[2024-01-24 15:19:52,600] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:52,602] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:52,603] [INFO] DQC Reference Directory: /var/lib/cwl/stg3283937d-5775-4aa7-8bb2-6f8d297b440c/dqc_reference
[2024-01-24 15:19:53,868] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:53,869] [INFO] Task started: Prodigal
[2024-01-24 15:19:53,870] [INFO] Running command: gunzip -c /var/lib/cwl/stge3e2edb0-de71-4346-a000-0b61088eeeb2/GCF_000964545.1_ASM96454v1_genomic.fna.gz | prodigal -d GCF_000964545.1_ASM96454v1_genomic.fna/cds.fna -a GCF_000964545.1_ASM96454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:20:12,008] [INFO] Task succeeded: Prodigal
[2024-01-24 15:20:12,009] [INFO] Task started: HMMsearch
[2024-01-24 15:20:12,009] [INFO] Running command: hmmsearch --tblout GCF_000964545.1_ASM96454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3283937d-5775-4aa7-8bb2-6f8d297b440c/dqc_reference/reference_markers.hmm GCF_000964545.1_ASM96454v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:20:12,382] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:20:12,383] [INFO] Found 6/6 markers.
[2024-01-24 15:20:12,429] [INFO] Query marker FASTA was written to GCF_000964545.1_ASM96454v1_genomic.fna/markers.fasta
[2024-01-24 15:20:12,429] [INFO] Task started: Blastn
[2024-01-24 15:20:12,429] [INFO] Running command: blastn -query GCF_000964545.1_ASM96454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3283937d-5775-4aa7-8bb2-6f8d297b440c/dqc_reference/reference_markers.fasta -out GCF_000964545.1_ASM96454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:13,483] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:13,487] [INFO] Selected 10 target genomes.
[2024-01-24 15:20:13,488] [INFO] Target genome list was writen to GCF_000964545.1_ASM96454v1_genomic.fna/target_genomes.txt
[2024-01-24 15:20:13,492] [INFO] Task started: fastANI
[2024-01-24 15:20:13,493] [INFO] Running command: fastANI --query /var/lib/cwl/stge3e2edb0-de71-4346-a000-0b61088eeeb2/GCF_000964545.1_ASM96454v1_genomic.fna.gz --refList GCF_000964545.1_ASM96454v1_genomic.fna/target_genomes.txt --output GCF_000964545.1_ASM96454v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:20:25,018] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:25,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3283937d-5775-4aa7-8bb2-6f8d297b440c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:20:25,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3283937d-5775-4aa7-8bb2-6f8d297b440c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:20:25,028] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:20:25,029] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:20:25,029] [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
Comamonas thiooxydans	strain=DSM 17888	GCA_000964545.1	363952	363952	type	True	100.0	1722	1725	95	conclusive
Comamonas thiooxydans	strain=DSM 17888	GCA_001418295.1	363952	363952	type	True	99.9968	1721	1725	95	conclusive
Comamonas thiooxydans	strain=DSM 17888	GCA_001517325.1	363952	363952	type	True	99.9968	1721	1725	95	conclusive
Comamonas testosteroni	strain=ATCC 11996	GCA_000241525.2	285	285	suspected-type	True	94.3917	1490	1725	95	below_threshold
Comamonas testosteroni	strain=NCTC10698	GCA_900461225.1	285	285	suspected-type	True	94.3774	1507	1725	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	84.7	1098	1725	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	80.213	684	1725	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.3347	618	1725	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	78.5756	416	1725	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.3405	484	1725	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:20:25,031] [INFO] DFAST Taxonomy check result was written to GCF_000964545.1_ASM96454v1_genomic.fna/tc_result.tsv
[2024-01-24 15:20:25,031] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:20:25,031] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:20:25,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3283937d-5775-4aa7-8bb2-6f8d297b440c/dqc_reference/checkm_data
[2024-01-24 15:20:25,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:20:25,081] [INFO] Task started: CheckM
[2024-01-24 15:20:25,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000964545.1_ASM96454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000964545.1_ASM96454v1_genomic.fna/checkm_input GCF_000964545.1_ASM96454v1_genomic.fna/checkm_result
[2024-01-24 15:21:21,043] [INFO] Task succeeded: CheckM
[2024-01-24 15:21:21,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:21:21,068] [INFO] ===== Completeness check finished =====
[2024-01-24 15:21:21,068] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:21:21,069] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000964545.1_ASM96454v1_genomic.fna/markers.fasta)
[2024-01-24 15:21:21,069] [INFO] Task started: Blastn
[2024-01-24 15:21:21,069] [INFO] Running command: blastn -query GCF_000964545.1_ASM96454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3283937d-5775-4aa7-8bb2-6f8d297b440c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000964545.1_ASM96454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:21:23,061] [INFO] Task succeeded: Blastn
[2024-01-24 15:21:23,065] [INFO] Selected 6 target genomes.
[2024-01-24 15:21:23,066] [INFO] Target genome list was writen to GCF_000964545.1_ASM96454v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:21:23,071] [INFO] Task started: fastANI
[2024-01-24 15:21:23,071] [INFO] Running command: fastANI --query /var/lib/cwl/stge3e2edb0-de71-4346-a000-0b61088eeeb2/GCF_000964545.1_ASM96454v1_genomic.fna.gz --refList GCF_000964545.1_ASM96454v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000964545.1_ASM96454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:31,372] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:31,383] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:31,383] [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_000964545.1	s__Comamonas thiooxydans	100.0	1722	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.51	95.23	0.90	0.87	29	conclusive
GCF_014076415.1	s__Comamonas testosteroni_F	94.4189	1504	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241525.1	s__Comamonas testosteroni	94.3916	1490	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	99.74	98.70	0.99	0.94	6	-
GCF_000761245.1	s__Comamonas testosteroni_C	94.237	1501	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.84	98.53	0.90	0.90	4	-
GCF_000739375.1	s__Comamonas testosteroni_B	92.4006	1444	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.94	95.50	0.89	0.85	10	-
GCA_009360615.1	s__Comamonas sp009360615	90.916	1270	1725	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:21:31,385] [INFO] GTDB search result was written to GCF_000964545.1_ASM96454v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:31,385] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:31,388] [INFO] DFAST_QC result json was written to GCF_000964545.1_ASM96454v1_genomic.fna/dqc_result.json
[2024-01-24 15:21:31,388] [INFO] DFAST_QC completed!
[2024-01-24 15:21:31,388] [INFO] Total running time: 0h1m39s