[2023-06-28 23:28:43,918] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:28:43,920] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:28:43,920] [INFO] DQC Reference Directory: /var/lib/cwl/stg31cd7854-c2c8-4e51-96c4-6cca980bd5f7/dqc_reference
[2023-06-28 23:28:45,096] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:28:45,097] [INFO] Task started: Prodigal
[2023-06-28 23:28:45,097] [INFO] Running command: gunzip -c /var/lib/cwl/stgfde8f235-9c5e-4ef8-bf6a-ba9e4a2d7061/GCA_017940005.1_ASM1794000v1_genomic.fna.gz | prodigal -d GCA_017940005.1_ASM1794000v1_genomic.fna/cds.fna -a GCA_017940005.1_ASM1794000v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:28:52,720] [INFO] Task succeeded: Prodigal
[2023-06-28 23:28:52,720] [INFO] Task started: HMMsearch
[2023-06-28 23:28:52,721] [INFO] Running command: hmmsearch --tblout GCA_017940005.1_ASM1794000v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31cd7854-c2c8-4e51-96c4-6cca980bd5f7/dqc_reference/reference_markers.hmm GCA_017940005.1_ASM1794000v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:28:52,970] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:28:52,972] [INFO] Found 6/6 markers.
[2023-06-28 23:28:52,997] [INFO] Query marker FASTA was written to GCA_017940005.1_ASM1794000v1_genomic.fna/markers.fasta
[2023-06-28 23:28:52,998] [INFO] Task started: Blastn
[2023-06-28 23:28:52,998] [INFO] Running command: blastn -query GCA_017940005.1_ASM1794000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31cd7854-c2c8-4e51-96c4-6cca980bd5f7/dqc_reference/reference_markers.fasta -out GCA_017940005.1_ASM1794000v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:28:53,557] [INFO] Task succeeded: Blastn
[2023-06-28 23:28:53,562] [INFO] Selected 14 target genomes.
[2023-06-28 23:28:53,562] [INFO] Target genome list was writen to GCA_017940005.1_ASM1794000v1_genomic.fna/target_genomes.txt
[2023-06-28 23:28:53,582] [INFO] Task started: fastANI
[2023-06-28 23:28:53,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgfde8f235-9c5e-4ef8-bf6a-ba9e4a2d7061/GCA_017940005.1_ASM1794000v1_genomic.fna.gz --refList GCA_017940005.1_ASM1794000v1_genomic.fna/target_genomes.txt --output GCA_017940005.1_ASM1794000v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:29:00,754] [INFO] Task succeeded: fastANI
[2023-06-28 23:29:00,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31cd7854-c2c8-4e51-96c4-6cca980bd5f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:29:00,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31cd7854-c2c8-4e51-96c4-6cca980bd5f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:29:00,757] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:29:00,758] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 23:29:00,758] [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 23:29:00,760] [INFO] DFAST Taxonomy check result was written to GCA_017940005.1_ASM1794000v1_genomic.fna/tc_result.tsv
[2023-06-28 23:29:00,760] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:29:00,761] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:29:00,761] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31cd7854-c2c8-4e51-96c4-6cca980bd5f7/dqc_reference/checkm_data
[2023-06-28 23:29:00,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:29:00,794] [INFO] Task started: CheckM
[2023-06-28 23:29:00,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017940005.1_ASM1794000v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017940005.1_ASM1794000v1_genomic.fna/checkm_input GCA_017940005.1_ASM1794000v1_genomic.fna/checkm_result
[2023-06-28 23:29:28,883] [INFO] Task succeeded: CheckM
[2023-06-28 23:29:28,885] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:29:28,907] [INFO] ===== Completeness check finished =====
[2023-06-28 23:29:28,908] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:29:28,908] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017940005.1_ASM1794000v1_genomic.fna/markers.fasta)
[2023-06-28 23:29:28,908] [INFO] Task started: Blastn
[2023-06-28 23:29:28,909] [INFO] Running command: blastn -query GCA_017940005.1_ASM1794000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31cd7854-c2c8-4e51-96c4-6cca980bd5f7/dqc_reference/reference_markers_gtdb.fasta -out GCA_017940005.1_ASM1794000v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:29:29,639] [INFO] Task succeeded: Blastn
[2023-06-28 23:29:29,643] [INFO] Selected 16 target genomes.
[2023-06-28 23:29:29,643] [INFO] Target genome list was writen to GCA_017940005.1_ASM1794000v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:29:29,655] [INFO] Task started: fastANI
[2023-06-28 23:29:29,655] [INFO] Running command: fastANI --query /var/lib/cwl/stgfde8f235-9c5e-4ef8-bf6a-ba9e4a2d7061/GCA_017940005.1_ASM1794000v1_genomic.fna.gz --refList GCA_017940005.1_ASM1794000v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017940005.1_ASM1794000v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:29:37,512] [INFO] Task succeeded: fastANI
[2023-06-28 23:29:37,522] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 23:29:37,523] [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_017940005.1	s__Treponema_D sp017940005	100.0	788	790	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_017470085.1	s__Treponema_D sp017470085	86.0856	123	790	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_017446265.1	s__Treponema_D sp017446265	83.9308	480	790	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_014334325.1	s__Treponema_D sp014334325	76.4108	125	790	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	95.62	95.62	0.82	0.82	2	-
GCF_902983995.1	s__Treponema_D buccale	76.3675	111	790	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_000413015.1	s__Treponema_D paredis	76.3658	112	790	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	95.58	95.58	0.90	0.90	2	-
GCF_000468115.1	s__Treponema_D socranskii	76.1221	121	790	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.97	99.97	0.95	0.95	2	-
GCA_002399405.1	s__Treponema_D sp002399405	75.9555	82	790	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.20	98.20	0.94	0.94	2	-
GCA_002314445.1	s__Treponema_D sp002314445	75.8324	57	790	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 23:29:37,524] [INFO] GTDB search result was written to GCA_017940005.1_ASM1794000v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:29:37,525] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:29:37,528] [INFO] DFAST_QC result json was written to GCA_017940005.1_ASM1794000v1_genomic.fna/dqc_result.json
[2023-06-28 23:29:37,528] [INFO] DFAST_QC completed!
[2023-06-28 23:29:37,528] [INFO] Total running time: 0h0m54s