[2024-01-24 11:26:08,308] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:08,312] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:08,313] [INFO] DQC Reference Directory: /var/lib/cwl/stg2396db11-c4f2-45f6-b93e-620eaa717e87/dqc_reference
[2024-01-24 11:26:09,574] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:09,575] [INFO] Task started: Prodigal
[2024-01-24 11:26:09,575] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d872294-a435-47b8-91c5-c359d4f3dbb2/GCF_012844455.2_ASM1284445v2_genomic.fna.gz | prodigal -d GCF_012844455.2_ASM1284445v2_genomic.fna/cds.fna -a GCF_012844455.2_ASM1284445v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:25,618] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:25,618] [INFO] Task started: HMMsearch
[2024-01-24 11:26:25,618] [INFO] Running command: hmmsearch --tblout GCF_012844455.2_ASM1284445v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2396db11-c4f2-45f6-b93e-620eaa717e87/dqc_reference/reference_markers.hmm GCF_012844455.2_ASM1284445v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:25,932] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:25,933] [INFO] Found 6/6 markers.
[2024-01-24 11:26:25,976] [INFO] Query marker FASTA was written to GCF_012844455.2_ASM1284445v2_genomic.fna/markers.fasta
[2024-01-24 11:26:25,977] [INFO] Task started: Blastn
[2024-01-24 11:26:25,977] [INFO] Running command: blastn -query GCF_012844455.2_ASM1284445v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2396db11-c4f2-45f6-b93e-620eaa717e87/dqc_reference/reference_markers.fasta -out GCF_012844455.2_ASM1284445v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:26,987] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:26,991] [INFO] Selected 16 target genomes.
[2024-01-24 11:26:26,991] [INFO] Target genome list was writen to GCF_012844455.2_ASM1284445v2_genomic.fna/target_genomes.txt
[2024-01-24 11:26:26,997] [INFO] Task started: fastANI
[2024-01-24 11:26:26,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d872294-a435-47b8-91c5-c359d4f3dbb2/GCF_012844455.2_ASM1284445v2_genomic.fna.gz --refList GCF_012844455.2_ASM1284445v2_genomic.fna/target_genomes.txt --output GCF_012844455.2_ASM1284445v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:44,019] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:44,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2396db11-c4f2-45f6-b93e-620eaa717e87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:44,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2396db11-c4f2-45f6-b93e-620eaa717e87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:44,034] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:44,035] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:44,035] [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 suwonensis	strain=EJ-4	GCA_012844455.2	2606214	2606214	type	True	100.0	1542	1544	95	conclusive
Comamonas testosteroni	strain=NCTC10698	GCA_900461225.1	285	285	suspected-type	True	84.7787	1197	1544	95	below_threshold
Comamonas testosteroni	strain=NBRC 14951	GCA_000740035.1	285	285	suspected-type	True	84.7735	1173	1544	95	below_threshold
Comamonas testosteroni	strain=ATCC 11996	GCA_000241525.2	285	285	suspected-type	True	84.7576	1172	1544	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_000964545.1	363952	363952	type	True	84.631	1158	1544	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001517325.1	363952	363952	type	True	84.6077	1173	1544	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001418295.1	363952	363952	type	True	84.6016	1174	1544	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	84.4468	1108	1544	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	82.0188	815	1544	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	81.6899	951	1544	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	80.9505	697	1544	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	80.3463	611	1544	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	79.4884	514	1544	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	78.8321	535	1544	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	77.511	292	1544	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	77.4925	355	1544	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:44,037] [INFO] DFAST Taxonomy check result was written to GCF_012844455.2_ASM1284445v2_genomic.fna/tc_result.tsv
[2024-01-24 11:26:44,037] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:44,037] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:44,038] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2396db11-c4f2-45f6-b93e-620eaa717e87/dqc_reference/checkm_data
[2024-01-24 11:26:44,039] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:44,112] [INFO] Task started: CheckM
[2024-01-24 11:26:44,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012844455.2_ASM1284445v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012844455.2_ASM1284445v2_genomic.fna/checkm_input GCF_012844455.2_ASM1284445v2_genomic.fna/checkm_result
[2024-01-24 11:27:34,040] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:34,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:34,062] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:34,063] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:34,063] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012844455.2_ASM1284445v2_genomic.fna/markers.fasta)
[2024-01-24 11:27:34,064] [INFO] Task started: Blastn
[2024-01-24 11:27:34,064] [INFO] Running command: blastn -query GCF_012844455.2_ASM1284445v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2396db11-c4f2-45f6-b93e-620eaa717e87/dqc_reference/reference_markers_gtdb.fasta -out GCF_012844455.2_ASM1284445v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:35,715] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:35,719] [INFO] Selected 13 target genomes.
[2024-01-24 11:27:35,720] [INFO] Target genome list was writen to GCF_012844455.2_ASM1284445v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:35,731] [INFO] Task started: fastANI
[2024-01-24 11:27:35,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d872294-a435-47b8-91c5-c359d4f3dbb2/GCF_012844455.2_ASM1284445v2_genomic.fna.gz --refList GCF_012844455.2_ASM1284445v2_genomic.fna/target_genomes_gtdb.txt --output GCF_012844455.2_ASM1284445v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:49,775] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:49,791] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:49,791] [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_012844455.2	s__Comamonas suwonensis	100.0	1542	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002754475.1	s__Comamonas sp002754475	93.2357	1301	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761245.1	s__Comamonas testosteroni_C	84.7531	1161	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.84	98.53	0.90	0.90	4	-
GCF_000241525.1	s__Comamonas testosteroni	84.7489	1173	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	99.74	98.70	0.99	0.94	6	-
GCF_000739375.1	s__Comamonas testosteroni_B	84.6879	1162	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.94	95.50	0.89	0.85	10	-
GCF_000964545.1	s__Comamonas thiooxydans	84.6223	1159	1544	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	84.4468	1108	1544	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	84.3175	1080	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009360615.1	s__Comamonas sp009360615	83.8187	1058	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900564145.1	s__Comamonas sp900564145	83.5688	1064	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637085.1	s__Comamonas phosphati	82.028	814	1544	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	81.7303	945	1544	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	80.9506	697	1544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.97	95.46	0.95	0.91	7	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:49,793] [INFO] GTDB search result was written to GCF_012844455.2_ASM1284445v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:49,794] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:49,797] [INFO] DFAST_QC result json was written to GCF_012844455.2_ASM1284445v2_genomic.fna/dqc_result.json
[2024-01-24 11:27:49,798] [INFO] DFAST_QC completed!
[2024-01-24 11:27:49,798] [INFO] Total running time: 0h1m41s