[2024-01-25 19:08:20,948] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:08:20,950] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:08:20,951] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b39ad1d-8794-48ed-b4ef-118db41b2eea/dqc_reference
[2024-01-25 19:08:22,097] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:08:22,098] [INFO] Task started: Prodigal
[2024-01-25 19:08:22,098] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c7435d1-3f48-4ef1-821b-149364b2bf01/GCF_014652295.1_ASM1465229v1_genomic.fna.gz | prodigal -d GCF_014652295.1_ASM1465229v1_genomic.fna/cds.fna -a GCF_014652295.1_ASM1465229v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:08:30,798] [INFO] Task succeeded: Prodigal
[2024-01-25 19:08:30,798] [INFO] Task started: HMMsearch
[2024-01-25 19:08:30,798] [INFO] Running command: hmmsearch --tblout GCF_014652295.1_ASM1465229v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b39ad1d-8794-48ed-b4ef-118db41b2eea/dqc_reference/reference_markers.hmm GCF_014652295.1_ASM1465229v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:08:31,043] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:08:31,044] [INFO] Found 6/6 markers.
[2024-01-25 19:08:31,071] [INFO] Query marker FASTA was written to GCF_014652295.1_ASM1465229v1_genomic.fna/markers.fasta
[2024-01-25 19:08:31,071] [INFO] Task started: Blastn
[2024-01-25 19:08:31,071] [INFO] Running command: blastn -query GCF_014652295.1_ASM1465229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b39ad1d-8794-48ed-b4ef-118db41b2eea/dqc_reference/reference_markers.fasta -out GCF_014652295.1_ASM1465229v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:31,838] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:31,841] [INFO] Selected 18 target genomes.
[2024-01-25 19:08:31,841] [INFO] Target genome list was writen to GCF_014652295.1_ASM1465229v1_genomic.fna/target_genomes.txt
[2024-01-25 19:08:31,849] [INFO] Task started: fastANI
[2024-01-25 19:08:31,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c7435d1-3f48-4ef1-821b-149364b2bf01/GCF_014652295.1_ASM1465229v1_genomic.fna.gz --refList GCF_014652295.1_ASM1465229v1_genomic.fna/target_genomes.txt --output GCF_014652295.1_ASM1465229v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:08:46,313] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:46,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b39ad1d-8794-48ed-b4ef-118db41b2eea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:08:46,314] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b39ad1d-8794-48ed-b4ef-118db41b2eea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:08:46,324] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:08:46,325] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:08:46,325] [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 persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	100.0	1036	1039	95	conclusive
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	99.9838	1034	1039	95	conclusive
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	81.4609	593	1039	95	below_threshold
Marinobacter oulmenensis	strain=DSM 22359	GCA_014201735.1	643747	643747	type	True	80.8911	591	1039	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	80.5277	527	1039	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	80.4441	521	1039	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	80.3354	426	1039	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.2127	533	1039	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	79.9489	388	1039	95	below_threshold
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	79.9057	486	1039	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	79.8739	459	1039	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	79.752	419	1039	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	79.6524	423	1039	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	79.5841	444	1039	95	below_threshold
Marinobacter alexandrii	strain=LZ-8	GCA_005871205.1	2570351	2570351	type	True	79.5553	427	1039	95	below_threshold
Marinobacter santoriniensis	strain=NKSG1	GCA_000347775.1	523742	523742	type	True	79.4572	382	1039	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	79.0715	385	1039	95	below_threshold
Marinobacter salinus	strain=Hb8	GCA_001854125.1	1874317	1874317	type	True	78.8733	369	1039	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:08:46,326] [INFO] DFAST Taxonomy check result was written to GCF_014652295.1_ASM1465229v1_genomic.fna/tc_result.tsv
[2024-01-25 19:08:46,327] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:08:46,328] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:08:46,328] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b39ad1d-8794-48ed-b4ef-118db41b2eea/dqc_reference/checkm_data
[2024-01-25 19:08:46,329] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:08:46,362] [INFO] Task started: CheckM
[2024-01-25 19:08:46,362] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652295.1_ASM1465229v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652295.1_ASM1465229v1_genomic.fna/checkm_input GCF_014652295.1_ASM1465229v1_genomic.fna/checkm_result
[2024-01-25 19:09:14,705] [INFO] Task succeeded: CheckM
[2024-01-25 19:09:14,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:09:14,724] [INFO] ===== Completeness check finished =====
[2024-01-25 19:09:14,724] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:09:14,725] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652295.1_ASM1465229v1_genomic.fna/markers.fasta)
[2024-01-25 19:09:14,725] [INFO] Task started: Blastn
[2024-01-25 19:09:14,725] [INFO] Running command: blastn -query GCF_014652295.1_ASM1465229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b39ad1d-8794-48ed-b4ef-118db41b2eea/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652295.1_ASM1465229v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:16,044] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:16,047] [INFO] Selected 13 target genomes.
[2024-01-25 19:09:16,047] [INFO] Target genome list was writen to GCF_014652295.1_ASM1465229v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:09:16,049] [INFO] Task started: fastANI
[2024-01-25 19:09:16,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c7435d1-3f48-4ef1-821b-149364b2bf01/GCF_014652295.1_ASM1465229v1_genomic.fna.gz --refList GCF_014652295.1_ASM1465229v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652295.1_ASM1465229v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:09:25,589] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:25,597] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:09:25,598] [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_900114155.1	s__Marinobacter persicus	99.9838	1034	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCA_013393545.1	s__Marinobacter sp013393545	87.5978	686	1039	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	84.0293	730	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	0.99	0.99	3	-
GCF_002258215.1	s__Marinobacter vinifirmus	81.4529	594	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_003315345.1	s__Marinobacter pelagius_A	80.8774	505	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201735.1	s__Marinobacter oulmenensis	80.8728	592	1039	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	80.4301	418	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114925.1	s__Marinobacter pelagius	80.2046	533	1039	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	79.8881	488	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003007675.1	s__Marinobacter fuscus	79.8739	459	1039	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	79.757	368	1039	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	79.752	419	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871205.1	s__Marinobacter alexandrii	79.5456	426	1039	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.69	98.69	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:09:25,599] [INFO] GTDB search result was written to GCF_014652295.1_ASM1465229v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:09:25,600] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:09:25,604] [INFO] DFAST_QC result json was written to GCF_014652295.1_ASM1465229v1_genomic.fna/dqc_result.json
[2024-01-25 19:09:25,604] [INFO] DFAST_QC completed!
[2024-01-25 19:09:25,604] [INFO] Total running time: 0h1m5s