[2024-01-24 13:48:59,918] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,920] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,921] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f83cdb4-4205-4175-9429-b1fc0dbc8688/dqc_reference
[2024-01-24 13:49:01,186] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,187] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,187] [INFO] Running command: gunzip -c /var/lib/cwl/stg035b160d-e3f4-4f8e-8a4c-ebdcb6ec2429/GCF_004342885.1_ASM434288v1_genomic.fna.gz | prodigal -d GCF_004342885.1_ASM434288v1_genomic.fna/cds.fna -a GCF_004342885.1_ASM434288v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:05,993] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:05,994] [INFO] Task started: HMMsearch
[2024-01-24 13:49:05,994] [INFO] Running command: hmmsearch --tblout GCF_004342885.1_ASM434288v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f83cdb4-4205-4175-9429-b1fc0dbc8688/dqc_reference/reference_markers.hmm GCF_004342885.1_ASM434288v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:06,240] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:06,242] [INFO] Found 6/6 markers.
[2024-01-24 13:49:06,267] [INFO] Query marker FASTA was written to GCF_004342885.1_ASM434288v1_genomic.fna/markers.fasta
[2024-01-24 13:49:06,267] [INFO] Task started: Blastn
[2024-01-24 13:49:06,268] [INFO] Running command: blastn -query GCF_004342885.1_ASM434288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f83cdb4-4205-4175-9429-b1fc0dbc8688/dqc_reference/reference_markers.fasta -out GCF_004342885.1_ASM434288v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:06,861] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:06,864] [INFO] Selected 21 target genomes.
[2024-01-24 13:49:06,864] [INFO] Target genome list was writen to GCF_004342885.1_ASM434288v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:06,872] [INFO] Task started: fastANI
[2024-01-24 13:49:06,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg035b160d-e3f4-4f8e-8a4c-ebdcb6ec2429/GCF_004342885.1_ASM434288v1_genomic.fna.gz --refList GCF_004342885.1_ASM434288v1_genomic.fna/target_genomes.txt --output GCF_004342885.1_ASM434288v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:19,383] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:19,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f83cdb4-4205-4175-9429-b1fc0dbc8688/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:19,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f83cdb4-4205-4175-9429-b1fc0dbc8688/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:19,391] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:19,391] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:19,391] [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
Tepidibacillus fermentans	strain=DSM 23802	GCA_004342885.1	1281767	1281767	type	True	100.0	784	789	95	conclusive
Tepidibacillus decaturensis	strain=Z9	GCA_001561915.1	1413211	1413211	type	True	80.261	210	789	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:19,393] [INFO] DFAST Taxonomy check result was written to GCF_004342885.1_ASM434288v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:19,393] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:19,393] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:19,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f83cdb4-4205-4175-9429-b1fc0dbc8688/dqc_reference/checkm_data
[2024-01-24 13:49:19,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:19,424] [INFO] Task started: CheckM
[2024-01-24 13:49:19,424] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004342885.1_ASM434288v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004342885.1_ASM434288v1_genomic.fna/checkm_input GCF_004342885.1_ASM434288v1_genomic.fna/checkm_result
[2024-01-24 13:49:41,897] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:41,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:41,922] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:41,922] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:41,922] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004342885.1_ASM434288v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:41,923] [INFO] Task started: Blastn
[2024-01-24 13:49:41,923] [INFO] Running command: blastn -query GCF_004342885.1_ASM434288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f83cdb4-4205-4175-9429-b1fc0dbc8688/dqc_reference/reference_markers_gtdb.fasta -out GCF_004342885.1_ASM434288v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:42,882] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:42,886] [INFO] Selected 23 target genomes.
[2024-01-24 13:49:42,886] [INFO] Target genome list was writen to GCF_004342885.1_ASM434288v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:42,901] [INFO] Task started: fastANI
[2024-01-24 13:49:42,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg035b160d-e3f4-4f8e-8a4c-ebdcb6ec2429/GCF_004342885.1_ASM434288v1_genomic.fna.gz --refList GCF_004342885.1_ASM434288v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004342885.1_ASM434288v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:56,701] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:56,706] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:56,706] [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_004342885.1	s__Tepidibacillus fermentans	100.0	784	789	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tepidibacillales;f__Tepidibacillaceae;g__Tepidibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001561915.1	s__Tepidibacillus_A decaturensis	80.2603	210	789	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tepidibacillales;f__Tepidibacillaceae;g__Tepidibacillus_A	95.0	98.42	98.42	0.91	0.91	2	-
GCA_016841555.1	s__JAENYW01 sp016841555	76.5538	58	789	d__Bacteria;p__Firmicutes;c__Bacilli;o__Tepidibacillales;f__Tepidibacillaceae;g__JAENYW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:56,708] [INFO] GTDB search result was written to GCF_004342885.1_ASM434288v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:56,708] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:56,711] [INFO] DFAST_QC result json was written to GCF_004342885.1_ASM434288v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:56,711] [INFO] DFAST_QC completed!
[2024-01-24 13:49:56,711] [INFO] Total running time: 0h0m57s