[2023-03-17 09:33:10,008] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:33:10,008] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:33:10,008] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f334fa3-9e7c-4fde-8022-4c8c62bc90ab/dqc_reference
[2023-03-17 09:33:11,111] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:33:11,111] [INFO] Task started: Prodigal
[2023-03-17 09:33:11,112] [INFO] Running command: cat /var/lib/cwl/stg82894d68-d68b-4968-acaa-5f6dfc615570/OceanDNA-b33284.fa | prodigal -d OceanDNA-b33284/cds.fna -a OceanDNA-b33284/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:33:30,477] [INFO] Task succeeded: Prodigal
[2023-03-17 09:33:30,477] [INFO] Task started: HMMsearch
[2023-03-17 09:33:30,477] [INFO] Running command: hmmsearch --tblout OceanDNA-b33284/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f334fa3-9e7c-4fde-8022-4c8c62bc90ab/dqc_reference/reference_markers.hmm OceanDNA-b33284/protein.faa > /dev/null
[2023-03-17 09:33:30,709] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:33:30,710] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg82894d68-d68b-4968-acaa-5f6dfc615570/OceanDNA-b33284.fa]
[2023-03-17 09:33:30,745] [INFO] Query marker FASTA was written to OceanDNA-b33284/markers.fasta
[2023-03-17 09:33:30,746] [INFO] Task started: Blastn
[2023-03-17 09:33:30,746] [INFO] Running command: blastn -query OceanDNA-b33284/markers.fasta -db /var/lib/cwl/stg2f334fa3-9e7c-4fde-8022-4c8c62bc90ab/dqc_reference/reference_markers.fasta -out OceanDNA-b33284/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:33:31,396] [INFO] Task succeeded: Blastn
[2023-03-17 09:33:31,396] [INFO] Selected 11 target genomes.
[2023-03-17 09:33:31,397] [INFO] Target genome list was writen to OceanDNA-b33284/target_genomes.txt
[2023-03-17 09:33:31,431] [INFO] Task started: fastANI
[2023-03-17 09:33:31,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg82894d68-d68b-4968-acaa-5f6dfc615570/OceanDNA-b33284.fa --refList OceanDNA-b33284/target_genomes.txt --output OceanDNA-b33284/fastani_result.tsv --threads 1
[2023-03-17 09:33:43,535] [INFO] Task succeeded: fastANI
[2023-03-17 09:33:43,535] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f334fa3-9e7c-4fde-8022-4c8c62bc90ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:33:43,535] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f334fa3-9e7c-4fde-8022-4c8c62bc90ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:33:43,543] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:33:43,543] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:33:43,544] [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
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	94.2856	656	736	95	below_threshold
Achromobacter dolens	strain=LMG 26840	GCA_902859745.1	1287738	1287738	type	True	92.6536	629	736	95	below_threshold
Achromobacter ruhlandii	strain=LMG 1866	GCA_902859695.1	72557	72557	type	True	91.7923	619	736	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	91.5304	624	736	95	below_threshold
Achromobacter xylosoxidans	strain=FDAARGOS_789	GCA_013343135.1	85698	85698	type	True	91.5063	622	736	95	below_threshold
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	91.4894	617	736	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	91.4672	624	736	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	84.4716	498	736	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	81.5334	368	736	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.5645	124	736	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.419	201	736	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:33:43,544] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33284/tc_result.tsv
[2023-03-17 09:33:43,544] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:33:43,544] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:33:43,544] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f334fa3-9e7c-4fde-8022-4c8c62bc90ab/dqc_reference/checkm_data
[2023-03-17 09:33:43,545] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:33:43,582] [INFO] Task started: CheckM
[2023-03-17 09:33:43,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33284/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33284/checkm_input OceanDNA-b33284/checkm_result
[2023-03-17 09:34:33,061] [INFO] Task succeeded: CheckM
[2023-03-17 09:34:33,061] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:34:33,065] [INFO] ===== Completeness check finished =====
[2023-03-17 09:34:33,065] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:34:33,065] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33284/markers.fasta)
[2023-03-17 09:34:33,066] [INFO] Task started: Blastn
[2023-03-17 09:34:33,066] [INFO] Running command: blastn -query OceanDNA-b33284/markers.fasta -db /var/lib/cwl/stg2f334fa3-9e7c-4fde-8022-4c8c62bc90ab/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33284/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:34:34,174] [INFO] Task succeeded: Blastn
[2023-03-17 09:34:34,175] [INFO] Selected 6 target genomes.
[2023-03-17 09:34:34,175] [INFO] Target genome list was writen to OceanDNA-b33284/target_genomes_gtdb.txt
[2023-03-17 09:34:34,352] [INFO] Task started: fastANI
[2023-03-17 09:34:34,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg82894d68-d68b-4968-acaa-5f6dfc615570/OceanDNA-b33284.fa --refList OceanDNA-b33284/target_genomes_gtdb.txt --output OceanDNA-b33284/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:34:41,627] [INFO] Task succeeded: fastANI
[2023-03-17 09:34:41,632] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:34:41,632] [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_016127315.1	s__Achromobacter insuavis_A	97.2651	682	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	97.14	97.13	0.90	0.90	4	conclusive
GCF_902859645.1	s__Achromobacter insuavis	94.2553	657	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	99.48	98.86	0.95	0.90	7	-
GCF_902859745.1	s__Achromobacter dolens	92.6247	630	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0063	99.05	99.03	0.93	0.90	8	-
GCF_902859695.1	s__Achromobacter ruhlandii	91.7088	622	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0063	98.29	97.95	0.91	0.85	19	-
GCF_001457475.1	s__Achromobacter xylosoxidans	91.4675	624	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.72	96.70	0.93	0.87	75	-
GCF_902859765.1	s__Achromobacter pulmonis	90.1491	559	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.40	99.40	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-17 09:34:41,632] [INFO] GTDB search result was written to OceanDNA-b33284/result_gtdb.tsv
[2023-03-17 09:34:41,632] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:34:41,634] [INFO] DFAST_QC result json was written to OceanDNA-b33284/dqc_result.json
[2023-03-17 09:34:41,634] [INFO] DFAST_QC completed!
[2023-03-17 09:34:41,634] [INFO] Total running time: 0h1m32s