[2024-01-24 11:51:10,237] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:10,240] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:10,240] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d779fa1-52a5-44e5-9540-197262e32fc1/dqc_reference
[2024-01-24 11:51:11,447] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:11,448] [INFO] Task started: Prodigal
[2024-01-24 11:51:11,448] [INFO] Running command: gunzip -c /var/lib/cwl/stgcacfaaaa-f013-4d7c-993d-57c1d78fd751/GCF_000621965.1_ASM62196v1_genomic.fna.gz | prodigal -d GCF_000621965.1_ASM62196v1_genomic.fna/cds.fna -a GCF_000621965.1_ASM62196v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:14,168] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:14,169] [INFO] Task started: HMMsearch
[2024-01-24 11:51:14,169] [INFO] Running command: hmmsearch --tblout GCF_000621965.1_ASM62196v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d779fa1-52a5-44e5-9540-197262e32fc1/dqc_reference/reference_markers.hmm GCF_000621965.1_ASM62196v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:14,408] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:14,409] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgcacfaaaa-f013-4d7c-993d-57c1d78fd751/GCF_000621965.1_ASM62196v1_genomic.fna.gz]
[2024-01-24 11:51:14,434] [INFO] Query marker FASTA was written to GCF_000621965.1_ASM62196v1_genomic.fna/markers.fasta
[2024-01-24 11:51:14,435] [INFO] Task started: Blastn
[2024-01-24 11:51:14,435] [INFO] Running command: blastn -query GCF_000621965.1_ASM62196v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d779fa1-52a5-44e5-9540-197262e32fc1/dqc_reference/reference_markers.fasta -out GCF_000621965.1_ASM62196v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:14,981] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:14,984] [INFO] Selected 5 target genomes.
[2024-01-24 11:51:14,984] [INFO] Target genome list was writen to GCF_000621965.1_ASM62196v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:15,008] [INFO] Task started: fastANI
[2024-01-24 11:51:15,008] [INFO] Running command: fastANI --query /var/lib/cwl/stgcacfaaaa-f013-4d7c-993d-57c1d78fd751/GCF_000621965.1_ASM62196v1_genomic.fna.gz --refList GCF_000621965.1_ASM62196v1_genomic.fna/target_genomes.txt --output GCF_000621965.1_ASM62196v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:18,232] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:18,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d779fa1-52a5-44e5-9540-197262e32fc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:18,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d779fa1-52a5-44e5-9540-197262e32fc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:18,242] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:18,242] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:18,242] [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 wolinii	strain=SH	GCA_000621965.1	190977	190977	type	True	100.0	667	667	95	conclusive
Methanobrevibacter boviskoreani	strain=JH1	GCA_000320505.2	1348249	1348249	type	True	80.0714	341	667	95	below_threshold
Methanobrevibacter smithii	strain=ATCC 35061; PS; DSMZ 861	GCA_000016525.1	2173	2173	type	True	77.2581	167	667	95	below_threshold
Methanobrevibacter olleyae	strain=DSM 16632	GCA_900114585.1	294671	294671	type	True	76.9117	251	667	95	below_threshold
Methanobrevibacter cuticularis	strain=DSM 11139	GCA_001639285.1	47311	47311	type	True	75.7202	190	667	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:18,244] [INFO] DFAST Taxonomy check result was written to GCF_000621965.1_ASM62196v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:18,245] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:18,245] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:18,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d779fa1-52a5-44e5-9540-197262e32fc1/dqc_reference/checkm_data
[2024-01-24 11:51:18,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:18,271] [INFO] Task started: CheckM
[2024-01-24 11:51:18,271] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621965.1_ASM62196v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621965.1_ASM62196v1_genomic.fna/checkm_input GCF_000621965.1_ASM62196v1_genomic.fna/checkm_result
[2024-01-24 11:51:35,262] [INFO] Task succeeded: CheckM
[2024-01-24 11:51:35,264] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:51:35,291] [INFO] ===== Completeness check finished =====
[2024-01-24 11:51:35,291] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:51:35,292] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621965.1_ASM62196v1_genomic.fna/markers.fasta)
[2024-01-24 11:51:35,292] [INFO] Task started: Blastn
[2024-01-24 11:51:35,292] [INFO] Running command: blastn -query GCF_000621965.1_ASM62196v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d779fa1-52a5-44e5-9540-197262e32fc1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621965.1_ASM62196v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:35,863] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:35,866] [INFO] Selected 5 target genomes.
[2024-01-24 11:51:35,866] [INFO] Target genome list was writen to GCF_000621965.1_ASM62196v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:51:35,875] [INFO] Task started: fastANI
[2024-01-24 11:51:35,875] [INFO] Running command: fastANI --query /var/lib/cwl/stgcacfaaaa-f013-4d7c-993d-57c1d78fd751/GCF_000621965.1_ASM62196v1_genomic.fna.gz --refList GCF_000621965.1_ASM62196v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621965.1_ASM62196v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:51:39,089] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:39,095] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:51:39,096] [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_000621965.1	s__Methanobrevibacter_B wolinii	100.0	667	667	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002208625.1	s__Methanobrevibacter_B sp002208625	90.0836	426	667	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000320505.1	s__Methanobrevibacter_B boviskoreani	80.1085	338	667	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_B	95.0	98.28	97.74	0.94	0.93	6	-
GCA_905235195.1	s__Methanobrevibacter_B sp905235195	79.4998	329	667	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252585.1	s__Methanobrevibacter_A smithii_A	77.4004	167	667	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	98.86	98.61	0.93	0.90	16	-
--------------------------------------------------------------------------------
[2024-01-24 11:51:39,102] [INFO] GTDB search result was written to GCF_000621965.1_ASM62196v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:51:39,103] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:51:39,106] [INFO] DFAST_QC result json was written to GCF_000621965.1_ASM62196v1_genomic.fna/dqc_result.json
[2024-01-24 11:51:39,106] [INFO] DFAST_QC completed!
[2024-01-24 11:51:39,106] [INFO] Total running time: 0h0m29s