[2024-01-24 12:06:24,780] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,782] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,782] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd8c906c-0745-4d1a-8c40-660c560812bb/dqc_reference
[2024-01-24 12:06:26,159] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:26,160] [INFO] Task started: Prodigal
[2024-01-24 12:06:26,160] [INFO] Running command: gunzip -c /var/lib/cwl/stg056a3297-7c7c-434a-86a7-a39f71404eba/GCF_028743435.1_ASM2874343v1_genomic.fna.gz | prodigal -d GCF_028743435.1_ASM2874343v1_genomic.fna/cds.fna -a GCF_028743435.1_ASM2874343v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:29,407] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:29,408] [INFO] Task started: HMMsearch
[2024-01-24 12:06:29,408] [INFO] Running command: hmmsearch --tblout GCF_028743435.1_ASM2874343v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd8c906c-0745-4d1a-8c40-660c560812bb/dqc_reference/reference_markers.hmm GCF_028743435.1_ASM2874343v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:29,602] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:29,603] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg056a3297-7c7c-434a-86a7-a39f71404eba/GCF_028743435.1_ASM2874343v1_genomic.fna.gz]
[2024-01-24 12:06:29,631] [INFO] Query marker FASTA was written to GCF_028743435.1_ASM2874343v1_genomic.fna/markers.fasta
[2024-01-24 12:06:29,632] [INFO] Task started: Blastn
[2024-01-24 12:06:29,632] [INFO] Running command: blastn -query GCF_028743435.1_ASM2874343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd8c906c-0745-4d1a-8c40-660c560812bb/dqc_reference/reference_markers.fasta -out GCF_028743435.1_ASM2874343v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:30,124] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:30,129] [INFO] Selected 6 target genomes.
[2024-01-24 12:06:30,130] [INFO] Target genome list was writen to GCF_028743435.1_ASM2874343v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:30,135] [INFO] Task started: fastANI
[2024-01-24 12:06:30,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg056a3297-7c7c-434a-86a7-a39f71404eba/GCF_028743435.1_ASM2874343v1_genomic.fna.gz --refList GCF_028743435.1_ASM2874343v1_genomic.fna/target_genomes.txt --output GCF_028743435.1_ASM2874343v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:32,577] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:32,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd8c906c-0745-4d1a-8c40-660c560812bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:32,578] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd8c906c-0745-4d1a-8c40-660c560812bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:32,584] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:32,584] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:32,584] [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 smithii	strain=ATCC 35061; PS; DSMZ 861	GCA_000016525.1	2173	2173	type	True	100.0	616	617	95	conclusive
Methanobrevibacter woesei	strain=DSM 11979	GCA_003111605.1	190976	190976	type	True	80.1353	273	617	95	below_threshold
Methanobrevibacter oralis	strain=DSM 7256	GCA_001639275.1	66851	66851	type	True	79.723	280	617	95	below_threshold
Methanobrevibacter gottschalkii	strain=DSM 11977	GCA_003814835.1	190974	190974	type	True	79.5253	262	617	95	below_threshold
Methanobrevibacter arboriphilus	strain=DH1	GCA_002072215.1	39441	39441	type	True	76.7998	113	617	95	below_threshold
Methanobrevibacter cuticularis	strain=DSM 11139	GCA_001639285.1	47311	47311	type	True	76.7182	100	617	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:32,587] [INFO] DFAST Taxonomy check result was written to GCF_028743435.1_ASM2874343v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:32,588] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:32,588] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:32,588] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd8c906c-0745-4d1a-8c40-660c560812bb/dqc_reference/checkm_data
[2024-01-24 12:06:32,589] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:32,609] [INFO] Task started: CheckM
[2024-01-24 12:06:32,610] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028743435.1_ASM2874343v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028743435.1_ASM2874343v1_genomic.fna/checkm_input GCF_028743435.1_ASM2874343v1_genomic.fna/checkm_result
[2024-01-24 12:06:49,327] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:49,328] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:49,344] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:49,344] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:49,344] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028743435.1_ASM2874343v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:49,345] [INFO] Task started: Blastn
[2024-01-24 12:06:49,345] [INFO] Running command: blastn -query GCF_028743435.1_ASM2874343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd8c906c-0745-4d1a-8c40-660c560812bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_028743435.1_ASM2874343v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:49,843] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:49,847] [INFO] Selected 8 target genomes.
[2024-01-24 12:06:49,847] [INFO] Target genome list was writen to GCF_028743435.1_ASM2874343v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:49,855] [INFO] Task started: fastANI
[2024-01-24 12:06:49,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg056a3297-7c7c-434a-86a7-a39f71404eba/GCF_028743435.1_ASM2874343v1_genomic.fna.gz --refList GCF_028743435.1_ASM2874343v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028743435.1_ASM2874343v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:06:53,546] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:53,554] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:06:53,554] [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_000016525.1	s__Methanobrevibacter_A smithii	100.0	616	617	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	98.32	97.88	0.94	0.83	24	conclusive
GCF_002252585.1	s__Methanobrevibacter_A smithii_A	93.6613	551	617	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	98.86	98.61	0.93	0.90	16	-
GCF_003111605.1	s__Methanobrevibacter_A woesei	80.1756	271	617	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	96.82	96.82	0.93	0.93	2	-
GCF_001639275.1	s__Methanobrevibacter_A oralis	79.7614	278	617	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	99.88	99.83	0.98	0.97	4	-
GCF_003814835.1	s__Methanobrevibacter_A gottschalkii	79.507	263	617	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	99.46	98.93	0.95	0.91	3	-
GCA_900317865.1	s__Methanobrevibacter_A sp900317865	79.0543	237	617	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	98.42	95.98	0.84	0.76	8	-
GCA_017460025.1	s__Methanobrevibacter_A sp017460025	79.0131	180	617	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_902783085.1	s__Methanobrevibacter_A sp902783085	78.1964	219	617	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 12:06:53,556] [INFO] GTDB search result was written to GCF_028743435.1_ASM2874343v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:06:53,557] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:06:53,559] [INFO] DFAST_QC result json was written to GCF_028743435.1_ASM2874343v1_genomic.fna/dqc_result.json
[2024-01-24 12:06:53,560] [INFO] DFAST_QC completed!
[2024-01-24 12:06:53,560] [INFO] Total running time: 0h0m29s