[2024-01-24 15:03:14,641] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:14,643] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:14,643] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4508572-d904-440f-9744-cf42c91a527a/dqc_reference
[2024-01-24 15:03:15,914] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:15,915] [INFO] Task started: Prodigal
[2024-01-24 15:03:15,916] [INFO] Running command: gunzip -c /var/lib/cwl/stge332f04f-7e60-42fb-bbe6-a50c3508b410/GCF_902859685.1_LMG_1873_genomic.fna.gz | prodigal -d GCF_902859685.1_LMG_1873_genomic.fna/cds.fna -a GCF_902859685.1_LMG_1873_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:45,908] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:45,909] [INFO] Task started: HMMsearch
[2024-01-24 15:03:45,909] [INFO] Running command: hmmsearch --tblout GCF_902859685.1_LMG_1873_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4508572-d904-440f-9744-cf42c91a527a/dqc_reference/reference_markers.hmm GCF_902859685.1_LMG_1873_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:46,256] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:46,258] [INFO] Found 6/6 markers.
[2024-01-24 15:03:46,315] [INFO] Query marker FASTA was written to GCF_902859685.1_LMG_1873_genomic.fna/markers.fasta
[2024-01-24 15:03:46,315] [INFO] Task started: Blastn
[2024-01-24 15:03:46,316] [INFO] Running command: blastn -query GCF_902859685.1_LMG_1873_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4508572-d904-440f-9744-cf42c91a527a/dqc_reference/reference_markers.fasta -out GCF_902859685.1_LMG_1873_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:47,400] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:47,404] [INFO] Selected 14 target genomes.
[2024-01-24 15:03:47,404] [INFO] Target genome list was writen to GCF_902859685.1_LMG_1873_genomic.fna/target_genomes.txt
[2024-01-24 15:03:47,411] [INFO] Task started: fastANI
[2024-01-24 15:03:47,411] [INFO] Running command: fastANI --query /var/lib/cwl/stge332f04f-7e60-42fb-bbe6-a50c3508b410/GCF_902859685.1_LMG_1873_genomic.fna.gz --refList GCF_902859685.1_LMG_1873_genomic.fna/target_genomes.txt --output GCF_902859685.1_LMG_1873_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:04:11,334] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:11,335] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4508572-d904-440f-9744-cf42c91a527a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:04:11,335] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4508572-d904-440f-9744-cf42c91a527a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:04:11,346] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:04:11,347] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:04:11,347] [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 piechaudii	strain=LMG 1873	GCA_902859685.1	72556	72556	type	True	100.0	2106	2106	95	conclusive
Achromobacter piechaudii	strain=NBRC 102461	GCA_001571245.1	72556	72556	type	True	99.9907	2092	2106	95	conclusive
Achromobacter spanius	strain=LMG 5911	GCA_902859605.1	217203	217203	suspected-type	True	88.4621	1674	2106	95	below_threshold
Achromobacter spanius	strain=DSM 23806	GCA_002812705.1	217203	217203	suspected-type	True	88.3906	1710	2106	95	below_threshold
Achromobacter kerstersii	strain=LMG 3441	GCA_902859595.1	1353890	1353890	type	True	87.0582	1686	2106	95	below_threshold
Achromobacter marplatensis	strain=LMG 26219	GCA_902859635.1	470868	470868	type	True	86.9373	1582	2106	95	below_threshold
Achromobacter marplatensis	strain=B2	GCA_002209535.1	470868	470868	type	True	86.9123	1590	2106	95	below_threshold
Achromobacter marplatensis	strain=CECT 7342	GCA_003315095.1	470868	470868	type	True	86.9075	1597	2106	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	85.8114	1473	2106	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	85.1069	1460	2106	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	84.4474	1406	2106	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	81.5729	835	2106	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.3778	449	2106	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.7315	438	2106	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:04:11,348] [INFO] DFAST Taxonomy check result was written to GCF_902859685.1_LMG_1873_genomic.fna/tc_result.tsv
[2024-01-24 15:04:11,349] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:04:11,349] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:04:11,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4508572-d904-440f-9744-cf42c91a527a/dqc_reference/checkm_data
[2024-01-24 15:04:11,351] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:04:11,414] [INFO] Task started: CheckM
[2024-01-24 15:04:11,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902859685.1_LMG_1873_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902859685.1_LMG_1873_genomic.fna/checkm_input GCF_902859685.1_LMG_1873_genomic.fna/checkm_result
[2024-01-24 15:05:31,261] [INFO] Task succeeded: CheckM
[2024-01-24 15:05:31,262] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:05:31,282] [INFO] ===== Completeness check finished =====
[2024-01-24 15:05:31,283] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:05:31,283] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902859685.1_LMG_1873_genomic.fna/markers.fasta)
[2024-01-24 15:05:31,284] [INFO] Task started: Blastn
[2024-01-24 15:05:31,284] [INFO] Running command: blastn -query GCF_902859685.1_LMG_1873_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4508572-d904-440f-9744-cf42c91a527a/dqc_reference/reference_markers_gtdb.fasta -out GCF_902859685.1_LMG_1873_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:05:33,425] [INFO] Task succeeded: Blastn
[2024-01-24 15:05:33,429] [INFO] Selected 8 target genomes.
[2024-01-24 15:05:33,430] [INFO] Target genome list was writen to GCF_902859685.1_LMG_1873_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:05:33,436] [INFO] Task started: fastANI
[2024-01-24 15:05:33,436] [INFO] Running command: fastANI --query /var/lib/cwl/stge332f04f-7e60-42fb-bbe6-a50c3508b410/GCF_902859685.1_LMG_1873_genomic.fna.gz --refList GCF_902859685.1_LMG_1873_genomic.fna/target_genomes_gtdb.txt --output GCF_902859685.1_LMG_1873_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:48,643] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:48,654] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:48,654] [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_001571245.1	s__Achromobacter piechaudii	99.9907	2092	2106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.00	98.18	0.96	0.93	8	conclusive
GCF_003600685.1	s__Achromobacter spanius_B	89.2353	1718	2106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.56	98.20	0.94	0.92	5	-
GCF_002812705.1	s__Achromobacter spanius	88.3974	1709	2106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.99	99.98	0.99	0.98	4	-
GCF_003994415.1	s__Achromobacter spanius_C	87.9167	1647	2106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.60	98.60	0.94	0.94	2	-
GCF_902859595.1	s__Achromobacter kerstersii	87.0823	1683	2106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.61	98.61	0.95	0.95	2	-
GCF_014170335.1	s__Achromobacter sp014170335	87.0664	1570	2106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002209535.1	s__Achromobacter marplatensis	86.9154	1589	2106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.15	97.44	0.96	0.90	4	-
GCF_012928505.1	s__Achromobacter sp012928505	86.7356	1563	2106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:48,656] [INFO] GTDB search result was written to GCF_902859685.1_LMG_1873_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:48,661] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:48,664] [INFO] DFAST_QC result json was written to GCF_902859685.1_LMG_1873_genomic.fna/dqc_result.json
[2024-01-24 15:05:48,665] [INFO] DFAST_QC completed!
[2024-01-24 15:05:48,665] [INFO] Total running time: 0h2m34s