[2023-06-19 14:29:47,008] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:29:47,015] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:29:47,015] [INFO] DQC Reference Directory: /var/lib/cwl/stg34af6674-dd7c-45a9-99c0-12660b272c29/dqc_reference
[2023-06-19 14:29:48,607] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:29:48,608] [INFO] Task started: Prodigal
[2023-06-19 14:29:48,608] [INFO] Running command: gunzip -c /var/lib/cwl/stgd53a4d55-0f14-4eac-8f20-cc3926e087e9/GCA_018882795.1_ASM1888279v1_genomic.fna.gz | prodigal -d GCA_018882795.1_ASM1888279v1_genomic.fna/cds.fna -a GCA_018882795.1_ASM1888279v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:29:54,870] [INFO] Task succeeded: Prodigal
[2023-06-19 14:29:54,871] [INFO] Task started: HMMsearch
[2023-06-19 14:29:54,871] [INFO] Running command: hmmsearch --tblout GCA_018882795.1_ASM1888279v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34af6674-dd7c-45a9-99c0-12660b272c29/dqc_reference/reference_markers.hmm GCA_018882795.1_ASM1888279v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:29:55,122] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:29:55,124] [INFO] Found 6/6 markers.
[2023-06-19 14:29:55,156] [INFO] Query marker FASTA was written to GCA_018882795.1_ASM1888279v1_genomic.fna/markers.fasta
[2023-06-19 14:29:55,156] [INFO] Task started: Blastn
[2023-06-19 14:29:55,156] [INFO] Running command: blastn -query GCA_018882795.1_ASM1888279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34af6674-dd7c-45a9-99c0-12660b272c29/dqc_reference/reference_markers.fasta -out GCA_018882795.1_ASM1888279v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:29:55,910] [INFO] Task succeeded: Blastn
[2023-06-19 14:29:55,915] [INFO] Selected 39 target genomes.
[2023-06-19 14:29:55,915] [INFO] Target genome list was writen to GCA_018882795.1_ASM1888279v1_genomic.fna/target_genomes.txt
[2023-06-19 14:29:55,929] [INFO] Task started: fastANI
[2023-06-19 14:29:55,929] [INFO] Running command: fastANI --query /var/lib/cwl/stgd53a4d55-0f14-4eac-8f20-cc3926e087e9/GCA_018882795.1_ASM1888279v1_genomic.fna.gz --refList GCA_018882795.1_ASM1888279v1_genomic.fna/target_genomes.txt --output GCA_018882795.1_ASM1888279v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:30:21,594] [INFO] Task succeeded: fastANI
[2023-06-19 14:30:21,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34af6674-dd7c-45a9-99c0-12660b272c29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:30:21,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34af6674-dd7c-45a9-99c0-12660b272c29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:30:21,612] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:30:21,612] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 14:30:21,613] [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
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	76.1147	53	634	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	75.9582	55	634	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_008801845.1	36863	36863	type	True	75.9581	55	634	95	below_threshold
Bordetella hinzii	strain=NCTC13199	GCA_900637615.1	103855	103855	type	True	75.9428	51	634	95	below_threshold
Bordetella hinzii	strain=LMG 13501	GCA_001548475.1	103855	103855	type	True	75.9284	50	634	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=NBRC 102523	GCA_001591225.1	80842	80842	type	True	75.7458	50	634	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=DSM 11543	GCA_003719195.1	80842	80842	type	True	75.7458	50	634	95	below_threshold
Achromobacter anxifer	strain=LMG 26857	GCA_903652925.1	1287737	1287737	type	True	75.6286	59	634	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 14:30:21,618] [INFO] DFAST Taxonomy check result was written to GCA_018882795.1_ASM1888279v1_genomic.fna/tc_result.tsv
[2023-06-19 14:30:21,621] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:30:21,621] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:30:21,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34af6674-dd7c-45a9-99c0-12660b272c29/dqc_reference/checkm_data
[2023-06-19 14:30:21,623] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:30:21,656] [INFO] Task started: CheckM
[2023-06-19 14:30:21,657] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018882795.1_ASM1888279v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018882795.1_ASM1888279v1_genomic.fna/checkm_input GCA_018882795.1_ASM1888279v1_genomic.fna/checkm_result
[2023-06-19 14:30:46,980] [INFO] Task succeeded: CheckM
[2023-06-19 14:30:46,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 14:30:47,004] [INFO] ===== Completeness check finished =====
[2023-06-19 14:30:47,005] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:30:47,005] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018882795.1_ASM1888279v1_genomic.fna/markers.fasta)
[2023-06-19 14:30:47,006] [INFO] Task started: Blastn
[2023-06-19 14:30:47,006] [INFO] Running command: blastn -query GCA_018882795.1_ASM1888279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34af6674-dd7c-45a9-99c0-12660b272c29/dqc_reference/reference_markers_gtdb.fasta -out GCA_018882795.1_ASM1888279v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:30:48,013] [INFO] Task succeeded: Blastn
[2023-06-19 14:30:48,018] [INFO] Selected 20 target genomes.
[2023-06-19 14:30:48,018] [INFO] Target genome list was writen to GCA_018882795.1_ASM1888279v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:30:48,030] [INFO] Task started: fastANI
[2023-06-19 14:30:48,031] [INFO] Running command: fastANI --query /var/lib/cwl/stgd53a4d55-0f14-4eac-8f20-cc3926e087e9/GCA_018882795.1_ASM1888279v1_genomic.fna.gz --refList GCA_018882795.1_ASM1888279v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018882795.1_ASM1888279v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:30:58,909] [INFO] Task succeeded: fastANI
[2023-06-19 14:30:58,918] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:30:58,919] [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
GCA_018882795.1	s__UBA954 sp018882795	100.0	627	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA954	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018882785.1	s__UBA954 sp018882785	78.0162	240	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA954	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970545.1	s__UBA954 sp018970545	77.921	193	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA954	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009924525.1	s__UBA954 sp009924525	77.9158	158	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA954	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969705.1	s__UBA954 sp018969705	77.4502	132	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA954	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002293155.1	s__UBA954 sp002293155	76.9631	82	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA954	95.0	98.25	97.64	0.86	0.78	18	-
GCA_009646425.1	s__UBA2463 sp009646425	76.7202	81	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2463	95.0	95.85	95.85	0.97	0.97	2	-
GCA_903934795.1	s__CAIZPE01 sp903934795	76.0464	68	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIZPE01	95.0	99.53	99.52	0.90	0.89	3	-
GCA_002342295.1	s__UBA2463 sp002342295	75.9845	54	634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2463	95.0	99.64	99.37	0.90	0.83	6	-
--------------------------------------------------------------------------------
[2023-06-19 14:30:58,920] [INFO] GTDB search result was written to GCA_018882795.1_ASM1888279v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:30:58,921] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:30:58,927] [INFO] DFAST_QC result json was written to GCA_018882795.1_ASM1888279v1_genomic.fna/dqc_result.json
[2023-06-19 14:30:58,927] [INFO] DFAST_QC completed!
[2023-06-19 14:30:58,927] [INFO] Total running time: 0h1m12s