[2024-01-25 17:52:06,190] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:52:06,191] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:52:06,192] [INFO] DQC Reference Directory: /var/lib/cwl/stg69bfb123-b2a6-4a45-bc6b-127c56b90209/dqc_reference
[2024-01-25 17:52:07,385] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:52:07,386] [INFO] Task started: Prodigal
[2024-01-25 17:52:07,386] [INFO] Running command: gunzip -c /var/lib/cwl/stg79d55f65-0eb4-4cec-8cd6-e4035d606eef/GCF_000255555.1_ASM25555v2_genomic.fna.gz | prodigal -d GCF_000255555.1_ASM25555v2_genomic.fna/cds.fna -a GCF_000255555.1_ASM25555v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:52:15,349] [INFO] Task succeeded: Prodigal
[2024-01-25 17:52:15,349] [INFO] Task started: HMMsearch
[2024-01-25 17:52:15,349] [INFO] Running command: hmmsearch --tblout GCF_000255555.1_ASM25555v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69bfb123-b2a6-4a45-bc6b-127c56b90209/dqc_reference/reference_markers.hmm GCF_000255555.1_ASM25555v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:52:15,603] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:52:15,604] [INFO] Found 6/6 markers.
[2024-01-25 17:52:15,632] [INFO] Query marker FASTA was written to GCF_000255555.1_ASM25555v2_genomic.fna/markers.fasta
[2024-01-25 17:52:15,632] [INFO] Task started: Blastn
[2024-01-25 17:52:15,632] [INFO] Running command: blastn -query GCF_000255555.1_ASM25555v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg69bfb123-b2a6-4a45-bc6b-127c56b90209/dqc_reference/reference_markers.fasta -out GCF_000255555.1_ASM25555v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:16,170] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:16,172] [INFO] Selected 17 target genomes.
[2024-01-25 17:52:16,173] [INFO] Target genome list was writen to GCF_000255555.1_ASM25555v2_genomic.fna/target_genomes.txt
[2024-01-25 17:52:16,182] [INFO] Task started: fastANI
[2024-01-25 17:52:16,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg79d55f65-0eb4-4cec-8cd6-e4035d606eef/GCF_000255555.1_ASM25555v2_genomic.fna.gz --refList GCF_000255555.1_ASM25555v2_genomic.fna/target_genomes.txt --output GCF_000255555.1_ASM25555v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:29,370] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:29,371] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69bfb123-b2a6-4a45-bc6b-127c56b90209/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:29,371] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69bfb123-b2a6-4a45-bc6b-127c56b90209/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:29,374] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:52:29,375] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:52:29,375] [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	100.0	1124	1127	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 17:52:29,376] [INFO] DFAST Taxonomy check result was written to GCF_000255555.1_ASM25555v2_genomic.fna/tc_result.tsv
[2024-01-25 17:52:29,377] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:29,377] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:29,377] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69bfb123-b2a6-4a45-bc6b-127c56b90209/dqc_reference/checkm_data
[2024-01-25 17:52:29,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:29,414] [INFO] Task started: CheckM
[2024-01-25 17:52:29,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000255555.1_ASM25555v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000255555.1_ASM25555v2_genomic.fna/checkm_input GCF_000255555.1_ASM25555v2_genomic.fna/checkm_result
[2024-01-25 17:52:55,489] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:55,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:55,510] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:55,510] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:55,511] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000255555.1_ASM25555v2_genomic.fna/markers.fasta)
[2024-01-25 17:52:55,511] [INFO] Task started: Blastn
[2024-01-25 17:52:55,511] [INFO] Running command: blastn -query GCF_000255555.1_ASM25555v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg69bfb123-b2a6-4a45-bc6b-127c56b90209/dqc_reference/reference_markers_gtdb.fasta -out GCF_000255555.1_ASM25555v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:56,331] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:56,334] [INFO] Selected 19 target genomes.
[2024-01-25 17:52:56,334] [INFO] Target genome list was writen to GCF_000255555.1_ASM25555v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:56,355] [INFO] Task started: fastANI
[2024-01-25 17:52:56,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg79d55f65-0eb4-4cec-8cd6-e4035d606eef/GCF_000255555.1_ASM25555v2_genomic.fna.gz --refList GCF_000255555.1_ASM25555v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000255555.1_ASM25555v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:53:06,540] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:06,547] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:53:06,547] [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
GCF_000255555.1	s__Treponema_D saccharophilum	100.0	1124	1127	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.00	98.95	0.97	0.97	3	conclusive
GCA_017934745.1	s__Treponema_D sp017934745	80.2491	420	1127	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.63	96.63	0.83	0.83	2	-
GCA_017525605.1	s__Treponema_D sp017525605	79.5193	390	1127	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.48	98.48	0.92	0.92	2	-
GCA_017412405.1	s__Treponema_D sp017412405	77.1217	129	1127	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_900316905.1	s__Treponema_D sp900316905	77.0718	56	1127	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.02	96.19	0.87	0.83	16	-
GCA_902783155.1	s__Treponema_D sp902783155	76.4262	53	1127	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.40	97.49	0.92	0.88	4	-
GCA_002404895.1	s__Treponema_D sp002404895	76.3632	95	1127	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_902799665.1	s__Treponema_D sp902799665	76.315	60	1127	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.67	96.44	0.88	0.84	3	-
GCA_017450845.1	s__Treponema_D sp017450845	75.9855	78	1127	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:53:06,548] [INFO] GTDB search result was written to GCF_000255555.1_ASM25555v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:53:06,549] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:53:06,551] [INFO] DFAST_QC result json was written to GCF_000255555.1_ASM25555v2_genomic.fna/dqc_result.json
[2024-01-25 17:53:06,551] [INFO] DFAST_QC completed!
[2024-01-25 17:53:06,551] [INFO] Total running time: 0h1m0s