[2023-06-28 18:28:48,430] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:28:48,433] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:28:48,433] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbff3e51-b94a-4ae5-ad22-5b05ea69e533/dqc_reference
[2023-06-28 18:28:51,654] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:28:51,655] [INFO] Task started: Prodigal
[2023-06-28 18:28:51,656] [INFO] Running command: gunzip -c /var/lib/cwl/stg057cfe58-0154-4202-ac78-3cc67669f849/GCA_017412405.1_ASM1741240v1_genomic.fna.gz | prodigal -d GCA_017412405.1_ASM1741240v1_genomic.fna/cds.fna -a GCA_017412405.1_ASM1741240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:28:57,838] [INFO] Task succeeded: Prodigal
[2023-06-28 18:28:57,838] [INFO] Task started: HMMsearch
[2023-06-28 18:28:57,838] [INFO] Running command: hmmsearch --tblout GCA_017412405.1_ASM1741240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbff3e51-b94a-4ae5-ad22-5b05ea69e533/dqc_reference/reference_markers.hmm GCA_017412405.1_ASM1741240v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:28:58,056] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:28:58,059] [INFO] Found 6/6 markers.
[2023-06-28 18:28:58,084] [INFO] Query marker FASTA was written to GCA_017412405.1_ASM1741240v1_genomic.fna/markers.fasta
[2023-06-28 18:28:58,085] [INFO] Task started: Blastn
[2023-06-28 18:28:58,085] [INFO] Running command: blastn -query GCA_017412405.1_ASM1741240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbff3e51-b94a-4ae5-ad22-5b05ea69e533/dqc_reference/reference_markers.fasta -out GCA_017412405.1_ASM1741240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:28:58,709] [INFO] Task succeeded: Blastn
[2023-06-28 18:28:58,713] [INFO] Selected 14 target genomes.
[2023-06-28 18:28:58,713] [INFO] Target genome list was writen to GCA_017412405.1_ASM1741240v1_genomic.fna/target_genomes.txt
[2023-06-28 18:28:58,718] [INFO] Task started: fastANI
[2023-06-28 18:28:58,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg057cfe58-0154-4202-ac78-3cc67669f849/GCA_017412405.1_ASM1741240v1_genomic.fna.gz --refList GCA_017412405.1_ASM1741240v1_genomic.fna/target_genomes.txt --output GCA_017412405.1_ASM1741240v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:29:11,063] [INFO] Task succeeded: fastANI
[2023-06-28 18:29:11,064] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbff3e51-b94a-4ae5-ad22-5b05ea69e533/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:29:11,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbff3e51-b94a-4ae5-ad22-5b05ea69e533/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:29:11,071] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:29:11,072] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:29:11,072] [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 saccharophilum	strain=DSM 2985	GCA_000255555.2	165	165	type	True	77.3708	104	644	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:29:11,074] [INFO] DFAST Taxonomy check result was written to GCA_017412405.1_ASM1741240v1_genomic.fna/tc_result.tsv
[2023-06-28 18:29:11,075] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:29:11,075] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:29:11,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbff3e51-b94a-4ae5-ad22-5b05ea69e533/dqc_reference/checkm_data
[2023-06-28 18:29:11,076] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:29:11,106] [INFO] Task started: CheckM
[2023-06-28 18:29:11,107] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017412405.1_ASM1741240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017412405.1_ASM1741240v1_genomic.fna/checkm_input GCA_017412405.1_ASM1741240v1_genomic.fna/checkm_result
[2023-06-28 18:29:36,000] [INFO] Task succeeded: CheckM
[2023-06-28 18:29:36,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:29:36,025] [INFO] ===== Completeness check finished =====
[2023-06-28 18:29:36,025] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:29:36,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017412405.1_ASM1741240v1_genomic.fna/markers.fasta)
[2023-06-28 18:29:36,026] [INFO] Task started: Blastn
[2023-06-28 18:29:36,026] [INFO] Running command: blastn -query GCA_017412405.1_ASM1741240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbff3e51-b94a-4ae5-ad22-5b05ea69e533/dqc_reference/reference_markers_gtdb.fasta -out GCA_017412405.1_ASM1741240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:29:36,993] [INFO] Task succeeded: Blastn
[2023-06-28 18:29:36,998] [INFO] Selected 20 target genomes.
[2023-06-28 18:29:36,998] [INFO] Target genome list was writen to GCA_017412405.1_ASM1741240v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:29:37,012] [INFO] Task started: fastANI
[2023-06-28 18:29:37,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg057cfe58-0154-4202-ac78-3cc67669f849/GCA_017412405.1_ASM1741240v1_genomic.fna.gz --refList GCA_017412405.1_ASM1741240v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017412405.1_ASM1741240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:29:46,864] [INFO] Task succeeded: fastANI
[2023-06-28 18:29:46,873] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:29:46,873] [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_017412405.1	s__Treponema_D sp017412405	100.0	638	644	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_017449265.1	s__Treponema_D sp017449265	80.2039	355	644	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_017934745.1	s__Treponema_D sp017934745	78.2536	131	644	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.63	96.63	0.83	0.83	2	-
GCF_000255555.1	s__Treponema_D saccharophilum	77.4231	103	644	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.00	98.95	0.97	0.97	3	-
GCA_017464425.1	s__Treponema_D sp017464425	77.4139	97	644	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	77.2157	73	644	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	77.0032	122	644	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_002404895.1	s__Treponema_D sp002404895	76.1381	70	644	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 18:29:46,875] [INFO] GTDB search result was written to GCA_017412405.1_ASM1741240v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:29:46,876] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:29:46,879] [INFO] DFAST_QC result json was written to GCA_017412405.1_ASM1741240v1_genomic.fna/dqc_result.json
[2023-06-28 18:29:46,879] [INFO] DFAST_QC completed!
[2023-06-28 18:29:46,880] [INFO] Total running time: 0h0m58s