[2024-01-24 14:42:14,594] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:42:14,596] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:42:14,596] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f836b80-1285-4776-a150-c1be906bf834/dqc_reference
[2024-01-24 14:42:15,868] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:42:15,869] [INFO] Task started: Prodigal
[2024-01-24 14:42:15,869] [INFO] Running command: gunzip -c /var/lib/cwl/stga16c1711-b147-4d33-a19f-e86a7bcf29eb/GCF_005871095.1_ASM587109v1_genomic.fna.gz | prodigal -d GCF_005871095.1_ASM587109v1_genomic.fna/cds.fna -a GCF_005871095.1_ASM587109v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:42:29,791] [INFO] Task succeeded: Prodigal
[2024-01-24 14:42:29,792] [INFO] Task started: HMMsearch
[2024-01-24 14:42:29,792] [INFO] Running command: hmmsearch --tblout GCF_005871095.1_ASM587109v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f836b80-1285-4776-a150-c1be906bf834/dqc_reference/reference_markers.hmm GCF_005871095.1_ASM587109v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:42:30,165] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:42:30,167] [INFO] Found 6/6 markers.
[2024-01-24 14:42:30,231] [INFO] Query marker FASTA was written to GCF_005871095.1_ASM587109v1_genomic.fna/markers.fasta
[2024-01-24 14:42:30,232] [INFO] Task started: Blastn
[2024-01-24 14:42:30,232] [INFO] Running command: blastn -query GCF_005871095.1_ASM587109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f836b80-1285-4776-a150-c1be906bf834/dqc_reference/reference_markers.fasta -out GCF_005871095.1_ASM587109v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:31,110] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:31,116] [INFO] Selected 19 target genomes.
[2024-01-24 14:42:31,117] [INFO] Target genome list was writen to GCF_005871095.1_ASM587109v1_genomic.fna/target_genomes.txt
[2024-01-24 14:42:31,126] [INFO] Task started: fastANI
[2024-01-24 14:42:31,127] [INFO] Running command: fastANI --query /var/lib/cwl/stga16c1711-b147-4d33-a19f-e86a7bcf29eb/GCF_005871095.1_ASM587109v1_genomic.fna.gz --refList GCF_005871095.1_ASM587109v1_genomic.fna/target_genomes.txt --output GCF_005871095.1_ASM587109v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:42:47,446] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:47,447] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f836b80-1285-4776-a150-c1be906bf834/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:42:47,448] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f836b80-1285-4776-a150-c1be906bf834/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:42:47,467] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:42:47,468] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:42:47,468] [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 subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	100.0	1523	1524	95	conclusive
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	96.602	1200	1524	95	conclusive
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	83.6612	783	1524	95	below_threshold
Marinobacter halophilus	strain=CGMCC 1.12481	GCA_014637865.1	1323740	1323740	type	True	81.7584	850	1524	95	below_threshold
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	81.7451	855	1524	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	81.7106	760	1524	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	80.8887	615	1524	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.4387	627	1524	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	80.0758	585	1524	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	79.9973	631	1524	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	79.7884	558	1524	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	79.7792	587	1524	95	below_threshold
Marinobacter alexandrii	strain=LZ-8	GCA_005871205.1	2570351	2570351	type	True	79.7572	527	1524	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	79.4861	512	1524	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	79.4046	395	1524	95	below_threshold
Marinobacter nitratireducens	strain=AK21	GCA_000708045.1	1137280	1137280	type	True	79.1509	527	1524	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.6538	457	1524	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	78.2374	374	1524	95	below_threshold
Marinobacter caseinilyticus	strain=M3-13	GCA_011074955.1	2692195	2692195	type	True	77.8944	266	1524	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:42:47,469] [INFO] DFAST Taxonomy check result was written to GCF_005871095.1_ASM587109v1_genomic.fna/tc_result.tsv
[2024-01-24 14:42:47,470] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:42:47,470] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:42:47,471] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f836b80-1285-4776-a150-c1be906bf834/dqc_reference/checkm_data
[2024-01-24 14:42:47,472] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:42:47,521] [INFO] Task started: CheckM
[2024-01-24 14:42:47,521] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005871095.1_ASM587109v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005871095.1_ASM587109v1_genomic.fna/checkm_input GCF_005871095.1_ASM587109v1_genomic.fna/checkm_result
[2024-01-24 14:43:31,692] [INFO] Task succeeded: CheckM
[2024-01-24 14:43:31,694] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:43:31,716] [INFO] ===== Completeness check finished =====
[2024-01-24 14:43:31,717] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:43:31,717] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005871095.1_ASM587109v1_genomic.fna/markers.fasta)
[2024-01-24 14:43:31,717] [INFO] Task started: Blastn
[2024-01-24 14:43:31,718] [INFO] Running command: blastn -query GCF_005871095.1_ASM587109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f836b80-1285-4776-a150-c1be906bf834/dqc_reference/reference_markers_gtdb.fasta -out GCF_005871095.1_ASM587109v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:43:33,639] [INFO] Task succeeded: Blastn
[2024-01-24 14:43:33,643] [INFO] Selected 14 target genomes.
[2024-01-24 14:43:33,644] [INFO] Target genome list was writen to GCF_005871095.1_ASM587109v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:43:33,656] [INFO] Task started: fastANI
[2024-01-24 14:43:33,657] [INFO] Running command: fastANI --query /var/lib/cwl/stga16c1711-b147-4d33-a19f-e86a7bcf29eb/GCF_005871095.1_ASM587109v1_genomic.fna.gz --refList GCF_005871095.1_ASM587109v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005871095.1_ASM587109v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:43:46,843] [INFO] Task succeeded: fastANI
[2024-01-24 14:43:46,860] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:43:46,861] [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	96.5786	1202	1524	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	94.6336	1198	1524	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	83.673	782	1524	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	82.5535	865	1524	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	82.4645	817	1524	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	82.4053	712	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284615.1	s__Marinobacter hydrocarbonoclasticus	81.91	774	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.10	96.48	0.88	0.81	26	-
GCF_003007685.1	s__Marinobacter halophilus	81.738	857	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900115175.1	s__Marinobacter gudaonensis	79.9895	633	1524	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	79.9647	465	1524	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	79.7794	524	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.69	98.69	0.90	0.90	2	-
GCF_016820575.1	s__Marinobacter sediminum	79.4958	510	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004327985.1	s__Marinobacter_A halodurans	78.2437	372	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011074955.1	s__Marinobacter caseinilyticus	77.8976	265	1524	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 14:43:46,863] [INFO] GTDB search result was written to GCF_005871095.1_ASM587109v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:43:46,863] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:43:46,867] [INFO] DFAST_QC result json was written to GCF_005871095.1_ASM587109v1_genomic.fna/dqc_result.json
[2024-01-24 14:43:46,867] [INFO] DFAST_QC completed!
[2024-01-24 14:43:46,867] [INFO] Total running time: 0h1m32s