[2024-01-25 17:39:05,633] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:05,635] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:05,635] [INFO] DQC Reference Directory: /var/lib/cwl/stga442e323-09a3-43cf-aef6-192e0f79f1e8/dqc_reference
[2024-01-25 17:39:06,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:06,765] [INFO] Task started: Prodigal
[2024-01-25 17:39:06,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg3db5eb11-fa50-476a-a862-b1305e8314c3/GCF_017161305.1_ASM1716130v1_genomic.fna.gz | prodigal -d GCF_017161305.1_ASM1716130v1_genomic.fna/cds.fna -a GCF_017161305.1_ASM1716130v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:13,147] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:13,148] [INFO] Task started: HMMsearch
[2024-01-25 17:39:13,148] [INFO] Running command: hmmsearch --tblout GCF_017161305.1_ASM1716130v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga442e323-09a3-43cf-aef6-192e0f79f1e8/dqc_reference/reference_markers.hmm GCF_017161305.1_ASM1716130v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:13,402] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:13,404] [INFO] Found 6/6 markers.
[2024-01-25 17:39:13,436] [INFO] Query marker FASTA was written to GCF_017161305.1_ASM1716130v1_genomic.fna/markers.fasta
[2024-01-25 17:39:13,436] [INFO] Task started: Blastn
[2024-01-25 17:39:13,436] [INFO] Running command: blastn -query GCF_017161305.1_ASM1716130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga442e323-09a3-43cf-aef6-192e0f79f1e8/dqc_reference/reference_markers.fasta -out GCF_017161305.1_ASM1716130v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:13,966] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:13,969] [INFO] Selected 14 target genomes.
[2024-01-25 17:39:13,969] [INFO] Target genome list was writen to GCF_017161305.1_ASM1716130v1_genomic.fna/target_genomes.txt
[2024-01-25 17:39:14,008] [INFO] Task started: fastANI
[2024-01-25 17:39:14,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg3db5eb11-fa50-476a-a862-b1305e8314c3/GCF_017161305.1_ASM1716130v1_genomic.fna.gz --refList GCF_017161305.1_ASM1716130v1_genomic.fna/target_genomes.txt --output GCF_017161305.1_ASM1716130v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:21,299] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:21,300] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga442e323-09a3-43cf-aef6-192e0f79f1e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:21,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga442e323-09a3-43cf-aef6-192e0f79f1e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:21,304] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:39:21,304] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:39:21,304] [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 ruminis	strain=DSM 103462	GCA_014201975.1	744515	744515	type	True	99.9701	891	965	95	conclusive
Treponema berlinense	strain=ATCC BAA-909	GCA_900167025.1	225004	225004	type	True	77.5312	106	965	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:21,305] [INFO] DFAST Taxonomy check result was written to GCF_017161305.1_ASM1716130v1_genomic.fna/tc_result.tsv
[2024-01-25 17:39:21,306] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:21,306] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:21,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga442e323-09a3-43cf-aef6-192e0f79f1e8/dqc_reference/checkm_data
[2024-01-25 17:39:21,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:21,337] [INFO] Task started: CheckM
[2024-01-25 17:39:21,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017161305.1_ASM1716130v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017161305.1_ASM1716130v1_genomic.fna/checkm_input GCF_017161305.1_ASM1716130v1_genomic.fna/checkm_result
[2024-01-25 17:39:44,959] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:44,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:44,977] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:44,977] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:44,977] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017161305.1_ASM1716130v1_genomic.fna/markers.fasta)
[2024-01-25 17:39:44,978] [INFO] Task started: Blastn
[2024-01-25 17:39:44,978] [INFO] Running command: blastn -query GCF_017161305.1_ASM1716130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga442e323-09a3-43cf-aef6-192e0f79f1e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_017161305.1_ASM1716130v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:45,781] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:45,783] [INFO] Selected 12 target genomes.
[2024-01-25 17:39:45,783] [INFO] Target genome list was writen to GCF_017161305.1_ASM1716130v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:45,792] [INFO] Task started: fastANI
[2024-01-25 17:39:45,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg3db5eb11-fa50-476a-a862-b1305e8314c3/GCF_017161305.1_ASM1716130v1_genomic.fna.gz --refList GCF_017161305.1_ASM1716130v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017161305.1_ASM1716130v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:39:52,920] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:52,928] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:39:52,928] [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_017161305.1	s__Treponema_D ruminis	100.0	965	965	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.98	99.98	0.92	0.92	2	conclusive
GCA_902785455.1	s__Treponema_D sp902785455	87.0558	546	965	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_017430385.1	s__Treponema_D sp017430385	83.0807	475	965	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_017469785.1	s__Treponema_D sp017469785	80.618	347	965	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.36	97.36	0.82	0.82	2	-
GCA_002368605.1	s__Treponema_D sp002368605	80.2037	343	965	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.93	96.81	0.81	0.77	3	-
GCA_017395545.1	s__Treponema_D sp017395545	80.0642	288	965	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_002393835.1	s__Treponema_D sp002393835	79.5156	265	965	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	96.83	96.83	0.78	0.78	2	-
GCA_017484285.1	s__Treponema_D sp017484285	79.1704	312	965	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_017464425.1	s__Treponema_D sp017464425	78.9572	270	965	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_017449265.1	s__Treponema_D sp017449265	78.8603	140	965	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_902803735.1	s__Treponema_D sp902803735	78.133	90	965	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_017449285.1	s__Treponema_D sp017449285	77.6714	103	965	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 17:39:52,930] [INFO] GTDB search result was written to GCF_017161305.1_ASM1716130v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:39:52,930] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:39:52,933] [INFO] DFAST_QC result json was written to GCF_017161305.1_ASM1716130v1_genomic.fna/dqc_result.json
[2024-01-25 17:39:52,933] [INFO] DFAST_QC completed!
[2024-01-25 17:39:52,933] [INFO] Total running time: 0h0m47s