[2024-01-24 13:57:42,144] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,147] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,147] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e09a7f4-c523-4872-aace-cdf1853eef65/dqc_reference
[2024-01-24 13:57:43,527] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:43,528] [INFO] Task started: Prodigal
[2024-01-24 13:57:43,529] [INFO] Running command: gunzip -c /var/lib/cwl/stgf96f97c2-3cb5-4c3b-ae26-911fb876b89a/GCF_014836675.1_ASM1483667v1_genomic.fna.gz | prodigal -d GCF_014836675.1_ASM1483667v1_genomic.fna/cds.fna -a GCF_014836675.1_ASM1483667v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:58,041] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:58,041] [INFO] Task started: HMMsearch
[2024-01-24 13:57:58,042] [INFO] Running command: hmmsearch --tblout GCF_014836675.1_ASM1483667v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e09a7f4-c523-4872-aace-cdf1853eef65/dqc_reference/reference_markers.hmm GCF_014836675.1_ASM1483667v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:58,346] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:58,348] [INFO] Found 6/6 markers.
[2024-01-24 13:57:58,385] [INFO] Query marker FASTA was written to GCF_014836675.1_ASM1483667v1_genomic.fna/markers.fasta
[2024-01-24 13:57:58,385] [INFO] Task started: Blastn
[2024-01-24 13:57:58,386] [INFO] Running command: blastn -query GCF_014836675.1_ASM1483667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e09a7f4-c523-4872-aace-cdf1853eef65/dqc_reference/reference_markers.fasta -out GCF_014836675.1_ASM1483667v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:59,270] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:59,275] [INFO] Selected 13 target genomes.
[2024-01-24 13:57:59,276] [INFO] Target genome list was writen to GCF_014836675.1_ASM1483667v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:59,282] [INFO] Task started: fastANI
[2024-01-24 13:57:59,282] [INFO] Running command: fastANI --query /var/lib/cwl/stgf96f97c2-3cb5-4c3b-ae26-911fb876b89a/GCF_014836675.1_ASM1483667v1_genomic.fna.gz --refList GCF_014836675.1_ASM1483667v1_genomic.fna/target_genomes.txt --output GCF_014836675.1_ASM1483667v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:10,387] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:10,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e09a7f4-c523-4872-aace-cdf1853eef65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:10,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e09a7f4-c523-4872-aace-cdf1853eef65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:10,399] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:10,399] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:10,399] [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 avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	100.0	1298	1299	95	conclusive
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	81.529	763	1299	95	below_threshold
Comamonas kerstersii	strain=CCUG 15333	GCA_008801935.1	225992	225992	type	True	81.3423	716	1299	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	80.0573	648	1299	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	79.8459	507	1299	95	below_threshold
Comamonas suwonensis	strain=EJ-4	GCA_012844455.2	2606214	2606214	type	True	79.5757	513	1299	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_000964545.1	363952	363952	type	True	79.156	519	1299	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001517325.1	363952	363952	type	True	79.0833	522	1299	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	78.7333	422	1299	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	78.4015	398	1299	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	78.2925	410	1299	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	78.1761	343	1299	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	77.2045	220	1299	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:10,401] [INFO] DFAST Taxonomy check result was written to GCF_014836675.1_ASM1483667v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:10,401] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:10,401] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:10,401] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e09a7f4-c523-4872-aace-cdf1853eef65/dqc_reference/checkm_data
[2024-01-24 13:58:10,402] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:10,464] [INFO] Task started: CheckM
[2024-01-24 13:58:10,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836675.1_ASM1483667v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836675.1_ASM1483667v1_genomic.fna/checkm_input GCF_014836675.1_ASM1483667v1_genomic.fna/checkm_result
[2024-01-24 13:58:56,124] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:56,125] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:56,147] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:56,147] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:56,148] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836675.1_ASM1483667v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:56,148] [INFO] Task started: Blastn
[2024-01-24 13:58:56,148] [INFO] Running command: blastn -query GCF_014836675.1_ASM1483667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e09a7f4-c523-4872-aace-cdf1853eef65/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836675.1_ASM1483667v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:57,797] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:57,801] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:57,802] [INFO] Target genome list was writen to GCF_014836675.1_ASM1483667v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:57,813] [INFO] Task started: fastANI
[2024-01-24 13:58:57,814] [INFO] Running command: fastANI --query /var/lib/cwl/stgf96f97c2-3cb5-4c3b-ae26-911fb876b89a/GCF_014836675.1_ASM1483667v1_genomic.fna.gz --refList GCF_014836675.1_ASM1483667v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836675.1_ASM1483667v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:08,718] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:08,729] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:08,729] [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_014836675.1	s__Comamonas sp014836675	100.0	1298	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.72	98.72	0.93	0.93	2	conclusive
GCF_902829245.1	s__Comamonas jiangduensis	82.1656	548	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	95.84	95.73	0.85	0.79	3	-
GCA_015478895.1	s__Comamonas sp015478895	81.8097	686	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739875.1	s__Comamonas aquatica	81.5014	766	1299	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	81.335	717	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.88	98.82	0.91	0.88	10	-
GCF_900461435.1	s__Comamonas terrigena	80.0877	643	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.97	95.46	0.95	0.91	7	-
GCF_019186805.1	s__Comamonas sp019186805	79.8359	509	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727115.1	s__Comamonas testosteroni_E	79.6682	497	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754475.1	s__Comamonas sp002754475	79.5804	533	1299	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	79.5477	515	1299	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	79.3408	535	1299	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.94	95.50	0.89	0.85	10	-
GCF_014076415.1	s__Comamonas testosteroni_F	79.3199	515	1299	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 13:59:08,731] [INFO] GTDB search result was written to GCF_014836675.1_ASM1483667v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:08,732] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:08,735] [INFO] DFAST_QC result json was written to GCF_014836675.1_ASM1483667v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:08,736] [INFO] DFAST_QC completed!
[2024-01-24 13:59:08,736] [INFO] Total running time: 0h1m27s