[2024-01-25 20:24:05,501] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:24:05,503] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:24:05,503] [INFO] DQC Reference Directory: /var/lib/cwl/stgf17bd4a0-2c7f-4e8c-a6e9-087fccf34eb9/dqc_reference
[2024-01-25 20:24:06,673] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:24:06,674] [INFO] Task started: Prodigal
[2024-01-25 20:24:06,674] [INFO] Running command: gunzip -c /var/lib/cwl/stg1dbd8012-ed73-44d4-b0f1-776836bfaec1/GCF_902859735.1_LMG_26852_genomic.fna.gz | prodigal -d GCF_902859735.1_LMG_26852_genomic.fna/cds.fna -a GCF_902859735.1_LMG_26852_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:24:26,826] [INFO] Task succeeded: Prodigal
[2024-01-25 20:24:26,826] [INFO] Task started: HMMsearch
[2024-01-25 20:24:26,827] [INFO] Running command: hmmsearch --tblout GCF_902859735.1_LMG_26852_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf17bd4a0-2c7f-4e8c-a6e9-087fccf34eb9/dqc_reference/reference_markers.hmm GCF_902859735.1_LMG_26852_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:24:27,136] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:24:27,137] [INFO] Found 6/6 markers.
[2024-01-25 20:24:27,190] [INFO] Query marker FASTA was written to GCF_902859735.1_LMG_26852_genomic.fna/markers.fasta
[2024-01-25 20:24:27,190] [INFO] Task started: Blastn
[2024-01-25 20:24:27,190] [INFO] Running command: blastn -query GCF_902859735.1_LMG_26852_genomic.fna/markers.fasta -db /var/lib/cwl/stgf17bd4a0-2c7f-4e8c-a6e9-087fccf34eb9/dqc_reference/reference_markers.fasta -out GCF_902859735.1_LMG_26852_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:28,203] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:28,206] [INFO] Selected 10 target genomes.
[2024-01-25 20:24:28,206] [INFO] Target genome list was writen to GCF_902859735.1_LMG_26852_genomic.fna/target_genomes.txt
[2024-01-25 20:24:28,214] [INFO] Task started: fastANI
[2024-01-25 20:24:28,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dbd8012-ed73-44d4-b0f1-776836bfaec1/GCF_902859735.1_LMG_26852_genomic.fna.gz --refList GCF_902859735.1_LMG_26852_genomic.fna/target_genomes.txt --output GCF_902859735.1_LMG_26852_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:24:44,272] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:44,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf17bd4a0-2c7f-4e8c-a6e9-087fccf34eb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:24:44,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf17bd4a0-2c7f-4e8c-a6e9-087fccf34eb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:24:44,280] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:24:44,280] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:24:44,280] [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 aegrifaciens	strain=LMG 26852	GCA_902859735.1	1287736	1287736	type	True	100.0	2140	2142	95	conclusive
Achromobacter anxifer	strain=LMG 26857	GCA_903652925.1	1287737	1287737	type	True	91.0013	1844	2142	95	below_threshold
Achromobacter insolitus	strain=LMG 6003	GCA_002209555.1	217204	217204	type	True	89.884	1832	2142	95	below_threshold
Achromobacter insolitus	strain=NCTC13520	GCA_900637265.1	217204	217204	type	True	89.8825	1858	2142	95	below_threshold
Achromobacter insolitus	strain=LMG 6003	GCA_902859615.1	217204	217204	type	True	89.8806	1844	2142	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	89.8501	1852	2142	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	86.3987	1512	2142	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	82.6555	912	2142	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.8857	326	2142	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.7806	528	2142	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:24:44,282] [INFO] DFAST Taxonomy check result was written to GCF_902859735.1_LMG_26852_genomic.fna/tc_result.tsv
[2024-01-25 20:24:44,285] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:24:44,285] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:24:44,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf17bd4a0-2c7f-4e8c-a6e9-087fccf34eb9/dqc_reference/checkm_data
[2024-01-25 20:24:44,286] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:24:44,349] [INFO] Task started: CheckM
[2024-01-25 20:24:44,350] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902859735.1_LMG_26852_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902859735.1_LMG_26852_genomic.fna/checkm_input GCF_902859735.1_LMG_26852_genomic.fna/checkm_result
[2024-01-25 20:25:41,725] [INFO] Task succeeded: CheckM
[2024-01-25 20:25:41,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:25:41,748] [INFO] ===== Completeness check finished =====
[2024-01-25 20:25:41,748] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:25:41,749] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902859735.1_LMG_26852_genomic.fna/markers.fasta)
[2024-01-25 20:25:41,749] [INFO] Task started: Blastn
[2024-01-25 20:25:41,749] [INFO] Running command: blastn -query GCF_902859735.1_LMG_26852_genomic.fna/markers.fasta -db /var/lib/cwl/stgf17bd4a0-2c7f-4e8c-a6e9-087fccf34eb9/dqc_reference/reference_markers_gtdb.fasta -out GCF_902859735.1_LMG_26852_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:25:43,796] [INFO] Task succeeded: Blastn
[2024-01-25 20:25:43,799] [INFO] Selected 8 target genomes.
[2024-01-25 20:25:43,799] [INFO] Target genome list was writen to GCF_902859735.1_LMG_26852_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:25:43,813] [INFO] Task started: fastANI
[2024-01-25 20:25:43,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dbd8012-ed73-44d4-b0f1-776836bfaec1/GCF_902859735.1_LMG_26852_genomic.fna.gz --refList GCF_902859735.1_LMG_26852_genomic.fna/target_genomes_gtdb.txt --output GCF_902859735.1_LMG_26852_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:25:59,158] [INFO] Task succeeded: fastANI
[2024-01-25 20:25:59,164] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:25:59,165] [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_902859735.1	s__Achromobacter aegrifaciens	100.0	2140	2142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.14	98.95	0.96	0.93	10	conclusive
GCF_014490035.1	s__Achromobacter bronchisepticus_A	94.9703	1946	2142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.75	98.99	0.98	0.93	5	-
GCF_002192695.1	s__Achromobacter xylosoxidans_C	93.9529	1923	2142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.40	98.40	0.91	0.91	2	-
GCF_013267355.1	s__Achromobacter pestifer_A	93.1615	1923	2142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000165835.1	s__Achromobacter xylosoxidans_B	92.3237	1956	2142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	96.34	96.34	0.92	0.92	2	-
GCF_903652925.1	s__Achromobacter anxifer	90.9909	1845	2142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.16	99.16	0.95	0.95	2	-
GCF_002209555.1	s__Achromobacter insolitus	89.8811	1832	2142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.13	98.86	0.96	0.89	17	-
GCF_002885955.2	s__Achromobacter pulmonis_A	87.4873	1509	2142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:25:59,166] [INFO] GTDB search result was written to GCF_902859735.1_LMG_26852_genomic.fna/result_gtdb.tsv
[2024-01-25 20:25:59,166] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:25:59,169] [INFO] DFAST_QC result json was written to GCF_902859735.1_LMG_26852_genomic.fna/dqc_result.json
[2024-01-25 20:25:59,169] [INFO] DFAST_QC completed!
[2024-01-25 20:25:59,169] [INFO] Total running time: 0h1m54s