[2024-01-25 19:47:35,624] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:35,625] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:35,625] [INFO] DQC Reference Directory: /var/lib/cwl/stg758da919-bf14-46a2-88bb-aa4d86999bd0/dqc_reference
[2024-01-25 19:47:36,738] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:36,738] [INFO] Task started: Prodigal
[2024-01-25 19:47:36,739] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4737853-738d-45f2-bfc4-d6eb2efe21cc/GCF_017874455.1_ASM1787445v1_genomic.fna.gz | prodigal -d GCF_017874455.1_ASM1787445v1_genomic.fna/cds.fna -a GCF_017874455.1_ASM1787445v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:41,386] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:41,387] [INFO] Task started: HMMsearch
[2024-01-25 19:47:41,387] [INFO] Running command: hmmsearch --tblout GCF_017874455.1_ASM1787445v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg758da919-bf14-46a2-88bb-aa4d86999bd0/dqc_reference/reference_markers.hmm GCF_017874455.1_ASM1787445v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:41,585] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:41,586] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgf4737853-738d-45f2-bfc4-d6eb2efe21cc/GCF_017874455.1_ASM1787445v1_genomic.fna.gz]
[2024-01-25 19:47:41,606] [INFO] Query marker FASTA was written to GCF_017874455.1_ASM1787445v1_genomic.fna/markers.fasta
[2024-01-25 19:47:41,606] [INFO] Task started: Blastn
[2024-01-25 19:47:41,606] [INFO] Running command: blastn -query GCF_017874455.1_ASM1787445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg758da919-bf14-46a2-88bb-aa4d86999bd0/dqc_reference/reference_markers.fasta -out GCF_017874455.1_ASM1787445v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:42,050] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:42,059] [INFO] Selected 2 target genomes.
[2024-01-25 19:47:42,059] [INFO] Target genome list was writen to GCF_017874455.1_ASM1787445v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:42,062] [INFO] Task started: fastANI
[2024-01-25 19:47:42,062] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4737853-738d-45f2-bfc4-d6eb2efe21cc/GCF_017874455.1_ASM1787445v1_genomic.fna.gz --refList GCF_017874455.1_ASM1787445v1_genomic.fna/target_genomes.txt --output GCF_017874455.1_ASM1787445v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:43,254] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:43,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg758da919-bf14-46a2-88bb-aa4d86999bd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:43,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg758da919-bf14-46a2-88bb-aa4d86999bd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:43,258] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:43,258] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:43,258] [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 aggregans	strain=DSM 29428	GCA_017874455.1	1615586	1615586	type	True	100.0	775	775	95	conclusive
Methanobacterium subterraneum	strain=A8p	GCA_002813695.1	59277	59277	type	True	76.9821	80	775	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:43,262] [INFO] DFAST Taxonomy check result was written to GCF_017874455.1_ASM1787445v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:43,262] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:43,262] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:43,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg758da919-bf14-46a2-88bb-aa4d86999bd0/dqc_reference/checkm_data
[2024-01-25 19:47:43,263] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:43,288] [INFO] Task started: CheckM
[2024-01-25 19:47:43,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874455.1_ASM1787445v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874455.1_ASM1787445v1_genomic.fna/checkm_input GCF_017874455.1_ASM1787445v1_genomic.fna/checkm_result
[2024-01-25 19:48:02,580] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:02,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:02,595] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:02,595] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:02,595] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874455.1_ASM1787445v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:02,596] [INFO] Task started: Blastn
[2024-01-25 19:48:02,596] [INFO] Running command: blastn -query GCF_017874455.1_ASM1787445v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg758da919-bf14-46a2-88bb-aa4d86999bd0/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874455.1_ASM1787445v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:03,078] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:03,081] [INFO] Selected 7 target genomes.
[2024-01-25 19:48:03,081] [INFO] Target genome list was writen to GCF_017874455.1_ASM1787445v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:03,090] [INFO] Task started: fastANI
[2024-01-25 19:48:03,090] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4737853-738d-45f2-bfc4-d6eb2efe21cc/GCF_017874455.1_ASM1787445v1_genomic.fna.gz --refList GCF_017874455.1_ASM1787445v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874455.1_ASM1787445v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:06,558] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:06,563] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:06,564] [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_017874455.1	s__Methanobacterium_C aggregans	100.0	775	775	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
GCF_900095295.1	s__Methanobacterium_C congolense	87.5228	672	775	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_C	95.0	95.90	95.90	0.92	0.92	2	-
GCA_002498385.1	s__Methanobacterium_C sp002498385	78.7196	280	775	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_000744455.1	s__Methanobacterium_B sp000744455	77.7541	144	775	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_B	95.0	97.99	97.99	0.89	0.89	2	-
GCA_003162655.1	s__Methanobacterium_B sp003162655	77.4441	82	775	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813695.1	s__Methanobacterium subterraneum	76.9821	80	775	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium	95.0	98.21	95.41	0.94	0.87	10	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:06,565] [INFO] GTDB search result was written to GCF_017874455.1_ASM1787445v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:06,565] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:06,567] [INFO] DFAST_QC result json was written to GCF_017874455.1_ASM1787445v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:06,567] [INFO] DFAST_QC completed!
[2024-01-25 19:48:06,567] [INFO] Total running time: 0h0m31s