[2024-01-25 17:44:05,441] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:05,442] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:05,442] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f56eff2-0c3d-4826-ae5f-2de5e07d7496/dqc_reference
[2024-01-25 17:44:06,565] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:06,565] [INFO] Task started: Prodigal
[2024-01-25 17:44:06,565] [INFO] Running command: gunzip -c /var/lib/cwl/stg7da0cf44-2251-49f1-93ab-43f4b5b3626d/GCF_001571245.1_ASM157124v1_genomic.fna.gz | prodigal -d GCF_001571245.1_ASM157124v1_genomic.fna/cds.fna -a GCF_001571245.1_ASM157124v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:26,314] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:26,315] [INFO] Task started: HMMsearch
[2024-01-25 17:44:26,315] [INFO] Running command: hmmsearch --tblout GCF_001571245.1_ASM157124v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f56eff2-0c3d-4826-ae5f-2de5e07d7496/dqc_reference/reference_markers.hmm GCF_001571245.1_ASM157124v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:26,603] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:26,605] [INFO] Found 6/6 markers.
[2024-01-25 17:44:26,654] [INFO] Query marker FASTA was written to GCF_001571245.1_ASM157124v1_genomic.fna/markers.fasta
[2024-01-25 17:44:26,654] [INFO] Task started: Blastn
[2024-01-25 17:44:26,654] [INFO] Running command: blastn -query GCF_001571245.1_ASM157124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f56eff2-0c3d-4826-ae5f-2de5e07d7496/dqc_reference/reference_markers.fasta -out GCF_001571245.1_ASM157124v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:27,634] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:27,637] [INFO] Selected 14 target genomes.
[2024-01-25 17:44:27,637] [INFO] Target genome list was writen to GCF_001571245.1_ASM157124v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:27,659] [INFO] Task started: fastANI
[2024-01-25 17:44:27,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg7da0cf44-2251-49f1-93ab-43f4b5b3626d/GCF_001571245.1_ASM157124v1_genomic.fna.gz --refList GCF_001571245.1_ASM157124v1_genomic.fna/target_genomes.txt --output GCF_001571245.1_ASM157124v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:48,969] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:48,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f56eff2-0c3d-4826-ae5f-2de5e07d7496/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:48,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f56eff2-0c3d-4826-ae5f-2de5e07d7496/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:48,980] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:44:48,980] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:44:48,980] [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=NBRC 102461	GCA_001571245.1	72556	72556	type	True	100.0	2095	2095	95	conclusive
Achromobacter piechaudii	strain=LMG 1873	GCA_902859685.1	72556	72556	type	True	99.9992	2092	2095	95	conclusive
Achromobacter spanius	strain=LMG 5911	GCA_902859605.1	217203	217203	suspected-type	True	88.4393	1682	2095	95	below_threshold
Achromobacter spanius	strain=DSM 23806	GCA_002812705.1	217203	217203	suspected-type	True	88.3963	1717	2095	95	below_threshold
Achromobacter kerstersii	strain=LMG 3441	GCA_902859595.1	1353890	1353890	type	True	87.066	1672	2095	95	below_threshold
Achromobacter marplatensis	strain=CECT 7342	GCA_003315095.1	470868	470868	type	True	86.9554	1592	2095	95	below_threshold
Achromobacter marplatensis	strain=B2	GCA_002209535.1	470868	470868	type	True	86.9529	1587	2095	95	below_threshold
Achromobacter marplatensis	strain=LMG 26219	GCA_902859635.1	470868	470868	type	True	86.9403	1591	2095	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	85.7418	1467	2095	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	85.1778	1443	2095	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	84.5519	1389	2095	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	81.6647	811	2095	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.3257	456	2095	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.553	448	2095	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:48,982] [INFO] DFAST Taxonomy check result was written to GCF_001571245.1_ASM157124v1_genomic.fna/tc_result.tsv
[2024-01-25 17:44:48,982] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:48,982] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:48,982] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f56eff2-0c3d-4826-ae5f-2de5e07d7496/dqc_reference/checkm_data
[2024-01-25 17:44:48,983] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:49,046] [INFO] Task started: CheckM
[2024-01-25 17:44:49,046] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001571245.1_ASM157124v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001571245.1_ASM157124v1_genomic.fna/checkm_input GCF_001571245.1_ASM157124v1_genomic.fna/checkm_result
[2024-01-25 17:45:51,440] [INFO] Task succeeded: CheckM
[2024-01-25 17:45:51,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:45:51,459] [INFO] ===== Completeness check finished =====
[2024-01-25 17:45:51,459] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:45:51,460] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001571245.1_ASM157124v1_genomic.fna/markers.fasta)
[2024-01-25 17:45:51,461] [INFO] Task started: Blastn
[2024-01-25 17:45:51,461] [INFO] Running command: blastn -query GCF_001571245.1_ASM157124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f56eff2-0c3d-4826-ae5f-2de5e07d7496/dqc_reference/reference_markers_gtdb.fasta -out GCF_001571245.1_ASM157124v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:53,553] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:53,556] [INFO] Selected 8 target genomes.
[2024-01-25 17:45:53,556] [INFO] Target genome list was writen to GCF_001571245.1_ASM157124v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:45:53,565] [INFO] Task started: fastANI
[2024-01-25 17:45:53,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg7da0cf44-2251-49f1-93ab-43f4b5b3626d/GCF_001571245.1_ASM157124v1_genomic.fna.gz --refList GCF_001571245.1_ASM157124v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001571245.1_ASM157124v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:46:07,568] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:07,574] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:46:07,574] [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	100.0	2095	2095	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	89.2885	1737	2095	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	88.3826	1719	2095	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	87.9153	1635	2095	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	87.0935	1669	2095	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	87.0518	1570	2095	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	86.9731	1584	2095	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	86.8183	1553	2095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:46:07,576] [INFO] GTDB search result was written to GCF_001571245.1_ASM157124v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:46:07,576] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:46:07,579] [INFO] DFAST_QC result json was written to GCF_001571245.1_ASM157124v1_genomic.fna/dqc_result.json
[2024-01-25 17:46:07,579] [INFO] DFAST_QC completed!
[2024-01-25 17:46:07,579] [INFO] Total running time: 0h2m2s