[2024-01-24 13:09:48,640] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:48,642] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:48,642] [INFO] DQC Reference Directory: /var/lib/cwl/stg02a0432f-29de-4dcd-97a3-f32ae5f675fd/dqc_reference
[2024-01-24 13:09:49,843] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:49,844] [INFO] Task started: Prodigal
[2024-01-24 13:09:49,844] [INFO] Running command: gunzip -c /var/lib/cwl/stgf98ae08c-7e76-4a34-90dc-656032e59c20/GCF_008329945.1_ASM832994v1_genomic.fna.gz | prodigal -d GCF_008329945.1_ASM832994v1_genomic.fna/cds.fna -a GCF_008329945.1_ASM832994v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:55,600] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:55,600] [INFO] Task started: HMMsearch
[2024-01-24 13:09:55,600] [INFO] Running command: hmmsearch --tblout GCF_008329945.1_ASM832994v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02a0432f-29de-4dcd-97a3-f32ae5f675fd/dqc_reference/reference_markers.hmm GCF_008329945.1_ASM832994v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:55,887] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:55,889] [INFO] Found 6/6 markers.
[2024-01-24 13:09:55,925] [INFO] Query marker FASTA was written to GCF_008329945.1_ASM832994v1_genomic.fna/markers.fasta
[2024-01-24 13:09:55,925] [INFO] Task started: Blastn
[2024-01-24 13:09:55,925] [INFO] Running command: blastn -query GCF_008329945.1_ASM832994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02a0432f-29de-4dcd-97a3-f32ae5f675fd/dqc_reference/reference_markers.fasta -out GCF_008329945.1_ASM832994v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:56,478] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:56,485] [INFO] Selected 16 target genomes.
[2024-01-24 13:09:56,485] [INFO] Target genome list was writen to GCF_008329945.1_ASM832994v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:56,496] [INFO] Task started: fastANI
[2024-01-24 13:09:56,496] [INFO] Running command: fastANI --query /var/lib/cwl/stgf98ae08c-7e76-4a34-90dc-656032e59c20/GCF_008329945.1_ASM832994v1_genomic.fna.gz --refList GCF_008329945.1_ASM832994v1_genomic.fna/target_genomes.txt --output GCF_008329945.1_ASM832994v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:05,000] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:05,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02a0432f-29de-4dcd-97a3-f32ae5f675fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:05,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02a0432f-29de-4dcd-97a3-f32ae5f675fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:05,004] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:05,004] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:05,004] [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
Thiospirochaeta perfilievii	strain=P	GCA_008329945.1	252967	252967	type	True	100.0	1230	1232	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:10:05,005] [INFO] DFAST Taxonomy check result was written to GCF_008329945.1_ASM832994v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:05,006] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:05,006] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:05,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02a0432f-29de-4dcd-97a3-f32ae5f675fd/dqc_reference/checkm_data
[2024-01-24 13:10:05,007] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:05,044] [INFO] Task started: CheckM
[2024-01-24 13:10:05,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008329945.1_ASM832994v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008329945.1_ASM832994v1_genomic.fna/checkm_input GCF_008329945.1_ASM832994v1_genomic.fna/checkm_result
[2024-01-24 13:10:29,107] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:29,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:29,124] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:29,125] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:29,125] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008329945.1_ASM832994v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:29,126] [INFO] Task started: Blastn
[2024-01-24 13:10:29,126] [INFO] Running command: blastn -query GCF_008329945.1_ASM832994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02a0432f-29de-4dcd-97a3-f32ae5f675fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_008329945.1_ASM832994v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:29,914] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:29,917] [INFO] Selected 21 target genomes.
[2024-01-24 13:10:29,917] [INFO] Target genome list was writen to GCF_008329945.1_ASM832994v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:29,964] [INFO] Task started: fastANI
[2024-01-24 13:10:29,964] [INFO] Running command: fastANI --query /var/lib/cwl/stgf98ae08c-7e76-4a34-90dc-656032e59c20/GCF_008329945.1_ASM832994v1_genomic.fna.gz --refList GCF_008329945.1_ASM832994v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008329945.1_ASM832994v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:40,647] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:40,657] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:40,657] [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_008329945.1	s__Thiospirochaeta perfilievii	100.0	1230	1232	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Spirochaetales_E;f__DSM-19205;g__Thiospirochaeta	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003247135.1	s__Thiospirochaeta sp003247135	78.0238	175	1232	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Spirochaetales_E;f__DSM-19205;g__Thiospirochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936295.1	s__Thiospirochaeta sp016936295	77.8729	209	1232	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Spirochaetales_E;f__DSM-19205;g__Thiospirochaeta	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:40,659] [INFO] GTDB search result was written to GCF_008329945.1_ASM832994v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:40,660] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:40,662] [INFO] DFAST_QC result json was written to GCF_008329945.1_ASM832994v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:40,662] [INFO] DFAST_QC completed!
[2024-01-24 13:10:40,662] [INFO] Total running time: 0h0m52s