[2024-01-25 19:04:50,408] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:04:50,409] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:04:50,409] [INFO] DQC Reference Directory: /var/lib/cwl/stg7783bc52-c4b2-46d3-80cc-289d003a069f/dqc_reference
[2024-01-25 19:04:51,559] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:04:51,559] [INFO] Task started: Prodigal
[2024-01-25 19:04:51,560] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c36ba4a-698f-4d02-a0ab-a4d4afdcb6e8/GCF_003336705.1_ASM333670v1_genomic.fna.gz | prodigal -d GCF_003336705.1_ASM333670v1_genomic.fna/cds.fna -a GCF_003336705.1_ASM333670v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:05:00,574] [INFO] Task succeeded: Prodigal
[2024-01-25 19:05:00,574] [INFO] Task started: HMMsearch
[2024-01-25 19:05:00,574] [INFO] Running command: hmmsearch --tblout GCF_003336705.1_ASM333670v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7783bc52-c4b2-46d3-80cc-289d003a069f/dqc_reference/reference_markers.hmm GCF_003336705.1_ASM333670v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:05:00,805] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:05:00,806] [INFO] Found 6/6 markers.
[2024-01-25 19:05:00,836] [INFO] Query marker FASTA was written to GCF_003336705.1_ASM333670v1_genomic.fna/markers.fasta
[2024-01-25 19:05:00,836] [INFO] Task started: Blastn
[2024-01-25 19:05:00,836] [INFO] Running command: blastn -query GCF_003336705.1_ASM333670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7783bc52-c4b2-46d3-80cc-289d003a069f/dqc_reference/reference_markers.fasta -out GCF_003336705.1_ASM333670v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:01,559] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:01,562] [INFO] Selected 15 target genomes.
[2024-01-25 19:05:01,562] [INFO] Target genome list was writen to GCF_003336705.1_ASM333670v1_genomic.fna/target_genomes.txt
[2024-01-25 19:05:01,577] [INFO] Task started: fastANI
[2024-01-25 19:05:01,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c36ba4a-698f-4d02-a0ab-a4d4afdcb6e8/GCF_003336705.1_ASM333670v1_genomic.fna.gz --refList GCF_003336705.1_ASM333670v1_genomic.fna/target_genomes.txt --output GCF_003336705.1_ASM333670v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:05:14,533] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:14,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7783bc52-c4b2-46d3-80cc-289d003a069f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:05:14,534] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7783bc52-c4b2-46d3-80cc-289d003a069f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:05:14,543] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:05:14,543] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:05:14,543] [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 litoralis	strain=Sw-45	GCA_003336705.1	187981	187981	type	True	100.0	1147	1147	95	conclusive
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	80.8709	538	1147	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	80.0767	520	1147	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	80.0202	525	1147	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	79.8801	501	1147	95	below_threshold
Marinobacter halophilus	strain=CGMCC 1.12481	GCA_014637865.1	1323740	1323740	type	True	79.6222	495	1147	95	below_threshold
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	79.5948	496	1147	95	below_threshold
Marinobacter daepoensis	strain=DSM 16072	GCA_000421165.1	262077	262077	type	True	78.9515	451	1147	95	below_threshold
Marinobacter alexandrii	strain=LZ-8	GCA_005871205.1	2570351	2570351	type	True	78.8563	357	1147	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	78.7079	355	1147	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	78.6304	388	1147	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	78.5637	311	1147	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	76.533	82	1147	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	76.433	65	1147	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:05:14,544] [INFO] DFAST Taxonomy check result was written to GCF_003336705.1_ASM333670v1_genomic.fna/tc_result.tsv
[2024-01-25 19:05:14,545] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:05:14,545] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:05:14,545] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7783bc52-c4b2-46d3-80cc-289d003a069f/dqc_reference/checkm_data
[2024-01-25 19:05:14,546] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:05:14,581] [INFO] Task started: CheckM
[2024-01-25 19:05:14,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003336705.1_ASM333670v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003336705.1_ASM333670v1_genomic.fna/checkm_input GCF_003336705.1_ASM333670v1_genomic.fna/checkm_result
[2024-01-25 19:05:44,301] [INFO] Task succeeded: CheckM
[2024-01-25 19:05:44,302] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:05:44,319] [INFO] ===== Completeness check finished =====
[2024-01-25 19:05:44,319] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:05:44,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003336705.1_ASM333670v1_genomic.fna/markers.fasta)
[2024-01-25 19:05:44,320] [INFO] Task started: Blastn
[2024-01-25 19:05:44,320] [INFO] Running command: blastn -query GCF_003336705.1_ASM333670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7783bc52-c4b2-46d3-80cc-289d003a069f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003336705.1_ASM333670v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:45,559] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:45,561] [INFO] Selected 8 target genomes.
[2024-01-25 19:05:45,562] [INFO] Target genome list was writen to GCF_003336705.1_ASM333670v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:05:45,569] [INFO] Task started: fastANI
[2024-01-25 19:05:45,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c36ba4a-698f-4d02-a0ab-a4d4afdcb6e8/GCF_003336705.1_ASM333670v1_genomic.fna.gz --refList GCF_003336705.1_ASM333670v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003336705.1_ASM333670v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:51,947] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:51,953] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:05:51,953] [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_003336705.1	s__Marinobacter litoralis	100.0	1147	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.25	98.25	0.91	0.91	2	conclusive
GCF_004353225.1	s__Marinobacter sp004353225	87.1998	984	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016427555.1	s__Marinobacter litoralis_A	87.0607	924	1147	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	80.8783	537	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_003007715.1	s__Marinobacter shengliensis	80.0202	525	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.96	95.10	0.86	0.82	7	-
GCF_001447155.2	s__Marinobacter sp001447155	79.9498	530	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402255.1	s__Marinobacter sp018402255	79.8677	442	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.33	99.33	0.88	0.88	2	-
GCF_017301335.1	s__Marinobacter sp017301335	78.5421	302	1147	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:05:51,954] [INFO] GTDB search result was written to GCF_003336705.1_ASM333670v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:51,955] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:51,958] [INFO] DFAST_QC result json was written to GCF_003336705.1_ASM333670v1_genomic.fna/dqc_result.json
[2024-01-25 19:05:51,958] [INFO] DFAST_QC completed!
[2024-01-25 19:05:51,958] [INFO] Total running time: 0h1m2s