[2024-01-24 11:34:41,260] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:41,263] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:41,263] [INFO] DQC Reference Directory: /var/lib/cwl/stge3378ddd-fd6a-444d-b54a-2f6e22d049d0/dqc_reference
[2024-01-24 11:34:42,560] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:42,560] [INFO] Task started: Prodigal
[2024-01-24 11:34:42,561] [INFO] Running command: gunzip -c /var/lib/cwl/stg34e30177-7954-472e-95e9-e32a3bd1084c/GCF_900461435.1_46693_E02_genomic.fna.gz | prodigal -d GCF_900461435.1_46693_E02_genomic.fna/cds.fna -a GCF_900461435.1_46693_E02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:01,080] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:01,080] [INFO] Task started: HMMsearch
[2024-01-24 11:35:01,080] [INFO] Running command: hmmsearch --tblout GCF_900461435.1_46693_E02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3378ddd-fd6a-444d-b54a-2f6e22d049d0/dqc_reference/reference_markers.hmm GCF_900461435.1_46693_E02_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:01,401] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:01,402] [INFO] Found 6/6 markers.
[2024-01-24 11:35:01,441] [INFO] Query marker FASTA was written to GCF_900461435.1_46693_E02_genomic.fna/markers.fasta
[2024-01-24 11:35:01,442] [INFO] Task started: Blastn
[2024-01-24 11:35:01,442] [INFO] Running command: blastn -query GCF_900461435.1_46693_E02_genomic.fna/markers.fasta -db /var/lib/cwl/stge3378ddd-fd6a-444d-b54a-2f6e22d049d0/dqc_reference/reference_markers.fasta -out GCF_900461435.1_46693_E02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:02,525] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:02,528] [INFO] Selected 16 target genomes.
[2024-01-24 11:35:02,529] [INFO] Target genome list was writen to GCF_900461435.1_46693_E02_genomic.fna/target_genomes.txt
[2024-01-24 11:35:02,534] [INFO] Task started: fastANI
[2024-01-24 11:35:02,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg34e30177-7954-472e-95e9-e32a3bd1084c/GCF_900461435.1_46693_E02_genomic.fna.gz --refList GCF_900461435.1_46693_E02_genomic.fna/target_genomes.txt --output GCF_900461435.1_46693_E02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:19,407] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:19,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3378ddd-fd6a-444d-b54a-2f6e22d049d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:19,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3378ddd-fd6a-444d-b54a-2f6e22d049d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:19,421] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:19,421] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:19,421] [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 terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	100.0	1560	1564	95	conclusive
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	83.5413	866	1564	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	82.4982	780	1564	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	82.2916	862	1564	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	81.9477	920	1564	95	below_threshold
Comamonas testosteroni	strain=NCTC10698	GCA_900461225.1	285	285	suspected-type	True	81.9397	850	1564	95	below_threshold
Comamonas testosteroni	strain=ATCC 11996	GCA_000241525.2	285	285	suspected-type	True	81.9166	827	1564	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001418295.1	363952	363952	type	True	81.7673	820	1564	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001517325.1	363952	363952	type	True	81.7602	820	1564	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_000964545.1	363952	363952	type	True	81.6691	821	1564	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	81.6486	766	1564	95	below_threshold
Comamonas suwonensis	strain=EJ-4	GCA_012844455.2	2606214	2606214	type	True	80.9907	702	1564	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	80.0529	643	1564	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	80.0082	673	1564	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.1941	547	1564	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.9254	548	1564	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:19,423] [INFO] DFAST Taxonomy check result was written to GCF_900461435.1_46693_E02_genomic.fna/tc_result.tsv
[2024-01-24 11:35:19,424] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:19,424] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:19,424] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3378ddd-fd6a-444d-b54a-2f6e22d049d0/dqc_reference/checkm_data
[2024-01-24 11:35:19,425] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:19,477] [INFO] Task started: CheckM
[2024-01-24 11:35:19,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900461435.1_46693_E02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900461435.1_46693_E02_genomic.fna/checkm_input GCF_900461435.1_46693_E02_genomic.fna/checkm_result
[2024-01-24 11:36:27,988] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:27,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:28,016] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:28,017] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:28,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900461435.1_46693_E02_genomic.fna/markers.fasta)
[2024-01-24 11:36:28,017] [INFO] Task started: Blastn
[2024-01-24 11:36:28,018] [INFO] Running command: blastn -query GCF_900461435.1_46693_E02_genomic.fna/markers.fasta -db /var/lib/cwl/stge3378ddd-fd6a-444d-b54a-2f6e22d049d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900461435.1_46693_E02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:29,913] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:29,918] [INFO] Selected 17 target genomes.
[2024-01-24 11:36:29,918] [INFO] Target genome list was writen to GCF_900461435.1_46693_E02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:29,931] [INFO] Task started: fastANI
[2024-01-24 11:36:29,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg34e30177-7954-472e-95e9-e32a3bd1084c/GCF_900461435.1_46693_E02_genomic.fna.gz --refList GCF_900461435.1_46693_E02_genomic.fna/target_genomes_gtdb.txt --output GCF_900461435.1_46693_E02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:47,782] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:47,799] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:47,799] [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_900461435.1	s__Comamonas terrigena	100.0	1562	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.97	95.46	0.95	0.91	7	conclusive
GCF_000739875.1	s__Comamonas aquatica	83.5464	865	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	96.97	96.57	0.89	0.87	7	-
GCF_014637085.1	s__Comamonas phosphati	82.4645	783	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544075.1	s__Comamonas terrae	82.2967	862	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236485.1	s__Comamonas sp019236485	82.173	611	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739375.1	s__Comamonas testosteroni_B	81.9678	866	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.94	95.50	0.89	0.85	10	-
GCF_000241525.1	s__Comamonas testosteroni	81.8795	833	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	99.74	98.70	0.99	0.94	6	-
GCF_900564145.1	s__Comamonas sp900564145	81.8706	796	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014076415.1	s__Comamonas testosteroni_F	81.8595	832	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571325.1	s__Comamonas tsuruhatensis	81.8467	894	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.4801	98.55	98.21	0.90	0.80	27	-
GCF_000761245.1	s__Comamonas testosteroni_C	81.7816	835	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.84	98.53	0.90	0.90	4	-
GCF_003569915.1	s__Comamonas testosteroni_D	81.7814	781	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964545.1	s__Comamonas thiooxydans	81.6728	820	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.51	95.23	0.90	0.87	29	-
GCF_019186805.1	s__Comamonas sp019186805	81.6375	766	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008801935.1	s__Comamonas kerstersii	81.2573	681	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.88	98.82	0.91	0.88	10	-
GCF_014204315.1	s__Comamonas konjaci_A	81.1591	766	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000204645.1	s__Alicycliphilus denitrificans	80.7058	709	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	97.26	95.80	0.83	0.76	8	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:47,801] [INFO] GTDB search result was written to GCF_900461435.1_46693_E02_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:47,801] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:47,805] [INFO] DFAST_QC result json was written to GCF_900461435.1_46693_E02_genomic.fna/dqc_result.json
[2024-01-24 11:36:47,806] [INFO] DFAST_QC completed!
[2024-01-24 11:36:47,806] [INFO] Total running time: 0h2m7s