[2023-06-18 19:52:02,377] [INFO] DFAST_QC pipeline started.
[2023-06-18 19:52:02,379] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 19:52:02,380] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ba0f586-b0ad-4b6d-9f1c-c84558ba86d9/dqc_reference
[2023-06-18 19:52:03,655] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 19:52:03,656] [INFO] Task started: Prodigal
[2023-06-18 19:52:03,656] [INFO] Running command: gunzip -c /var/lib/cwl/stg2459c261-a61b-4eee-9438-ccdacd8f819c/GCA_018402345.1_ASM1840234v1_genomic.fna.gz | prodigal -d GCA_018402345.1_ASM1840234v1_genomic.fna/cds.fna -a GCA_018402345.1_ASM1840234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 19:52:25,905] [INFO] Task succeeded: Prodigal
[2023-06-18 19:52:25,906] [INFO] Task started: HMMsearch
[2023-06-18 19:52:25,906] [INFO] Running command: hmmsearch --tblout GCA_018402345.1_ASM1840234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ba0f586-b0ad-4b6d-9f1c-c84558ba86d9/dqc_reference/reference_markers.hmm GCA_018402345.1_ASM1840234v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 19:52:26,139] [INFO] Task succeeded: HMMsearch
[2023-06-18 19:52:26,140] [INFO] Found 6/6 markers.
[2023-06-18 19:52:26,170] [INFO] Query marker FASTA was written to GCA_018402345.1_ASM1840234v1_genomic.fna/markers.fasta
[2023-06-18 19:52:26,171] [INFO] Task started: Blastn
[2023-06-18 19:52:26,171] [INFO] Running command: blastn -query GCA_018402345.1_ASM1840234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ba0f586-b0ad-4b6d-9f1c-c84558ba86d9/dqc_reference/reference_markers.fasta -out GCA_018402345.1_ASM1840234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:52:26,815] [INFO] Task succeeded: Blastn
[2023-06-18 19:52:26,819] [INFO] Selected 20 target genomes.
[2023-06-18 19:52:26,820] [INFO] Target genome list was writen to GCA_018402345.1_ASM1840234v1_genomic.fna/target_genomes.txt
[2023-06-18 19:52:26,853] [INFO] Task started: fastANI
[2023-06-18 19:52:26,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg2459c261-a61b-4eee-9438-ccdacd8f819c/GCA_018402345.1_ASM1840234v1_genomic.fna.gz --refList GCA_018402345.1_ASM1840234v1_genomic.fna/target_genomes.txt --output GCA_018402345.1_ASM1840234v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 19:52:39,893] [INFO] Task succeeded: fastANI
[2023-06-18 19:52:39,893] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ba0f586-b0ad-4b6d-9f1c-c84558ba86d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 19:52:39,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ba0f586-b0ad-4b6d-9f1c-c84558ba86d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 19:52:39,904] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 19:52:39,905] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 19:52:39,905] [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
Terrimicrobium sacchariphilum	strain=NM-5	GCA_001613545.1	690879	690879	type	True	77.2989	100	1036	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	76.8929	51	1036	95	below_threshold
Chthoniobacter flavus	strain=Ellin428	GCA_000173075.1	191863	191863	type	True	76.6838	66	1036	95	below_threshold
Chthoniobacter flavus	strain=DSM 22515	GCA_004341915.1	191863	191863	type	True	76.5083	65	1036	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 19:52:39,911] [INFO] DFAST Taxonomy check result was written to GCA_018402345.1_ASM1840234v1_genomic.fna/tc_result.tsv
[2023-06-18 19:52:39,912] [INFO] ===== Taxonomy check completed =====
[2023-06-18 19:52:39,912] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 19:52:39,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ba0f586-b0ad-4b6d-9f1c-c84558ba86d9/dqc_reference/checkm_data
[2023-06-18 19:52:39,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 19:52:39,961] [INFO] Task started: CheckM
[2023-06-18 19:52:39,962] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018402345.1_ASM1840234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018402345.1_ASM1840234v1_genomic.fna/checkm_input GCA_018402345.1_ASM1840234v1_genomic.fna/checkm_result
[2023-06-18 19:53:40,705] [INFO] Task succeeded: CheckM
[2023-06-18 19:53:40,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 19:53:40,740] [INFO] ===== Completeness check finished =====
[2023-06-18 19:53:40,740] [INFO] ===== Start GTDB Search =====
[2023-06-18 19:53:40,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018402345.1_ASM1840234v1_genomic.fna/markers.fasta)
[2023-06-18 19:53:40,741] [INFO] Task started: Blastn
[2023-06-18 19:53:40,741] [INFO] Running command: blastn -query GCA_018402345.1_ASM1840234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ba0f586-b0ad-4b6d-9f1c-c84558ba86d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_018402345.1_ASM1840234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:53:41,634] [INFO] Task succeeded: Blastn
[2023-06-18 19:53:41,638] [INFO] Selected 13 target genomes.
[2023-06-18 19:53:41,639] [INFO] Target genome list was writen to GCA_018402345.1_ASM1840234v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 19:53:41,647] [INFO] Task started: fastANI
[2023-06-18 19:53:41,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg2459c261-a61b-4eee-9438-ccdacd8f819c/GCA_018402345.1_ASM1840234v1_genomic.fna.gz --refList GCA_018402345.1_ASM1840234v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018402345.1_ASM1840234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 19:53:50,925] [INFO] Task succeeded: fastANI
[2023-06-18 19:53:50,945] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 19:53:50,945] [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_018402345.1	s__UBA967 sp018402345	100.0	1036	1036	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018970255.1	s__UBA967 sp018970255	79.1709	286	1036	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002396485.1	s__UBA967 sp002396485	78.2262	254	1036	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009886045.1	s__UBA967 sp009886045	77.9411	219	1036	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002290555.1	s__UBA967 sp002290555	77.7128	169	1036	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	99.67	99.67	0.84	0.84	2	-
GCA_903915315.1	s__UBA967 sp903915315	77.5653	91	1036	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__UBA967	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613545.1	s__Terrimicrobium sacchariphilum	77.2989	100	1036	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__Terrimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305195.1	s__Terrimicrobium sp001897195	77.2351	114	1036	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__Terrimicrobium	95.0	99.90	99.90	0.94	0.94	2	-
GCA_003054655.1	s__Terrimicrobium sp003054655	76.8322	113	1036	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__Terrimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007280915.1	s__QYQL01 sp007280915	76.7308	132	1036	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Terrimicrobiaceae;g__QYQL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903874975.1	s__Chthoniobacter sp903874975	76.6024	62	1036	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__Chthoniobacter	95.0	97.99	97.82	0.84	0.83	3	-
--------------------------------------------------------------------------------
[2023-06-18 19:53:50,948] [INFO] GTDB search result was written to GCA_018402345.1_ASM1840234v1_genomic.fna/result_gtdb.tsv
[2023-06-18 19:53:50,948] [INFO] ===== GTDB Search completed =====
[2023-06-18 19:53:50,951] [INFO] DFAST_QC result json was written to GCA_018402345.1_ASM1840234v1_genomic.fna/dqc_result.json
[2023-06-18 19:53:50,951] [INFO] DFAST_QC completed!
[2023-06-18 19:53:50,951] [INFO] Total running time: 0h1m49s