[2024-01-24 12:23:03,883] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,887] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,887] [INFO] DQC Reference Directory: /var/lib/cwl/stg13ca7c1c-db01-4db4-a1db-5daad6d59755/dqc_reference
[2024-01-24 12:23:05,144] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,145] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,145] [INFO] Running command: gunzip -c /var/lib/cwl/stga4d607d6-66ca-4c60-b1ee-345b6c89b05d/GCF_003111625.1_ASM311162v1_genomic.fna.gz | prodigal -d GCF_003111625.1_ASM311162v1_genomic.fna/cds.fna -a GCF_003111625.1_ASM311162v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:10,614] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:10,615] [INFO] Task started: HMMsearch
[2024-01-24 12:23:10,615] [INFO] Running command: hmmsearch --tblout GCF_003111625.1_ASM311162v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13ca7c1c-db01-4db4-a1db-5daad6d59755/dqc_reference/reference_markers.hmm GCF_003111625.1_ASM311162v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:10,835] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:10,836] [WARNING] Found 2/6 markers. [/var/lib/cwl/stga4d607d6-66ca-4c60-b1ee-345b6c89b05d/GCF_003111625.1_ASM311162v1_genomic.fna.gz]
[2024-01-24 12:23:10,863] [INFO] Query marker FASTA was written to GCF_003111625.1_ASM311162v1_genomic.fna/markers.fasta
[2024-01-24 12:23:10,864] [INFO] Task started: Blastn
[2024-01-24 12:23:10,864] [INFO] Running command: blastn -query GCF_003111625.1_ASM311162v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13ca7c1c-db01-4db4-a1db-5daad6d59755/dqc_reference/reference_markers.fasta -out GCF_003111625.1_ASM311162v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:11,384] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:11,387] [INFO] Selected 1 target genomes.
[2024-01-24 12:23:11,388] [INFO] Target genome list was writen to GCF_003111625.1_ASM311162v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:11,390] [INFO] Task started: fastANI
[2024-01-24 12:23:11,390] [INFO] Running command: fastANI --query /var/lib/cwl/stga4d607d6-66ca-4c60-b1ee-345b6c89b05d/GCF_003111625.1_ASM311162v1_genomic.fna.gz --refList GCF_003111625.1_ASM311162v1_genomic.fna/target_genomes.txt --output GCF_003111625.1_ASM311162v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:12,206] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:12,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13ca7c1c-db01-4db4-a1db-5daad6d59755/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:12,207] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13ca7c1c-db01-4db4-a1db-5daad6d59755/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:12,212] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:12,212] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:12,212] [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
Methanobrevibacter thaueri	strain=DSM 11995	GCA_003111625.1	190975	190975	type	True	100.0	728	730	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:23:12,214] [INFO] DFAST Taxonomy check result was written to GCF_003111625.1_ASM311162v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:12,215] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:12,215] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:12,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13ca7c1c-db01-4db4-a1db-5daad6d59755/dqc_reference/checkm_data
[2024-01-24 12:23:12,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:12,254] [INFO] Task started: CheckM
[2024-01-24 12:23:12,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003111625.1_ASM311162v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003111625.1_ASM311162v1_genomic.fna/checkm_input GCF_003111625.1_ASM311162v1_genomic.fna/checkm_result
[2024-01-24 12:23:35,462] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:35,463] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:35,488] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:35,489] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:35,489] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003111625.1_ASM311162v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:35,490] [INFO] Task started: Blastn
[2024-01-24 12:23:35,490] [INFO] Running command: blastn -query GCF_003111625.1_ASM311162v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13ca7c1c-db01-4db4-a1db-5daad6d59755/dqc_reference/reference_markers_gtdb.fasta -out GCF_003111625.1_ASM311162v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:36,055] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:36,061] [INFO] Selected 8 target genomes.
[2024-01-24 12:23:36,061] [INFO] Target genome list was writen to GCF_003111625.1_ASM311162v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:36,100] [INFO] Task started: fastANI
[2024-01-24 12:23:36,100] [INFO] Running command: fastANI --query /var/lib/cwl/stga4d607d6-66ca-4c60-b1ee-345b6c89b05d/GCF_003111625.1_ASM311162v1_genomic.fna.gz --refList GCF_003111625.1_ASM311162v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003111625.1_ASM311162v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:40,854] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:40,862] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:40,862] [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_003111625.1	s__Methanobrevibacter_A thaueri	100.0	728	730	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	97.39	96.97	0.91	0.89	4	conclusive
GCA_015062915.1	s__Methanobrevibacter_A thaueri_B	84.1518	448	730	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015062905.1	s__Methanobrevibacter_A thaueri_A	82.5705	376	730	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774605.1	s__Methanobrevibacter_A sp902774605	81.951	381	730	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788255.1	s__Methanobrevibacter_A sp902788255	81.8407	395	730	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017634055.1	s__Methanobrevibacter_A sp017634055	81.6807	340	730	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017468685.1	s__Methanobrevibacter_A sp017468685	81.5225	381	730	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015062985.1	s__Methanobrevibacter_A sp015062985	80.2869	341	730	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:40,864] [INFO] GTDB search result was written to GCF_003111625.1_ASM311162v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:40,865] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:40,869] [INFO] DFAST_QC result json was written to GCF_003111625.1_ASM311162v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:40,870] [INFO] DFAST_QC completed!
[2024-01-24 12:23:40,870] [INFO] Total running time: 0h0m37s