[2024-01-24 13:31:33,513] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,517] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,517] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4eacec6-43d7-4140-bec7-821e20657117/dqc_reference
[2024-01-24 13:31:34,862] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,863] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,863] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6e91484-b7e7-48a6-b889-1e6bf66a9360/GCF_000214725.1_ASM21472v1_genomic.fna.gz | prodigal -d GCF_000214725.1_ASM21472v1_genomic.fna/cds.fna -a GCF_000214725.1_ASM21472v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:40,564] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:40,564] [INFO] Task started: HMMsearch
[2024-01-24 13:31:40,564] [INFO] Running command: hmmsearch --tblout GCF_000214725.1_ASM21472v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4eacec6-43d7-4140-bec7-821e20657117/dqc_reference/reference_markers.hmm GCF_000214725.1_ASM21472v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:40,796] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:40,798] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgc6e91484-b7e7-48a6-b889-1e6bf66a9360/GCF_000214725.1_ASM21472v1_genomic.fna.gz]
[2024-01-24 13:31:40,821] [INFO] Query marker FASTA was written to GCF_000214725.1_ASM21472v1_genomic.fna/markers.fasta
[2024-01-24 13:31:40,821] [INFO] Task started: Blastn
[2024-01-24 13:31:40,821] [INFO] Running command: blastn -query GCF_000214725.1_ASM21472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4eacec6-43d7-4140-bec7-821e20657117/dqc_reference/reference_markers.fasta -out GCF_000214725.1_ASM21472v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:41,362] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:41,366] [INFO] Selected 2 target genomes.
[2024-01-24 13:31:41,366] [INFO] Target genome list was writen to GCF_000214725.1_ASM21472v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:41,368] [INFO] Task started: fastANI
[2024-01-24 13:31:41,368] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6e91484-b7e7-48a6-b889-1e6bf66a9360/GCF_000214725.1_ASM21472v1_genomic.fna.gz --refList GCF_000214725.1_ASM21472v1_genomic.fna/target_genomes.txt --output GCF_000214725.1_ASM21472v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:42,800] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:42,801] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4eacec6-43d7-4140-bec7-821e20657117/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:42,801] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4eacec6-43d7-4140-bec7-821e20657117/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:42,805] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:31:42,805] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:31:42,806] [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	100.0	847	848	95	conclusive
Methanobacterium bryantii	strain=M.o.H.	GCA_002287175.1	2161	2161	type	True	76.8683	126	848	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:42,807] [INFO] DFAST Taxonomy check result was written to GCF_000214725.1_ASM21472v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:42,807] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:42,808] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:42,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4eacec6-43d7-4140-bec7-821e20657117/dqc_reference/checkm_data
[2024-01-24 13:31:42,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:42,837] [INFO] Task started: CheckM
[2024-01-24 13:31:42,837] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000214725.1_ASM21472v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000214725.1_ASM21472v1_genomic.fna/checkm_input GCF_000214725.1_ASM21472v1_genomic.fna/checkm_result
[2024-01-24 13:32:06,018] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:06,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:06,041] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:06,041] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:06,042] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000214725.1_ASM21472v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:06,042] [INFO] Task started: Blastn
[2024-01-24 13:32:06,042] [INFO] Running command: blastn -query GCF_000214725.1_ASM21472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4eacec6-43d7-4140-bec7-821e20657117/dqc_reference/reference_markers_gtdb.fasta -out GCF_000214725.1_ASM21472v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:06,568] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:06,573] [INFO] Selected 4 target genomes.
[2024-01-24 13:32:06,573] [INFO] Target genome list was writen to GCF_000214725.1_ASM21472v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:06,577] [INFO] Task started: fastANI
[2024-01-24 13:32:06,577] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6e91484-b7e7-48a6-b889-1e6bf66a9360/GCF_000214725.1_ASM21472v1_genomic.fna.gz --refList GCF_000214725.1_ASM21472v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000214725.1_ASM21472v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:09,323] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:09,329] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:09,329] [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_000214725.1	s__Methanobacterium_C paludis	100.0	847	848	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002498385.1	s__Methanobacterium_C sp002498385	80.2313	392	848	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_C	95.0	99.69	99.35	0.95	0.90	18	-
GCF_900095295.1	s__Methanobacterium_C congolense	78.8939	312	848	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_C	95.0	95.90	95.90	0.92	0.92	2	-
GCF_002287175.1	s__Methanobacterium_D bryantii	76.8683	126	848	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_D	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:09,331] [INFO] GTDB search result was written to GCF_000214725.1_ASM21472v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:09,331] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:09,334] [INFO] DFAST_QC result json was written to GCF_000214725.1_ASM21472v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:09,334] [INFO] DFAST_QC completed!
[2024-01-24 13:32:09,335] [INFO] Total running time: 0h0m36s