[2023-06-29 11:07:20,808] [INFO] DFAST_QC pipeline started.
[2023-06-29 11:07:20,810] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 11:07:20,810] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cb14e34-9e4e-4fe7-918f-debdab6d37f5/dqc_reference
[2023-06-29 11:07:22,187] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 11:07:22,188] [INFO] Task started: Prodigal
[2023-06-29 11:07:22,188] [INFO] Running command: gunzip -c /var/lib/cwl/stgef1f8235-4e39-4eab-be5c-7ec8581b0ade/GCA_012521115.1_ASM1252111v1_genomic.fna.gz | prodigal -d GCA_012521115.1_ASM1252111v1_genomic.fna/cds.fna -a GCA_012521115.1_ASM1252111v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 11:07:25,721] [INFO] Task succeeded: Prodigal
[2023-06-29 11:07:25,721] [INFO] Task started: HMMsearch
[2023-06-29 11:07:25,722] [INFO] Running command: hmmsearch --tblout GCA_012521115.1_ASM1252111v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cb14e34-9e4e-4fe7-918f-debdab6d37f5/dqc_reference/reference_markers.hmm GCA_012521115.1_ASM1252111v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 11:07:25,914] [INFO] Task succeeded: HMMsearch
[2023-06-29 11:07:25,915] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgef1f8235-4e39-4eab-be5c-7ec8581b0ade/GCA_012521115.1_ASM1252111v1_genomic.fna.gz]
[2023-06-29 11:07:25,941] [INFO] Query marker FASTA was written to GCA_012521115.1_ASM1252111v1_genomic.fna/markers.fasta
[2023-06-29 11:07:25,941] [INFO] Task started: Blastn
[2023-06-29 11:07:25,941] [INFO] Running command: blastn -query GCA_012521115.1_ASM1252111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cb14e34-9e4e-4fe7-918f-debdab6d37f5/dqc_reference/reference_markers.fasta -out GCA_012521115.1_ASM1252111v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:07:26,444] [INFO] Task succeeded: Blastn
[2023-06-29 11:07:26,448] [INFO] Selected 4 target genomes.
[2023-06-29 11:07:26,448] [INFO] Target genome list was writen to GCA_012521115.1_ASM1252111v1_genomic.fna/target_genomes.txt
[2023-06-29 11:07:26,452] [INFO] Task started: fastANI
[2023-06-29 11:07:26,452] [INFO] Running command: fastANI --query /var/lib/cwl/stgef1f8235-4e39-4eab-be5c-7ec8581b0ade/GCA_012521115.1_ASM1252111v1_genomic.fna.gz --refList GCA_012521115.1_ASM1252111v1_genomic.fna/target_genomes.txt --output GCA_012521115.1_ASM1252111v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 11:07:27,997] [INFO] Task succeeded: fastANI
[2023-06-29 11:07:27,998] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cb14e34-9e4e-4fe7-918f-debdab6d37f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 11:07:27,998] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cb14e34-9e4e-4fe7-918f-debdab6d37f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 11:07:28,008] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 11:07:28,008] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 11:07:28,009] [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
Methanothermobacter wolfeii	strain=DSM 2970	GCA_025397995.1	145261	145261	type	True	99.6616	460	467	95	conclusive
Methanothermobacter marburgensis	strain=Marburg	GCA_000145295.1	145263	145263	type	True	81.2808	312	467	95	below_threshold
Methanothermobacter defluvii	strain=DSM 7466	GCA_003385755.1	49339	49339	type	True	81.2135	347	467	95	below_threshold
Methanothermobacter thermautotrophicus	strain=Delta H	GCA_000008645.1	145262	145262	type	True	80.7836	351	467	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 11:07:28,011] [INFO] DFAST Taxonomy check result was written to GCA_012521115.1_ASM1252111v1_genomic.fna/tc_result.tsv
[2023-06-29 11:07:28,011] [INFO] ===== Taxonomy check completed =====
[2023-06-29 11:07:28,011] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 11:07:28,012] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cb14e34-9e4e-4fe7-918f-debdab6d37f5/dqc_reference/checkm_data
[2023-06-29 11:07:28,013] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 11:07:28,031] [INFO] Task started: CheckM
[2023-06-29 11:07:28,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012521115.1_ASM1252111v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012521115.1_ASM1252111v1_genomic.fna/checkm_input GCA_012521115.1_ASM1252111v1_genomic.fna/checkm_result
[2023-06-29 11:07:46,244] [INFO] Task succeeded: CheckM
[2023-06-29 11:07:46,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 11:07:46,262] [INFO] ===== Completeness check finished =====
[2023-06-29 11:07:46,262] [INFO] ===== Start GTDB Search =====
[2023-06-29 11:07:46,262] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012521115.1_ASM1252111v1_genomic.fna/markers.fasta)
[2023-06-29 11:07:46,263] [INFO] Task started: Blastn
[2023-06-29 11:07:46,263] [INFO] Running command: blastn -query GCA_012521115.1_ASM1252111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cb14e34-9e4e-4fe7-918f-debdab6d37f5/dqc_reference/reference_markers_gtdb.fasta -out GCA_012521115.1_ASM1252111v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:07:47,072] [INFO] Task succeeded: Blastn
[2023-06-29 11:07:47,076] [INFO] Selected 5 target genomes.
[2023-06-29 11:07:47,076] [INFO] Target genome list was writen to GCA_012521115.1_ASM1252111v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 11:07:47,087] [INFO] Task started: fastANI
[2023-06-29 11:07:47,087] [INFO] Running command: fastANI --query /var/lib/cwl/stgef1f8235-4e39-4eab-be5c-7ec8581b0ade/GCA_012521115.1_ASM1252111v1_genomic.fna.gz --refList GCA_012521115.1_ASM1252111v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012521115.1_ASM1252111v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 11:07:49,007] [INFO] Task succeeded: fastANI
[2023-06-29 11:07:49,017] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 11:07:49,017] [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_900095815.1	s__Methanothermobacter wolfeii	99.7954	465	467	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae;g__Methanothermobacter	95.0	99.47	99.15	0.98	0.96	3	conclusive
GCF_000145295.1	s__Methanothermobacter marburgensis	81.2808	312	467	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae;g__Methanothermobacter	95.0	97.04	96.76	0.96	0.96	3	-
GCF_000828575.1	s__Methanothermobacter sp000828575	80.9925	336	467	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae;g__Methanothermobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000008645.1	s__Methanothermobacter thermautotrophicus	80.7725	352	467	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae;g__Methanothermobacter	95.0	97.55	96.65	0.96	0.94	7	-
GCF_014889545.1	s__Methanothermobacter thermautotrophicus_A	80.7118	329	467	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanothermobacteraceae;g__Methanothermobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 11:07:49,019] [INFO] GTDB search result was written to GCA_012521115.1_ASM1252111v1_genomic.fna/result_gtdb.tsv
[2023-06-29 11:07:49,020] [INFO] ===== GTDB Search completed =====
[2023-06-29 11:07:49,022] [INFO] DFAST_QC result json was written to GCA_012521115.1_ASM1252111v1_genomic.fna/dqc_result.json
[2023-06-29 11:07:49,022] [INFO] DFAST_QC completed!
[2023-06-29 11:07:49,023] [INFO] Total running time: 0h0m28s