447155.2	s__Marinobacter sp001447155	79.7102	512	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188435.1	s__Marinobacter sp900188435	79.7077	614	1325	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	79.447	508	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.96	95.10	0.86	0.82	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:22,720] [INFO] GTDB search result was written to GCF_000347775.1_ASM34777v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:22,720] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:22,724] [INFO] DFAST_QC result json was written to GCF_000347775.1_ASM34777v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:22,724] [INFO] DFAST_QC completed!
[2024-01-24 12:17:22,724] [INFO] Total running time: 0h1m14s