[2024-01-24 13:01:38,050] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:38,052] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:38,052] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfd229ce-3269-4063-9c76-4e7a2722cb95/dqc_reference
[2024-01-24 13:01:40,904] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:40,905] [INFO] Task started: Prodigal
[2024-01-24 13:01:40,906] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfc37e7b-86f4-4da7-9de6-b7bf1a591eba/GCF_003387155.1_ASM338715v1_genomic.fna.gz | prodigal -d GCF_003387155.1_ASM338715v1_genomic.fna/cds.fna -a GCF_003387155.1_ASM338715v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:00,099] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:00,100] [INFO] Task started: HMMsearch
[2024-01-24 13:02:00,100] [INFO] Running command: hmmsearch --tblout GCF_003387155.1_ASM338715v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfd229ce-3269-4063-9c76-4e7a2722cb95/dqc_reference/reference_markers.hmm GCF_003387155.1_ASM338715v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:00,572] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:00,573] [INFO] Found 6/6 markers.
[2024-01-24 13:02:00,648] [INFO] Query marker FASTA was written to GCF_003387155.1_ASM338715v1_genomic.fna/markers.fasta
[2024-01-24 13:02:00,649] [INFO] Task started: Blastn
[2024-01-24 13:02:00,649] [INFO] Running command: blastn -query GCF_003387155.1_ASM338715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfd229ce-3269-4063-9c76-4e7a2722cb95/dqc_reference/reference_markers.fasta -out GCF_003387155.1_ASM338715v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:01,958] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:01,962] [INFO] Selected 16 target genomes.
[2024-01-24 13:02:01,963] [INFO] Target genome list was writen to GCF_003387155.1_ASM338715v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:01,975] [INFO] Task started: fastANI
[2024-01-24 13:02:01,975] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfc37e7b-86f4-4da7-9de6-b7bf1a591eba/GCF_003387155.1_ASM338715v1_genomic.fna.gz --refList GCF_003387155.1_ASM338715v1_genomic.fna/target_genomes.txt --output GCF_003387155.1_ASM338715v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:20,814] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:20,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfd229ce-3269-4063-9c76-4e7a2722cb95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:20,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfd229ce-3269-4063-9c76-4e7a2722cb95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:20,830] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:20,831] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:20,831] [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
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	100.0	1877	1878	95	conclusive
Roseateles terrae	strain=CECT 7247	GCA_014192155.1	431060	431060	type	True	87.0692	1542	1878	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	82.5784	1112	1878	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	80.1548	778	1878	95	below_threshold
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	80.0854	747	1878	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.8622	604	1878	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	79.6511	684	1878	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	79.6197	537	1878	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.526	602	1878	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	79.3698	541	1878	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	79.3697	532	1878	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	79.2682	568	1878	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	79.2578	538	1878	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	78.8812	639	1878	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	78.7459	525	1878	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.6684	491	1878	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:20,833] [INFO] DFAST Taxonomy check result was written to GCF_003387155.1_ASM338715v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:20,833] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:20,834] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:20,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfd229ce-3269-4063-9c76-4e7a2722cb95/dqc_reference/checkm_data
[2024-01-24 13:02:20,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:20,911] [INFO] Task started: CheckM
[2024-01-24 13:02:20,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003387155.1_ASM338715v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003387155.1_ASM338715v1_genomic.fna/checkm_input GCF_003387155.1_ASM338715v1_genomic.fna/checkm_result
[2024-01-24 13:04:00,626] [INFO] Task succeeded: CheckM
[2024-01-24 13:04:00,628] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:04:00,655] [INFO] ===== Completeness check finished =====
[2024-01-24 13:04:00,655] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:04:00,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003387155.1_ASM338715v1_genomic.fna/markers.fasta)
[2024-01-24 13:04:00,657] [INFO] Task started: Blastn
[2024-01-24 13:04:00,657] [INFO] Running command: blastn -query GCF_003387155.1_ASM338715v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfd229ce-3269-4063-9c76-4e7a2722cb95/dqc_reference/reference_markers_gtdb.fasta -out GCF_003387155.1_ASM338715v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:04:02,578] [INFO] Task succeeded: Blastn
[2024-01-24 13:04:02,582] [INFO] Selected 9 target genomes.
[2024-01-24 13:04:02,583] [INFO] Target genome list was writen to GCF_003387155.1_ASM338715v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:04:02,590] [INFO] Task started: fastANI
[2024-01-24 13:04:02,590] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfc37e7b-86f4-4da7-9de6-b7bf1a591eba/GCF_003387155.1_ASM338715v1_genomic.fna.gz --refList GCF_003387155.1_ASM338715v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003387155.1_ASM338715v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:04:14,994] [INFO] Task succeeded: fastANI
[2024-01-24 13:04:15,010] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:04:15,010] [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_003387155.1	s__Roseateles depolymerans	100.0	1877	1878	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Roseateles	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014192155.1	s__Roseateles terrae	87.0818	1540	1878	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Roseateles	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900109745.1	s__Roseateles sp900109745	84.4004	1311	1878	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Roseateles	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113225.1	s__Mitsuaria sp900113225	82.8167	1163	1878	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	98.36	98.28	0.95	0.95	4	-
GCF_002761755.1	s__Mitsuaria sp002761755	82.5905	1110	1878	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002205645.1	s__Mitsuaria aquatilis	82.5665	1118	1878	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598255.1	s__Mitsuaria chitosanitabida	82.5195	1155	1878	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	99.05	99.05	0.96	0.96	2	-
GCA_002205125.1	s__Mitsuaria noduli	82.2084	1124	1878	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653795.1	s__Mitsuaria sp001653795	81.915	1041	1878	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:04:15,012] [INFO] GTDB search result was written to GCF_003387155.1_ASM338715v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:04:15,013] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:04:15,018] [INFO] DFAST_QC result json was written to GCF_003387155.1_ASM338715v1_genomic.fna/dqc_result.json
[2024-01-24 13:04:15,018] [INFO] DFAST_QC completed!
[2024-01-24 13:04:15,018] [INFO] Total running time: 0h2m37s