[2024-01-24 12:47:12,237] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:12,240] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:12,240] [INFO] DQC Reference Directory: /var/lib/cwl/stg4258a2da-80d1-4a5f-aad3-750fe13052e1/dqc_reference
[2024-01-24 12:47:13,692] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:13,692] [INFO] Task started: Prodigal
[2024-01-24 12:47:13,693] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb75496f-9dd2-4e6a-9172-e4c8f543b1e4/GCF_000024185.1_ASM2418v1_genomic.fna.gz | prodigal -d GCF_000024185.1_ASM2418v1_genomic.fna/cds.fna -a GCF_000024185.1_ASM2418v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:19,520] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:19,520] [INFO] Task started: HMMsearch
[2024-01-24 12:47:19,520] [INFO] Running command: hmmsearch --tblout GCF_000024185.1_ASM2418v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4258a2da-80d1-4a5f-aad3-750fe13052e1/dqc_reference/reference_markers.hmm GCF_000024185.1_ASM2418v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:19,752] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:19,753] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgfb75496f-9dd2-4e6a-9172-e4c8f543b1e4/GCF_000024185.1_ASM2418v1_genomic.fna.gz]
[2024-01-24 12:47:19,780] [INFO] Query marker FASTA was written to GCF_000024185.1_ASM2418v1_genomic.fna/markers.fasta
[2024-01-24 12:47:19,780] [INFO] Task started: Blastn
[2024-01-24 12:47:19,780] [INFO] Running command: blastn -query GCF_000024185.1_ASM2418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4258a2da-80d1-4a5f-aad3-750fe13052e1/dqc_reference/reference_markers.fasta -out GCF_000024185.1_ASM2418v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:20,311] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:20,315] [INFO] Selected 5 target genomes.
[2024-01-24 12:47:20,315] [INFO] Target genome list was writen to GCF_000024185.1_ASM2418v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:20,317] [INFO] Task started: fastANI
[2024-01-24 12:47:20,317] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb75496f-9dd2-4e6a-9172-e4c8f543b1e4/GCF_000024185.1_ASM2418v1_genomic.fna.gz --refList GCF_000024185.1_ASM2418v1_genomic.fna/target_genomes.txt --output GCF_000024185.1_ASM2418v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:23,141] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:23,141] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4258a2da-80d1-4a5f-aad3-750fe13052e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:23,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4258a2da-80d1-4a5f-aad3-750fe13052e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:23,147] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:23,147] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:23,148] [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 ruminantium	strain=M1	GCA_000024185.1	83816	83816	type	True	100.0	979	979	95	conclusive
Methanobrevibacter olleyae	strain=DSM 16632	GCA_900114585.1	294671	294671	type	True	79.8996	357	979	95	below_threshold
Methanobrevibacter arboriphilus	strain=DH1	GCA_002072215.1	39441	39441	type	True	75.7614	109	979	95	below_threshold
Methanobrevibacter curvatus	strain=DSM 11111	GCA_001639295.1	49547	49547	type	True	75.4996	116	979	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:23,149] [INFO] DFAST Taxonomy check result was written to GCF_000024185.1_ASM2418v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:23,150] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:23,150] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:23,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4258a2da-80d1-4a5f-aad3-750fe13052e1/dqc_reference/checkm_data
[2024-01-24 12:47:23,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:23,186] [INFO] Task started: CheckM
[2024-01-24 12:47:23,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024185.1_ASM2418v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024185.1_ASM2418v1_genomic.fna/checkm_input GCF_000024185.1_ASM2418v1_genomic.fna/checkm_result
[2024-01-24 12:47:48,732] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:48,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:48,762] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:48,763] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:48,763] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024185.1_ASM2418v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:48,763] [INFO] Task started: Blastn
[2024-01-24 12:47:48,763] [INFO] Running command: blastn -query GCF_000024185.1_ASM2418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4258a2da-80d1-4a5f-aad3-750fe13052e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024185.1_ASM2418v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:49,328] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:49,354] [INFO] Selected 8 target genomes.
[2024-01-24 12:47:49,355] [INFO] Target genome list was writen to GCF_000024185.1_ASM2418v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:49,364] [INFO] Task started: fastANI
[2024-01-24 12:47:49,365] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb75496f-9dd2-4e6a-9172-e4c8f543b1e4/GCF_000024185.1_ASM2418v1_genomic.fna.gz --refList GCF_000024185.1_ASM2418v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024185.1_ASM2418v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:54,143] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:54,159] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:54,159] [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_000024185.1	s__Methanobrevibacter ruminantium	100.0	979	979	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015063035.1	s__Methanobrevibacter olleyae_A	81.1987	394	979	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004553595.1	s__Methanobrevibacter ruminantium_A	81.1359	411	979	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	99.31	99.31	0.95	0.95	2	-
GCA_017410345.1	s__Methanobrevibacter sp017410345	81.0316	399	979	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432245.1	s__Methanobrevibacter sp017432245	80.9533	345	979	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016838945.1	s__Methanobrevibacter sp016838945	80.8459	327	979	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	99.68	99.68	0.88	0.88	2	-
GCA_902774685.1	s__Methanobrevibacter sp902774685	80.7512	398	979	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235495.1	s__Methanobrevibacter sp905235495	80.6937	270	979	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:54,161] [INFO] GTDB search result was written to GCF_000024185.1_ASM2418v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:54,162] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:54,165] [INFO] DFAST_QC result json was written to GCF_000024185.1_ASM2418v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:54,165] [INFO] DFAST_QC completed!
[2024-01-24 12:47:54,165] [INFO] Total running time: 0h0m42s