[2023-06-18 19:52:17,880] [INFO] DFAST_QC pipeline started.
[2023-06-18 19:52:17,882] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 19:52:17,883] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4ad98f8-239e-4dc6-9836-704bbd81ed91/dqc_reference
[2023-06-18 19:52:19,163] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 19:52:19,163] [INFO] Task started: Prodigal
[2023-06-18 19:52:19,164] [INFO] Running command: gunzip -c /var/lib/cwl/stgab8586d8-3855-4f02-a59f-37603b6b63e1/GCA_018064525.1_ASM1806452v1_genomic.fna.gz | prodigal -d GCA_018064525.1_ASM1806452v1_genomic.fna/cds.fna -a GCA_018064525.1_ASM1806452v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 19:52:24,338] [INFO] Task succeeded: Prodigal
[2023-06-18 19:52:24,338] [INFO] Task started: HMMsearch
[2023-06-18 19:52:24,339] [INFO] Running command: hmmsearch --tblout GCA_018064525.1_ASM1806452v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4ad98f8-239e-4dc6-9836-704bbd81ed91/dqc_reference/reference_markers.hmm GCA_018064525.1_ASM1806452v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 19:52:24,588] [INFO] Task succeeded: HMMsearch
[2023-06-18 19:52:24,590] [INFO] Found 6/6 markers.
[2023-06-18 19:52:24,621] [INFO] Query marker FASTA was written to GCA_018064525.1_ASM1806452v1_genomic.fna/markers.fasta
[2023-06-18 19:52:24,622] [INFO] Task started: Blastn
[2023-06-18 19:52:24,622] [INFO] Running command: blastn -query GCA_018064525.1_ASM1806452v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4ad98f8-239e-4dc6-9836-704bbd81ed91/dqc_reference/reference_markers.fasta -out GCA_018064525.1_ASM1806452v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:52:25,220] [INFO] Task succeeded: Blastn
[2023-06-18 19:52:25,224] [INFO] Selected 19 target genomes.
[2023-06-18 19:52:25,225] [INFO] Target genome list was writen to GCA_018064525.1_ASM1806452v1_genomic.fna/target_genomes.txt
[2023-06-18 19:52:25,230] [INFO] Task started: fastANI
[2023-06-18 19:52:25,231] [INFO] Running command: fastANI --query /var/lib/cwl/stgab8586d8-3855-4f02-a59f-37603b6b63e1/GCA_018064525.1_ASM1806452v1_genomic.fna.gz --refList GCA_018064525.1_ASM1806452v1_genomic.fna/target_genomes.txt --output GCA_018064525.1_ASM1806452v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 19:52:35,810] [INFO] Task succeeded: fastANI
[2023-06-18 19:52:35,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4ad98f8-239e-4dc6-9836-704bbd81ed91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 19:52:35,811] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4ad98f8-239e-4dc6-9836-704bbd81ed91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 19:52:35,822] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 19:52:35,822] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 19:52:35,822] [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 berlinense	strain=ATCC BAA-909	GCA_900167025.1	225004	225004	type	True	76.9525	91	857	95	below_threshold
Treponema porcinum	strain=ATCC BAA-908	GCA_900167145.1	261392	261392	type	True	76.3888	69	857	95	below_threshold
Treponema rectale	strain=DSM 103679	GCA_014202035.1	744512	744512	suspected-type	True	76.3096	94	857	95	below_threshold
Treponema ruminis	strain=DSM 103462	GCA_014201975.1	744515	744515	type	True	76.1553	76	857	95	below_threshold
Treponema peruense	strain=RCC2812	GCA_016117655.1	2787628	2787628	type	True	75.7498	66	857	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 19:52:35,824] [INFO] DFAST Taxonomy check result was written to GCA_018064525.1_ASM1806452v1_genomic.fna/tc_result.tsv
[2023-06-18 19:52:35,825] [INFO] ===== Taxonomy check completed =====
[2023-06-18 19:52:35,825] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 19:52:35,826] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4ad98f8-239e-4dc6-9836-704bbd81ed91/dqc_reference/checkm_data
[2023-06-18 19:52:35,827] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 19:52:35,855] [INFO] Task started: CheckM
