[2023-06-28 13:27:06,336] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:27:06,747] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:27:06,747] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3dcdfda-e420-4887-8186-ddce00caf76a/dqc_reference
[2023-06-28 13:27:07,829] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:27:07,829] [INFO] Task started: Prodigal
[2023-06-28 13:27:07,830] [INFO] Running command: gunzip -c /var/lib/cwl/stgade58cda-5a64-44b6-8a52-3a2659293b05/GCA_020855015.1_ASM2085501v1_genomic.fna.gz | prodigal -d GCA_020855015.1_ASM2085501v1_genomic.fna/cds.fna -a GCA_020855015.1_ASM2085501v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:27:10,719] [INFO] Task succeeded: Prodigal
[2023-06-28 13:27:10,719] [INFO] Task started: HMMsearch
[2023-06-28 13:27:10,719] [INFO] Running command: hmmsearch --tblout GCA_020855015.1_ASM2085501v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3dcdfda-e420-4887-8186-ddce00caf76a/dqc_reference/reference_markers.hmm GCA_020855015.1_ASM2085501v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:27:10,872] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:27:10,874] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgade58cda-5a64-44b6-8a52-3a2659293b05/GCA_020855015.1_ASM2085501v1_genomic.fna.gz]
[2023-06-28 13:27:10,893] [INFO] Query marker FASTA was written to GCA_020855015.1_ASM2085501v1_genomic.fna/markers.fasta
[2023-06-28 13:27:10,894] [INFO] Task started: Blastn
[2023-06-28 13:27:10,894] [INFO] Running command: blastn -query GCA_020855015.1_ASM2085501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3dcdfda-e420-4887-8186-ddce00caf76a/dqc_reference/reference_markers.fasta -out GCA_020855015.1_ASM2085501v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:27:11,349] [INFO] Task succeeded: Blastn
[2023-06-28 13:27:11,352] [INFO] Selected 3 target genomes.
[2023-06-28 13:27:11,353] [INFO] Target genome list was writen to GCA_020855015.1_ASM2085501v1_genomic.fna/target_genomes.txt
[2023-06-28 13:27:11,354] [INFO] Task started: fastANI
[2023-06-28 13:27:11,354] [INFO] Running command: fastANI --query /var/lib/cwl/stgade58cda-5a64-44b6-8a52-3a2659293b05/GCA_020855015.1_ASM2085501v1_genomic.fna.gz --refList GCA_020855015.1_ASM2085501v1_genomic.fna/target_genomes.txt --output GCA_020855015.1_ASM2085501v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:27:12,737] [INFO] Task succeeded: fastANI
[2023-06-28 13:27:12,738] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3dcdfda-e420-4887-8186-ddce00caf76a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:27:12,738] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3dcdfda-e420-4887-8186-ddce00caf76a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:27:12,742] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:27:12,742] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:27:12,742] [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
Methanobacterium paludis	strain=SWAN1	GCA_000214725.1	868131	868131	type	True	75.5399	55	496	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:27:12,744] [INFO] DFAST Taxonomy check result was written to GCA_020855015.1_ASM2085501v1_genomic.fna/tc_result.tsv
[2023-06-28 13:27:12,744] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:27:12,744] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:27:12,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3dcdfda-e420-4887-8186-ddce00caf76a/dqc_reference/checkm_data
[2023-06-28 13:27:12,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:27:12,766] [INFO] Task started: CheckM
[2023-06-28 13:27:12,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020855015.1_ASM2085501v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020855015.1_ASM2085501v1_genomic.fna/checkm_input GCA_020855015.1_ASM2085501v1_genomic.fna/checkm_result
[2023-06-28 13:27:28,150] [INFO] Task succeeded: CheckM
[2023-06-28 13:27:28,151] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:27:28,169] [INFO] ===== Completeness check finished =====
[2023-06-28 13:27:28,169] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:27:28,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020855015.1_ASM2085501v1_genomic.fna/markers.fasta)
[2023-06-28 13:27:28,169] [INFO] Task started: Blastn
[2023-06-28 13:27:28,170] [INFO] Running command: blastn -query GCA_020855015.1_ASM2085501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3dcdfda-e420-4887-8186-ddce00caf76a/dqc_reference/reference_markers_gtdb.fasta -out GCA_020855015.1_ASM2085501v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:27:28,639] [INFO] Task succeeded: Blastn
[2023-06-28 13:27:28,642] [INFO] Selected 7 target genomes.
[2023-06-28 13:27:28,642] [INFO] Target genome list was writen to GCA_020855015.1_ASM2085501v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:27:28,656] [INFO] Task started: fastANI
[2023-06-28 13:27:28,657] [INFO] Running command: fastANI --query /var/lib/cwl/stgade58cda-5a64-44b6-8a52-3a2659293b05/GCA_020855015.1_ASM2085501v1_genomic.fna.gz --refList GCA_020855015.1_ASM2085501v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020855015.1_ASM2085501v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:27:31,721] [INFO] Task succeeded: fastANI
[2023-06-28 13:27:31,727] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 13:27:31,727] [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_002496805.1	s__Methanobacterium sp002496805	83.5533	392	496	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	99.15	97.17	0.91	0.89	5	-
GCA_012838205.1	s__Methanobacterium sp012838205	83.3041	373	496	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002067065.1	s__Methanobacterium sp002067065	79.7823	305	496	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016217785.1	s__Methanobacterium sp016217785	79.3605	254	496	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013403005.1	s__Methanobacterium sp013403005	78.7547	241	496	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 13:27:31,729] [INFO] GTDB search result was written to GCA_020855015.1_ASM2085501v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:27:31,730] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:27:31,733] [INFO] DFAST_QC result json was written to GCA_020855015.1_ASM2085501v1_genomic.fna/dqc_result.json
[2023-06-28 13:27:31,733] [INFO] DFAST_QC completed!
[2023-06-28 13:27:31,733] [INFO] Total running time: 0h0m25s