[2023-06-28 12:17:49,220] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:17:49,228] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:17:49,229] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4ed74d6-80bb-42ff-8bcc-7b965b41beeb/dqc_reference
[2023-06-28 12:17:50,473] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:17:50,474] [INFO] Task started: Prodigal
[2023-06-28 12:17:50,474] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b470ac5-6f3e-4228-a105-6c6ce1b53b38/GCA_017402295.1_ASM1740229v1_genomic.fna.gz | prodigal -d GCA_017402295.1_ASM1740229v1_genomic.fna/cds.fna -a GCA_017402295.1_ASM1740229v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:17:53,666] [INFO] Task succeeded: Prodigal
[2023-06-28 12:17:53,667] [INFO] Task started: HMMsearch
[2023-06-28 12:17:53,667] [INFO] Running command: hmmsearch --tblout GCA_017402295.1_ASM1740229v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4ed74d6-80bb-42ff-8bcc-7b965b41beeb/dqc_reference/reference_markers.hmm GCA_017402295.1_ASM1740229v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:17:53,813] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:17:53,814] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6b470ac5-6f3e-4228-a105-6c6ce1b53b38/GCA_017402295.1_ASM1740229v1_genomic.fna.gz]
[2023-06-28 12:17:53,833] [INFO] Query marker FASTA was written to GCA_017402295.1_ASM1740229v1_genomic.fna/markers.fasta
[2023-06-28 12:17:53,833] [INFO] Task started: Blastn
[2023-06-28 12:17:53,833] [INFO] Running command: blastn -query GCA_017402295.1_ASM1740229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4ed74d6-80bb-42ff-8bcc-7b965b41beeb/dqc_reference/reference_markers.fasta -out GCA_017402295.1_ASM1740229v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:17:54,383] [INFO] Task succeeded: Blastn
[2023-06-28 12:17:54,387] [INFO] Selected 13 target genomes.
[2023-06-28 12:17:54,387] [INFO] Target genome list was writen to GCA_017402295.1_ASM1740229v1_genomic.fna/target_genomes.txt
[2023-06-28 12:17:54,390] [INFO] Task started: fastANI
[2023-06-28 12:17:54,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b470ac5-6f3e-4228-a105-6c6ce1b53b38/GCA_017402295.1_ASM1740229v1_genomic.fna.gz --refList GCA_017402295.1_ASM1740229v1_genomic.fna/target_genomes.txt --output GCA_017402295.1_ASM1740229v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:18:00,270] [INFO] Task succeeded: fastANI
[2023-06-28 12:18:00,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4ed74d6-80bb-42ff-8bcc-7b965b41beeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:18:00,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4ed74d6-80bb-42ff-8bcc-7b965b41beeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:18:00,272] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:18:00,272] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:18:00,272] [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
--------------------------------------------------------------------------------
[2023-06-28 12:18:00,319] [INFO] DFAST Taxonomy check result was written to GCA_017402295.1_ASM1740229v1_genomic.fna/tc_result.tsv
[2023-06-28 12:18:00,320] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:18:00,320] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:18:00,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4ed74d6-80bb-42ff-8bcc-7b965b41beeb/dqc_reference/checkm_data
[2023-06-28 12:18:00,323] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:18:00,342] [INFO] Task started: CheckM
[2023-06-28 12:18:00,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017402295.1_ASM1740229v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017402295.1_ASM1740229v1_genomic.fna/checkm_input GCA_017402295.1_ASM1740229v1_genomic.fna/checkm_result
[2023-06-28 12:18:16,910] [INFO] Task succeeded: CheckM
[2023-06-28 12:18:16,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.32%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 12:18:16,931] [INFO] ===== Completeness check finished =====
[2023-06-28 12:18:16,931] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:18:16,931] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017402295.1_ASM1740229v1_genomic.fna/markers.fasta)
[2023-06-28 12:18:16,932] [INFO] Task started: Blastn
[2023-06-28 12:18:16,932] [INFO] Running command: blastn -query GCA_017402295.1_ASM1740229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4ed74d6-80bb-42ff-8bcc-7b965b41beeb/dqc_reference/reference_markers_gtdb.fasta -out GCA_017402295.1_ASM1740229v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:18:17,655] [INFO] Task succeeded: Blastn
[2023-06-28 12:18:17,659] [INFO] Selected 11 target genomes.
[2023-06-28 12:18:17,659] [INFO] Target genome list was writen to GCA_017402295.1_ASM1740229v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:18:17,661] [INFO] Task started: fastANI
[2023-06-28 12:18:17,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b470ac5-6f3e-4228-a105-6c6ce1b53b38/GCA_017402295.1_ASM1740229v1_genomic.fna.gz --refList GCA_017402295.1_ASM1740229v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017402295.1_ASM1740229v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:18:22,139] [INFO] Task succeeded: fastANI
[2023-06-28 12:18:22,145] [INFO] Found 5 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-28 12:18:22,145] [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_002373205.1	s__Treponema_D sp002373205	96.5686	117	132	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.79	96.03	0.78	0.67	16	inconclusive
GCA_002448445.1	s__Treponema_D sp002448445	95.1287	124	132	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.51	97.25	0.94	0.94	3	inconclusive
GCA_017961705.1	s__Treponema_D sp017961705	93.2411	126	132	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.01	97.01	0.82	0.82	2	-
GCA_017534445.1	s__Treponema_D sp017534445	93.0093	117	132	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.88	96.88	0.85	0.85	2	-
GCA_017614295.1	s__Treponema_D sp017614295	88.7486	111	132	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 12:18:22,147] [INFO] GTDB search result was written to GCA_017402295.1_ASM1740229v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:18:22,148] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:18:22,152] [INFO] DFAST_QC result json was written to GCA_017402295.1_ASM1740229v1_genomic.fna/dqc_result.json
[2023-06-28 12:18:22,153] [INFO] DFAST_QC completed!
[2023-06-28 12:18:22,153] [INFO] Total running time: 0h0m33s