[2023-06-18 19:52:35,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018064525.1_ASM1806452v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018064525.1_ASM1806452v1_genomic.fna/checkm_input GCA_018064525.1_ASM1806452v1_genomic.fna/checkm_result
[2023-06-18 19:52:59,112] [INFO] Task succeeded: CheckM
[2023-06-18 19:52:59,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 19:52:59,133] [INFO] ===== Completeness check finished =====
[2023-06-18 19:52:59,133] [INFO] ===== Start GTDB Search =====
[2023-06-18 19:52:59,134] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018064525.1_ASM1806452v1_genomic.fna/markers.fasta)
[2023-06-18 19:52:59,134] [INFO] Task started: Blastn
[2023-06-18 19:52:59,134] [INFO] Running command: blastn -query GCA_018064525.1_ASM1806452v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4ad98f8-239e-4dc6-9836-704bbd81ed91/dqc_reference/reference_markers_gtdb.fasta -out GCA_018064525.1_ASM1806452v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:52:59,941] [INFO] Task succeeded: Blastn
[2023-06-18 19:52:59,947] [INFO] Selected 14 target genomes.
[2023-06-18 19:52:59,947] [INFO] Target genome list was writen to GCA_018064525.1_ASM1806452v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 19:52:59,953] [INFO] Task started: fastANI
[2023-06-18 19:52:59,953] [INFO] Running command: fastANI --query /var/lib/cwl/stgab8586d8-3855-4f02-a59f-37603b6b63e1/GCA_018064525.1_ASM1806452v1_genomic.fna.gz --refList GCA_018064525.1_ASM1806452v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018064525.1_ASM1806452v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 19:53:06,640] [INFO] Task succeeded: fastANI
[2023-06-18 19:53:06,651] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 19:53:06,651] [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_018064525.1	s__Treponema_D sp018064525	100.0	851	857	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018066075.1	s__Treponema_D sp018066075	85.9278	491	857	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_017553635.1	s__Treponema_D sp017553635	79.8279	379	857	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.74	98.74	0.94	0.94	2	-
GCA_016293495.1	s__Treponema_D sp016293495	79.5543	332	857	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.53	98.51	0.86	0.85	3	-
GCA_018385415.1	s__Treponema_D sp018385415	79.5329	301	857	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_002309195.1	s__Treponema_D sp002309195	79.4499	235	857	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.61	98.42	0.71	0.58	5	-
GCA_900769985.1	s__Treponema_D sp900769985	78.3119	284	857	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.33	98.33	0.87	0.87	2	-
GCF_000260795.1	s__Treponema_D sp000260795	77.3865	124	857	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_016286535.1	s__Treponema_D sp016286535	77.0387	112	857	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_016296655.1	s__Treponema_D sp016296655	76.9197	85	857	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_902797305.1	s__Treponema_D sp902797305	76.3244	82	857	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_002394685.1	s__Treponema_D sp002394685	76.2508	93	857	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.10	97.94	0.89	0.88	4	-
GCA_900767955.1	s__Treponema_D sp900767955	76.1058	88	857	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.06	96.06	0.87	0.77	5	-
--------------------------------------------------------------------------------
[2023-06-18 19:53:06,653] [INFO] GTDB search result was written to GCA_018064525.1_ASM1806452v1_genomic.fna/result_gtdb.tsv
[2023-06-18 19:53:06,654] [INFO] ===== GTDB Search completed =====
[2023-06-18 19:53:06,657] [INFO] DFAST_QC result json was written to GCA_018064525.1_ASM1806452v1_genomic.fna/dqc_result.json
[2023-06-18 19:53:06,657] [INFO] DFAST_QC completed!
[2023-06-18 19:53:06,657] [INFO] Total running time: 0h0m49s