[2023-06-27 03:10:13,801] [INFO] DFAST_QC pipeline started.
[2023-06-27 03:10:13,805] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 03:10:13,806] [INFO] DQC Reference Directory: /var/lib/cwl/stg82102edb-dc1d-494b-b734-f63cef297052/dqc_reference
[2023-06-27 03:10:15,061] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 03:10:15,061] [INFO] Task started: Prodigal
[2023-06-27 03:10:15,062] [INFO] Running command: gunzip -c /var/lib/cwl/stg51d4cc0f-10c8-4f07-ba41-df954592d579/GCA_026415555.1_ASM2641555v1_genomic.fna.gz | prodigal -d GCA_026415555.1_ASM2641555v1_genomic.fna/cds.fna -a GCA_026415555.1_ASM2641555v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 03:10:17,282] [INFO] Task succeeded: Prodigal
[2023-06-27 03:10:17,286] [INFO] Task started: HMMsearch
[2023-06-27 03:10:17,287] [INFO] Running command: hmmsearch --tblout GCA_026415555.1_ASM2641555v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82102edb-dc1d-494b-b734-f63cef297052/dqc_reference/reference_markers.hmm GCA_026415555.1_ASM2641555v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 03:10:17,613] [INFO] Task succeeded: HMMsearch
[2023-06-27 03:10:17,614] [INFO] Found 6/6 markers.
[2023-06-27 03:10:17,658] [INFO] Query marker FASTA was written to GCA_026415555.1_ASM2641555v1_genomic.fna/markers.fasta
[2023-06-27 03:10:17,658] [INFO] Task started: Blastn
[2023-06-27 03:10:17,658] [INFO] Running command: blastn -query GCA_026415555.1_ASM2641555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82102edb-dc1d-494b-b734-f63cef297052/dqc_reference/reference_markers.fasta -out GCA_026415555.1_ASM2641555v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:10:18,965] [INFO] Task succeeded: Blastn
[2023-06-27 03:10:18,970] [INFO] Selected 11 target genomes.
[2023-06-27 03:10:18,970] [INFO] Target genome list was writen to GCA_026415555.1_ASM2641555v1_genomic.fna/target_genomes.txt
[2023-06-27 03:10:18,979] [INFO] Task started: fastANI
[2023-06-27 03:10:18,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg51d4cc0f-10c8-4f07-ba41-df954592d579/GCA_026415555.1_ASM2641555v1_genomic.fna.gz --refList GCA_026415555.1_ASM2641555v1_genomic.fna/target_genomes.txt --output GCA_026415555.1_ASM2641555v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 03:10:24,807] [INFO] Task succeeded: fastANI
[2023-06-27 03:10:24,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82102edb-dc1d-494b-b734-f63cef297052/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 03:10:24,809] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82102edb-dc1d-494b-b734-f63cef297052/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 03:10:24,815] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 03:10:24,816] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 03:10:24,816] [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
Thermodesulfobacterium hydrogeniphilum	strain=DSM 14290	GCA_000746255.1	161156	161156	type	True	76.5403	102	485	95	below_threshold
Thermodesulfobacterium geofontis	strain=OPF15	GCA_000215975.1	1295609	1295609	type	True	76.4746	141	485	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 03:10:24,840] [INFO] DFAST Taxonomy check result was written to GCA_026415555.1_ASM2641555v1_genomic.fna/tc_result.tsv
[2023-06-27 03:10:24,841] [INFO] ===== Taxonomy check completed =====
[2023-06-27 03:10:24,841] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 03:10:24,842] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82102edb-dc1d-494b-b734-f63cef297052/dqc_reference/checkm_data
[2023-06-27 03:10:24,843] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 03:10:24,877] [INFO] Task started: CheckM
[2023-06-27 03:10:24,878] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026415555.1_ASM2641555v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026415555.1_ASM2641555v1_genomic.fna/checkm_input GCA_026415555.1_ASM2641555v1_genomic.fna/checkm_result
[2023-06-27 03:10:41,604] [INFO] Task succeeded: CheckM
[2023-06-27 03:10:41,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.16%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 03:10:41,632] [INFO] ===== Completeness check finished =====
[2023-06-27 03:10:41,633] [INFO] ===== Start GTDB Search =====
[2023-06-27 03:10:41,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026415555.1_ASM2641555v1_genomic.fna/markers.fasta)
[2023-06-27 03:10:41,634] [INFO] Task started: Blastn
[2023-06-27 03:10:41,634] [INFO] Running command: blastn -query GCA_026415555.1_ASM2641555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82102edb-dc1d-494b-b734-f63cef297052/dqc_reference/reference_markers_gtdb.fasta -out GCA_026415555.1_ASM2641555v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:10:42,501] [INFO] Task succeeded: Blastn
[2023-06-27 03:10:42,558] [INFO] Selected 20 target genomes.
[2023-06-27 03:10:42,558] [INFO] Target genome list was writen to GCA_026415555.1_ASM2641555v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 03:10:42,607] [INFO] Task started: fastANI
[2023-06-27 03:10:42,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg51d4cc0f-10c8-4f07-ba41-df954592d579/GCA_026415555.1_ASM2641555v1_genomic.fna.gz --refList GCA_026415555.1_ASM2641555v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026415555.1_ASM2641555v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 03:10:48,958] [INFO] Task succeeded: fastANI
[2023-06-27 03:10:48,964] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 03:10:48,965] [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_000746255.1	s__Thermodesulfobacterium hydrogeniphilum	76.5403	102	485	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215975.1	s__Thermodesulfobacterium geofontis	76.4746	141	485	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	96.03	96.03	0.85	0.85	2	-
GCA_011361985.1	s__Thermodesulfobacterium geofontis_D	76.393	109	485	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003641645.1	s__Thermodesulfobacterium sp003641645	76.2422	80	485	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011380535.1	s__Thermodesulfobacterium geofontis_C	76.2311	113	485	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	99.32	99.32	0.91	0.91	2	-
GCA_017656385.1	s__Thermodesulfobacterium sp017656385	76.1218	88	485	d__Bacteria;p__Desulfobacterota;c__Thermodesulfobacteria;o__Thermodesulfobacteriales;f__Thermodesulfobacteriaceae;g__Thermodesulfobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 03:10:48,970] [INFO] GTDB search result was written to GCA_026415555.1_ASM2641555v1_genomic.fna/result_gtdb.tsv
[2023-06-27 03:10:48,971] [INFO] ===== GTDB Search completed =====
[2023-06-27 03:10:48,974] [INFO] DFAST_QC result json was written to GCA_026415555.1_ASM2641555v1_genomic.fna/dqc_result.json
[2023-06-27 03:10:48,974] [INFO] DFAST_QC completed!
[2023-06-27 03:10:48,974] [INFO] Total running time: 0h0m35s