[2023-07-01 04:21:50,969] [INFO] DFAST_QC pipeline started.
[2023-07-01 04:21:50,971] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 04:21:50,972] [INFO] DQC Reference Directory: /var/lib/cwl/stg412e7c3a-06a9-4715-8653-4825c65fe601/dqc_reference
[2023-07-01 04:21:52,393] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 04:21:52,393] [INFO] Task started: Prodigal
[2023-07-01 04:21:52,394] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0d4ef68-cc33-4878-89ef-948194e92205/GCA_024698325.1_ASM2469832v1_genomic.fna.gz | prodigal -d GCA_024698325.1_ASM2469832v1_genomic.fna/cds.fna -a GCA_024698325.1_ASM2469832v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 04:21:59,048] [INFO] Task succeeded: Prodigal
[2023-07-01 04:21:59,048] [INFO] Task started: HMMsearch
[2023-07-01 04:21:59,048] [INFO] Running command: hmmsearch --tblout GCA_024698325.1_ASM2469832v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg412e7c3a-06a9-4715-8653-4825c65fe601/dqc_reference/reference_markers.hmm GCA_024698325.1_ASM2469832v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 04:21:59,286] [INFO] Task succeeded: HMMsearch
[2023-07-01 04:21:59,288] [INFO] Found 6/6 markers.
[2023-07-01 04:21:59,317] [INFO] Query marker FASTA was written to GCA_024698325.1_ASM2469832v1_genomic.fna/markers.fasta
[2023-07-01 04:21:59,318] [INFO] Task started: Blastn
[2023-07-01 04:21:59,318] [INFO] Running command: blastn -query GCA_024698325.1_ASM2469832v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg412e7c3a-06a9-4715-8653-4825c65fe601/dqc_reference/reference_markers.fasta -out GCA_024698325.1_ASM2469832v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:21:59,886] [INFO] Task succeeded: Blastn
[2023-07-01 04:21:59,897] [INFO] Selected 13 target genomes.
[2023-07-01 04:21:59,898] [INFO] Target genome list was writen to GCA_024698325.1_ASM2469832v1_genomic.fna/target_genomes.txt
[2023-07-01 04:21:59,900] [INFO] Task started: fastANI
[2023-07-01 04:21:59,901] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0d4ef68-cc33-4878-89ef-948194e92205/GCA_024698325.1_ASM2469832v1_genomic.fna.gz --refList GCA_024698325.1_ASM2469832v1_genomic.fna/target_genomes.txt --output GCA_024698325.1_ASM2469832v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 04:22:06,351] [INFO] Task succeeded: fastANI
[2023-07-01 04:22:06,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg412e7c3a-06a9-4715-8653-4825c65fe601/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 04:22:06,353] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg412e7c3a-06a9-4715-8653-4825c65fe601/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 04:22:06,363] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 04:22:06,363] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 04:22:06,363] [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
Treponema ruminis	strain=DSM 103462	GCA_014201975.1	744515	744515	type	True	77.2678	120	880	95	below_threshold
Treponema berlinense	strain=ATCC BAA-909	GCA_900167025.1	225004	225004	type	True	76.8341	70	880	95	below_threshold
Treponema saccharophilum	strain=DSM 2985	GCA_000255555.2	165	165	type	True	76.72	78	880	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 04:22:06,366] [INFO] DFAST Taxonomy check result was written to GCA_024698325.1_ASM2469832v1_genomic.fna/tc_result.tsv
[2023-07-01 04:22:06,367] [INFO] ===== Taxonomy check completed =====
[2023-07-01 04:22:06,367] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 04:22:06,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg412e7c3a-06a9-4715-8653-4825c65fe601/dqc_reference/checkm_data
[2023-07-01 04:22:06,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 04:22:06,404] [INFO] Task started: CheckM
[2023-07-01 04:22:06,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024698325.1_ASM2469832v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024698325.1_ASM2469832v1_genomic.fna/checkm_input GCA_024698325.1_ASM2469832v1_genomic.fna/checkm_result
[2023-07-01 04:22:32,990] [INFO] Task succeeded: CheckM
[2023-07-01 04:22:32,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 04:22:33,015] [INFO] ===== Completeness check finished =====
[2023-07-01 04:22:33,015] [INFO] ===== Start GTDB Search =====
[2023-07-01 04:22:33,016] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024698325.1_ASM2469832v1_genomic.fna/markers.fasta)
[2023-07-01 04:22:33,016] [INFO] Task started: Blastn
[2023-07-01 04:22:33,016] [INFO] Running command: blastn -query GCA_024698325.1_ASM2469832v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg412e7c3a-06a9-4715-8653-4825c65fe601/dqc_reference/reference_markers_gtdb.fasta -out GCA_024698325.1_ASM2469832v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:22:33,790] [INFO] Task succeeded: Blastn
[2023-07-01 04:22:33,795] [INFO] Selected 21 target genomes.
[2023-07-01 04:22:33,795] [INFO] Target genome list was writen to GCA_024698325.1_ASM2469832v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 04:22:33,849] [INFO] Task started: fastANI
[2023-07-01 04:22:33,849] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0d4ef68-cc33-4878-89ef-948194e92205/GCA_024698325.1_ASM2469832v1_genomic.fna.gz --refList GCA_024698325.1_ASM2469832v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024698325.1_ASM2469832v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 04:22:43,694] [INFO] Task succeeded: fastANI
[2023-07-01 04:22:43,710] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 04:22:43,710] [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_017449285.1	s__Treponema_D sp017449285	77.8936	153	880	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017161305.1	s__Treponema_D ruminis	77.2858	106	880	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.98	99.98	0.92	0.92	2	-
GCA_017450535.1	s__Treponema_D sp017450535	77.2738	122	880	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017430385.1	s__Treponema_D sp017430385	77.1007	100	880	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017484285.1	s__Treponema_D sp017484285	77.0552	127	880	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002369025.1	s__Treponema_D sp002369025	77.0284	132	880	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.41	97.17	0.81	0.77	4	-
GCF_900167025.1	s__Treponema_D berlinense	76.8687	68	880	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.85	98.81	0.93	0.90	4	-
GCF_000619925.1	s__Treponema_D sp000619925	76.5562	62	880	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804085.1	s__Treponema_D sp014804085	76.4649	100	880	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	95.34	95.30	0.82	0.78	3	-
GCA_900770075.1	s__Treponema_D sp900770075	76.3888	62	880	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.11	97.11	0.86	0.86	2	-
GCA_002394465.1	s__Treponema_D sp002394465	76.2806	60	880	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902803735.1	s__Treponema_D sp902803735	76.2525	50	880	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 04:22:43,713] [INFO] GTDB search result was written to GCA_024698325.1_ASM2469832v1_genomic.fna/result_gtdb.tsv
[2023-07-01 04:22:43,713] [INFO] ===== GTDB Search completed =====
[2023-07-01 04:22:43,718] [INFO] DFAST_QC result json was written to GCA_024698325.1_ASM2469832v1_genomic.fna/dqc_result.json
[2023-07-01 04:22:43,718] [INFO] DFAST_QC completed!
[2023-07-01 04:22:43,718] [INFO] Total running time: 0h0m53s