[2023-06-28 12:49:38,743] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:49:38,752] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:49:38,752] [INFO] DQC Reference Directory: /var/lib/cwl/stg89c5036c-0ebe-4ccf-826b-ceeaca1f5b5a/dqc_reference
[2023-06-28 12:49:40,104] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:49:40,106] [INFO] Task started: Prodigal
[2023-06-28 12:49:40,107] [INFO] Running command: gunzip -c /var/lib/cwl/stg78623a8e-8138-494a-8fa8-f33d79d8fe42/GCA_017635005.1_ASM1763500v1_genomic.fna.gz | prodigal -d GCA_017635005.1_ASM1763500v1_genomic.fna/cds.fna -a GCA_017635005.1_ASM1763500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:49:46,202] [INFO] Task succeeded: Prodigal
[2023-06-28 12:49:46,202] [INFO] Task started: HMMsearch
[2023-06-28 12:49:46,202] [INFO] Running command: hmmsearch --tblout GCA_017635005.1_ASM1763500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89c5036c-0ebe-4ccf-826b-ceeaca1f5b5a/dqc_reference/reference_markers.hmm GCA_017635005.1_ASM1763500v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:49:46,485] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:49:46,487] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg78623a8e-8138-494a-8fa8-f33d79d8fe42/GCA_017635005.1_ASM1763500v1_genomic.fna.gz]
[2023-06-28 12:49:46,527] [INFO] Query marker FASTA was written to GCA_017635005.1_ASM1763500v1_genomic.fna/markers.fasta
[2023-06-28 12:49:46,527] [INFO] Task started: Blastn
[2023-06-28 12:49:46,527] [INFO] Running command: blastn -query GCA_017635005.1_ASM1763500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89c5036c-0ebe-4ccf-826b-ceeaca1f5b5a/dqc_reference/reference_markers.fasta -out GCA_017635005.1_ASM1763500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:49:47,198] [INFO] Task succeeded: Blastn
[2023-06-28 12:49:47,202] [INFO] Selected 8 target genomes.
[2023-06-28 12:49:47,203] [INFO] Target genome list was writen to GCA_017635005.1_ASM1763500v1_genomic.fna/target_genomes.txt
[2023-06-28 12:49:47,204] [INFO] Task started: fastANI
[2023-06-28 12:49:47,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg78623a8e-8138-494a-8fa8-f33d79d8fe42/GCA_017635005.1_ASM1763500v1_genomic.fna.gz --refList GCA_017635005.1_ASM1763500v1_genomic.fna/target_genomes.txt --output GCA_017635005.1_ASM1763500v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:49:51,893] [INFO] Task succeeded: fastANI
[2023-06-28 12:49:51,893] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89c5036c-0ebe-4ccf-826b-ceeaca1f5b5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:49:51,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89c5036c-0ebe-4ccf-826b-ceeaca1f5b5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:49:51,901] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:49:51,901] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:49:51,901] [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	80.0849	356	788	95	below_threshold
Treponema saccharophilum	strain=DSM 2985	GCA_000255555.2	165	165	type	True	77.4113	66	788	95	below_threshold
Treponema berlinense	strain=ATCC BAA-909	GCA_900167025.1	225004	225004	type	True	77.3637	81	788	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:49:51,903] [INFO] DFAST Taxonomy check result was written to GCA_017635005.1_ASM1763500v1_genomic.fna/tc_result.tsv
[2023-06-28 12:49:51,905] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:49:51,905] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:49:51,906] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89c5036c-0ebe-4ccf-826b-ceeaca1f5b5a/dqc_reference/checkm_data
[2023-06-28 12:49:51,907] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:49:51,943] [INFO] Task started: CheckM
[2023-06-28 12:49:51,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017635005.1_ASM1763500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017635005.1_ASM1763500v1_genomic.fna/checkm_input GCA_017635005.1_ASM1763500v1_genomic.fna/checkm_result
[2023-06-28 12:50:16,600] [INFO] Task succeeded: CheckM
[2023-06-28 12:50:16,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:50:16,623] [INFO] ===== Completeness check finished =====
[2023-06-28 12:50:16,623] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:50:16,624] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017635005.1_ASM1763500v1_genomic.fna/markers.fasta)
[2023-06-28 12:50:16,624] [INFO] Task started: Blastn
[2023-06-28 12:50:16,624] [INFO] Running command: blastn -query GCA_017635005.1_ASM1763500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89c5036c-0ebe-4ccf-826b-ceeaca1f5b5a/dqc_reference/reference_markers_gtdb.fasta -out GCA_017635005.1_ASM1763500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:50:17,482] [INFO] Task succeeded: Blastn
[2023-06-28 12:50:17,486] [INFO] Selected 12 target genomes.
[2023-06-28 12:50:17,486] [INFO] Target genome list was writen to GCA_017635005.1_ASM1763500v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:50:17,492] [INFO] Task started: fastANI
[2023-06-28 12:50:17,492] [INFO] Running command: fastANI --query /var/lib/cwl/stg78623a8e-8138-494a-8fa8-f33d79d8fe42/GCA_017635005.1_ASM1763500v1_genomic.fna.gz --refList GCA_017635005.1_ASM1763500v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017635005.1_ASM1763500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:50:24,347] [INFO] Task succeeded: fastANI
[2023-06-28 12:50:24,357] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:50:24,357] [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_002368605.1	s__Treponema_D sp002368605	96.8144	604	788	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.93	96.81	0.81	0.77	3	conclusive
GCA_017469785.1	s__Treponema_D sp017469785	85.759	446	788	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.36	97.36	0.82	0.82	2	-
GCA_017468745.1	s__Treponema_D sp017468745	84.879	291	788	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_002393835.1	s__Treponema_D sp002393835	81.4342	280	788	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.83	96.83	0.78	0.78	2	-
GCA_017430385.1	s__Treponema_D sp017430385	80.6609	339	788	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_902785455.1	s__Treponema_D sp902785455	80.2763	309	788	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	80.2295	294	788	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_017484285.1	s__Treponema_D sp017484285	80.0025	329	788	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_017464425.1	s__Treponema_D sp017464425	79.8213	296	788	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_017449265.1	s__Treponema_D sp017449265	79.79	124	788	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.79	97.79	0.82	0.82	2	-
GCA_017449285.1	s__Treponema_D sp017449285	77.3775	110	788	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:50:24,359] [INFO] GTDB search result was written to GCA_017635005.1_ASM1763500v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:50:24,360] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:50:24,363] [INFO] DFAST_QC result json was written to GCA_017635005.1_ASM1763500v1_genomic.fna/dqc_result.json
[2023-06-28 12:50:24,363] [INFO] DFAST_QC completed!
[2023-06-28 12:50:24,363] [INFO] Total running time: 0h0m46s