[2024-01-25 18:45:20,555] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:45:20,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:45:20,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg27d4b205-2af4-41e9-a5fb-053f3e1fb137/dqc_reference
[2024-01-25 18:45:21,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:45:21,686] [INFO] Task started: Prodigal
[2024-01-25 18:45:21,686] [INFO] Running command: gunzip -c /var/lib/cwl/stg6dfb7c66-1cd2-4511-af8b-f408e5825a0e/GCF_016127415.1_ASM1612741v1_genomic.fna.gz | prodigal -d GCF_016127415.1_ASM1612741v1_genomic.fna/cds.fna -a GCF_016127415.1_ASM1612741v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:45:50,300] [INFO] Task succeeded: Prodigal
[2024-01-25 18:45:50,300] [INFO] Task started: HMMsearch
[2024-01-25 18:45:50,300] [INFO] Running command: hmmsearch --tblout GCF_016127415.1_ASM1612741v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27d4b205-2af4-41e9-a5fb-053f3e1fb137/dqc_reference/reference_markers.hmm GCF_016127415.1_ASM1612741v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:45:50,613] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:45:50,614] [INFO] Found 6/6 markers.
[2024-01-25 18:45:50,666] [INFO] Query marker FASTA was written to GCF_016127415.1_ASM1612741v1_genomic.fna/markers.fasta
[2024-01-25 18:45:50,666] [INFO] Task started: Blastn
[2024-01-25 18:45:50,667] [INFO] Running command: blastn -query GCF_016127415.1_ASM1612741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27d4b205-2af4-41e9-a5fb-053f3e1fb137/dqc_reference/reference_markers.fasta -out GCF_016127415.1_ASM1612741v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:51,549] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:51,552] [INFO] Selected 19 target genomes.
[2024-01-25 18:45:51,553] [INFO] Target genome list was writen to GCF_016127415.1_ASM1612741v1_genomic.fna/target_genomes.txt
[2024-01-25 18:45:51,564] [INFO] Task started: fastANI
[2024-01-25 18:45:51,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dfb7c66-1cd2-4511-af8b-f408e5825a0e/GCF_016127415.1_ASM1612741v1_genomic.fna.gz --refList GCF_016127415.1_ASM1612741v1_genomic.fna/target_genomes.txt --output GCF_016127415.1_ASM1612741v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:46:14,785] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:14,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27d4b205-2af4-41e9-a5fb-053f3e1fb137/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:46:14,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27d4b205-2af4-41e9-a5fb-053f3e1fb137/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:46:14,797] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:46:14,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:46:14,797] [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
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	100.0	2265	2265	95	conclusive
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	99.971	2161	2265	95	conclusive
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	84.4963	1128	2265	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	84.4137	963	2265	95	below_threshold
Comamonas testosteroni	strain=ATCC 11996	GCA_000241525.2	285	285	suspected-type	True	82.1722	1009	2265	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_000964545.1	363952	363952	type	True	82.1283	1015	2265	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001517325.1	363952	363952	type	True	82.09	1015	2265	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	82.0882	816	2265	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	82.0827	946	2265	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	81.8274	918	2265	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	81.1523	880	2265	95	below_threshold
Diaphorobacter ruginosibacter	strain=DSM 27467	GCA_014395975.1	1715720	1715720	type	True	80.8598	841	2265	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	80.6701	827	2265	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	80.3933	964	2265	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.0189	692	2265	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.6492	605	2265	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.3163	716	2265	95	below_threshold
Caulobacter henricii	strain=CB4	GCA_001414055.1	69395	69395	type	True	75.4773	112	2265	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:46:14,799] [INFO] DFAST Taxonomy check result was written to GCF_016127415.1_ASM1612741v1_genomic.fna/tc_result.tsv
[2024-01-25 18:46:14,799] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:46:14,799] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:46:14,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27d4b205-2af4-41e9-a5fb-053f3e1fb137/dqc_reference/checkm_data
[2024-01-25 18:46:14,800] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:46:14,866] [INFO] Task started: CheckM
[2024-01-25 18:46:14,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016127415.1_ASM1612741v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016127415.1_ASM1612741v1_genomic.fna/checkm_input GCF_016127415.1_ASM1612741v1_genomic.fna/checkm_result
[2024-01-25 18:50:15,089] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:15,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:15,106] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:15,107] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:15,107] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016127415.1_ASM1612741v1_genomic.fna/markers.fasta)
[2024-01-25 18:50:15,108] [INFO] Task started: Blastn
[2024-01-25 18:50:15,108] [INFO] Running command: blastn -query GCF_016127415.1_ASM1612741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27d4b205-2af4-41e9-a5fb-053f3e1fb137/dqc_reference/reference_markers_gtdb.fasta -out GCF_016127415.1_ASM1612741v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:16,806] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:16,809] [INFO] Selected 18 target genomes.
[2024-01-25 18:50:16,809] [INFO] Target genome list was writen to GCF_016127415.1_ASM1612741v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:50:16,835] [INFO] Task started: fastANI
[2024-01-25 18:50:16,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dfb7c66-1cd2-4511-af8b-f408e5825a0e/GCF_016127415.1_ASM1612741v1_genomic.fna.gz --refList GCF_016127415.1_ASM1612741v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016127415.1_ASM1612741v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:50:37,369] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:37,378] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:50:37,379] [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_001598795.1	s__Comamonas acidovorans	99.971	2161	2265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.4801	97.72	96.19	0.89	0.80	41	conclusive
GCF_001571325.1	s__Comamonas tsuruhatensis	95.4596	1852	2265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.4801	98.55	98.21	0.90	0.80	27	-
GCF_001544075.1	s__Comamonas terrae	84.4573	1133	2265	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	84.4267	962	2265	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	83.2146	725	2265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429845.1	s__Comamonas composti	82.9261	975	2265	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	82.2226	1014	2265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.84	98.53	0.90	0.90	4	-
GCF_000964545.1	s__Comamonas thiooxydans	82.138	1014	2265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.51	95.23	0.90	0.87	29	-
GCF_000739875.1	s__Comamonas aquatica	82.1222	812	2265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	96.97	96.57	0.89	0.87	7	-
GCF_000400995.2	s__MR-S7 sp000400995	82.0984	912	2265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__MR-S7	95.0	97.31	97.31	0.83	0.83	2	-
GCF_900461435.1	s__Comamonas terrigena	81.8503	913	2265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.97	95.46	0.95	0.91	7	-
GCF_900564145.1	s__Comamonas sp900564145	81.7794	964	2265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350475.1	s__Pseudacidovorax intermedius	80.0298	880	2265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudacidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002794255.1	s__Streptomyces carminius	74.9684	166	2265	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:50:37,380] [INFO] GTDB search result was written to GCF_016127415.1_ASM1612741v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:50:37,381] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:50:37,384] [INFO] DFAST_QC result json was written to GCF_016127415.1_ASM1612741v1_genomic.fna/dqc_result.json
[2024-01-25 18:50:37,384] [INFO] DFAST_QC completed!
[2024-01-25 18:50:37,384] [INFO] Total running time: 0h5m17s