[2024-01-24 12:34:20,630] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:34:20,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:34:20,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg7064dd21-2bcd-436f-9bee-97bb03f6f0fe/dqc_reference
[2024-01-24 12:34:21,822] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:34:21,823] [INFO] Task started: Prodigal
[2024-01-24 12:34:21,823] [INFO] Running command: gunzip -c /var/lib/cwl/stg79ef03ad-f2a5-4d27-b1b7-1e60d6aa7ee1/GCF_030162955.1_ASM3016295v1_genomic.fna.gz | prodigal -d GCF_030162955.1_ASM3016295v1_genomic.fna/cds.fna -a GCF_030162955.1_ASM3016295v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:34:35,197] [INFO] Task succeeded: Prodigal
[2024-01-24 12:34:35,198] [INFO] Task started: HMMsearch
[2024-01-24 12:34:35,198] [INFO] Running command: hmmsearch --tblout GCF_030162955.1_ASM3016295v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7064dd21-2bcd-436f-9bee-97bb03f6f0fe/dqc_reference/reference_markers.hmm GCF_030162955.1_ASM3016295v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:34:35,494] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:34:35,495] [INFO] Found 6/6 markers.
[2024-01-24 12:34:35,525] [INFO] Query marker FASTA was written to GCF_030162955.1_ASM3016295v1_genomic.fna/markers.fasta
[2024-01-24 12:34:35,526] [INFO] Task started: Blastn
[2024-01-24 12:34:35,526] [INFO] Running command: blastn -query GCF_030162955.1_ASM3016295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7064dd21-2bcd-436f-9bee-97bb03f6f0fe/dqc_reference/reference_markers.fasta -out GCF_030162955.1_ASM3016295v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:36,359] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:36,363] [INFO] Selected 16 target genomes.
[2024-01-24 12:34:36,364] [INFO] Target genome list was writen to GCF_030162955.1_ASM3016295v1_genomic.fna/target_genomes.txt
[2024-01-24 12:34:36,371] [INFO] Task started: fastANI
[2024-01-24 12:34:36,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg79ef03ad-f2a5-4d27-b1b7-1e60d6aa7ee1/GCF_030162955.1_ASM3016295v1_genomic.fna.gz --refList GCF_030162955.1_ASM3016295v1_genomic.fna/target_genomes.txt --output GCF_030162955.1_ASM3016295v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:34:49,343] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:49,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7064dd21-2bcd-436f-9bee-97bb03f6f0fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:34:49,344] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7064dd21-2bcd-436f-9bee-97bb03f6f0fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:34:49,360] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:34:49,361] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:34:49,361] [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 aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	83.8944	822	1168	95	below_threshold
Comamonas kerstersii	strain=CCUG 15333	GCA_008801935.1	225992	225992	type	True	82.4568	727	1168	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	82.4428	789	1168	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	81.3466	633	1168	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	80.4784	548	1168	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	80.3949	498	1168	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_000964545.1	363952	363952	type	True	80.3698	513	1168	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001418295.1	363952	363952	type	True	80.3093	508	1168	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001517325.1	363952	363952	type	True	80.2977	509	1168	95	below_threshold
Comamonas suwonensis	strain=EJ-4	GCA_012844455.2	2606214	2606214	type	True	80.2203	533	1168	95	below_threshold
Comamonas testosteroni	strain=ATCC 11996	GCA_000241525.2	285	285	suspected-type	True	80.1041	561	1168	95	below_threshold
Comamonas testosteroni	strain=NCTC10698	GCA_900461225.1	285	285	suspected-type	True	80.0746	569	1168	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	79.5551	437	1168	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	79.1508	389	1168	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.1258	452	1168	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.2065	297	1168	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:34:49,362] [INFO] DFAST Taxonomy check result was written to GCF_030162955.1_ASM3016295v1_genomic.fna/tc_result.tsv
[2024-01-24 12:34:49,363] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:34:49,363] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:34:49,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7064dd21-2bcd-436f-9bee-97bb03f6f0fe/dqc_reference/checkm_data
[2024-01-24 12:34:49,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:34:49,398] [INFO] Task started: CheckM
[2024-01-24 12:34:49,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030162955.1_ASM3016295v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030162955.1_ASM3016295v1_genomic.fna/checkm_input GCF_030162955.1_ASM3016295v1_genomic.fna/checkm_result
[2024-01-24 12:35:30,501] [INFO] Task succeeded: CheckM
[2024-01-24 12:35:30,503] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:35:30,524] [INFO] ===== Completeness check finished =====
[2024-01-24 12:35:30,525] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:35:30,525] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030162955.1_ASM3016295v1_genomic.fna/markers.fasta)
[2024-01-24 12:35:30,526] [INFO] Task started: Blastn
[2024-01-24 12:35:30,526] [INFO] Running command: blastn -query GCF_030162955.1_ASM3016295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7064dd21-2bcd-436f-9bee-97bb03f6f0fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_030162955.1_ASM3016295v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:35:32,152] [INFO] Task succeeded: Blastn
[2024-01-24 12:35:32,155] [INFO] Selected 12 target genomes.
[2024-01-24 12:35:32,156] [INFO] Target genome list was writen to GCF_030162955.1_ASM3016295v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:35:32,167] [INFO] Task started: fastANI
[2024-01-24 12:35:32,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg79ef03ad-f2a5-4d27-b1b7-1e60d6aa7ee1/GCF_030162955.1_ASM3016295v1_genomic.fna.gz --refList GCF_030162955.1_ASM3016295v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030162955.1_ASM3016295v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:35:42,040] [INFO] Task succeeded: fastANI
[2024-01-24 12:35:42,061] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:35:42,062] [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_902829245.1	s__Comamonas jiangduensis	98.9751	745	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	95.84	95.73	0.85	0.79	3	conclusive
GCF_000739875.1	s__Comamonas aquatica	83.8941	822	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	96.97	96.57	0.89	0.87	7	-
GCF_008801935.1	s__Comamonas kerstersii	82.4568	727	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.88	98.82	0.91	0.88	10	-
GCF_014836675.1	s__Comamonas sp014836675	82.4301	791	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.72	98.72	0.93	0.93	2	-
GCA_015478895.1	s__Comamonas sp015478895	82.2168	707	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900461435.1	s__Comamonas terrigena	81.3388	634	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.97	95.46	0.95	0.91	7	-
GCF_008727115.1	s__Comamonas testosteroni_E	80.7549	520	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019186805.1	s__Comamonas sp019186805	80.4854	546	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569915.1	s__Comamonas testosteroni_D	80.3667	563	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012844455.2	s__Comamonas suwonensis	80.2412	531	1168	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	80.2319	543	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207855.1	s__Comamonas odontotermitis	79.5258	392	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:35:42,063] [INFO] GTDB search result was written to GCF_030162955.1_ASM3016295v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:35:42,064] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:35:42,067] [INFO] DFAST_QC result json was written to GCF_030162955.1_ASM3016295v1_genomic.fna/dqc_result.json
[2024-01-24 12:35:42,067] [INFO] DFAST_QC completed!
[2024-01-24 12:35:42,067] [INFO] Total running time: 0h1m21s