[2023-06-28 15:14:13,203] [INFO] DFAST_QC pipeline started.
[2023-06-28 15:14:13,206] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 15:14:13,206] [INFO] DQC Reference Directory: /var/lib/cwl/stgedf538c9-74cc-45e3-8f3e-e0bc6333c0ce/dqc_reference
[2023-06-28 15:14:14,509] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 15:14:14,510] [INFO] Task started: Prodigal
[2023-06-28 15:14:14,510] [INFO] Running command: gunzip -c /var/lib/cwl/stg1694b01a-2497-4a72-b22c-949c7b39173a/GCA_015063005.1_ASM1506300v1_genomic.fna.gz | prodigal -d GCA_015063005.1_ASM1506300v1_genomic.fna/cds.fna -a GCA_015063005.1_ASM1506300v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 15:14:19,239] [INFO] Task succeeded: Prodigal
[2023-06-28 15:14:19,239] [INFO] Task started: HMMsearch
[2023-06-28 15:14:19,239] [INFO] Running command: hmmsearch --tblout GCA_015063005.1_ASM1506300v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgedf538c9-74cc-45e3-8f3e-e0bc6333c0ce/dqc_reference/reference_markers.hmm GCA_015063005.1_ASM1506300v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 15:14:19,473] [INFO] Task succeeded: HMMsearch
[2023-06-28 15:14:19,475] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg1694b01a-2497-4a72-b22c-949c7b39173a/GCA_015063005.1_ASM1506300v1_genomic.fna.gz]
[2023-06-28 15:14:19,510] [INFO] Query marker FASTA was written to GCA_015063005.1_ASM1506300v1_genomic.fna/markers.fasta
[2023-06-28 15:14:19,510] [INFO] Task started: Blastn
[2023-06-28 15:14:19,511] [INFO] Running command: blastn -query GCA_015063005.1_ASM1506300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedf538c9-74cc-45e3-8f3e-e0bc6333c0ce/dqc_reference/reference_markers.fasta -out GCA_015063005.1_ASM1506300v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:14:20,214] [INFO] Task succeeded: Blastn
[2023-06-28 15:14:20,219] [INFO] Selected 5 target genomes.
[2023-06-28 15:14:20,220] [INFO] Target genome list was writen to GCA_015063005.1_ASM1506300v1_genomic.fna/target_genomes.txt
[2023-06-28 15:14:20,222] [INFO] Task started: fastANI
[2023-06-28 15:14:20,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg1694b01a-2497-4a72-b22c-949c7b39173a/GCA_015063005.1_ASM1506300v1_genomic.fna.gz --refList GCA_015063005.1_ASM1506300v1_genomic.fna/target_genomes.txt --output GCA_015063005.1_ASM1506300v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 15:14:22,449] [INFO] Task succeeded: fastANI
[2023-06-28 15:14:22,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgedf538c9-74cc-45e3-8f3e-e0bc6333c0ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 15:14:22,450] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgedf538c9-74cc-45e3-8f3e-e0bc6333c0ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 15:14:22,460] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 15:14:22,460] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 15:14:22,460] [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 millerae	strain=DSM 16643	GCA_900103415.1	230361	230361	type	True	80.5522	345	711	95	below_threshold
Methanobrevibacter thaueri	strain=DSM 11995	GCA_003111625.1	190975	190975	type	True	79.7827	225	711	95	below_threshold
Methanobrevibacter gottschalkii	strain=DSM 11977	GCA_003814835.1	190974	190974	type	True	79.314	240	711	95	below_threshold
Methanobrevibacter smithii	strain=ATCC 35061; PS; DSMZ 861	GCA_000016525.1	2173	2173	type	True	79.2833	216	711	95	below_threshold
Methanobrevibacter olleyae	strain=DSM 16632	GCA_900114585.1	294671	294671	type	True	77.1567	100	711	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 15:14:22,462] [INFO] DFAST Taxonomy check result was written to GCA_015063005.1_ASM1506300v1_genomic.fna/tc_result.tsv
[2023-06-28 15:14:22,463] [INFO] ===== Taxonomy check completed =====
[2023-06-28 15:14:22,463] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 15:14:22,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgedf538c9-74cc-45e3-8f3e-e0bc6333c0ce/dqc_reference/checkm_data
[2023-06-28 15:14:22,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 15:14:22,515] [INFO] Task started: CheckM
[2023-06-28 15:14:22,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015063005.1_ASM1506300v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015063005.1_ASM1506300v1_genomic.fna/checkm_input GCA_015063005.1_ASM1506300v1_genomic.fna/checkm_result
[2023-06-28 15:14:44,547] [INFO] Task succeeded: CheckM
[2023-06-28 15:14:44,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.37%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 15:14:44,573] [INFO] ===== Completeness check finished =====
[2023-06-28 15:14:44,574] [INFO] ===== Start GTDB Search =====
[2023-06-28 15:14:44,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015063005.1_ASM1506300v1_genomic.fna/markers.fasta)
[2023-06-28 15:14:44,574] [INFO] Task started: Blastn
[2023-06-28 15:14:44,575] [INFO] Running command: blastn -query GCA_015063005.1_ASM1506300v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedf538c9-74cc-45e3-8f3e-e0bc6333c0ce/dqc_reference/reference_markers_gtdb.fasta -out GCA_015063005.1_ASM1506300v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:14:45,100] [INFO] Task succeeded: Blastn
[2023-06-28 15:14:45,105] [INFO] Selected 7 target genomes.
[2023-06-28 15:14:45,105] [INFO] Target genome list was writen to GCA_015063005.1_ASM1506300v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 15:14:45,112] [INFO] Task started: fastANI
[2023-06-28 15:14:45,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg1694b01a-2497-4a72-b22c-949c7b39173a/GCA_015063005.1_ASM1506300v1_genomic.fna.gz --refList GCA_015063005.1_ASM1506300v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015063005.1_ASM1506300v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 15:14:48,579] [INFO] Task succeeded: fastANI
[2023-06-28 15:14:48,587] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 15:14:48,588] [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
GCA_015063005.1	s__Methanobrevibacter_A millerae_B	100.0	710	711	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	97.89	97.89	0.85	0.85	2	conclusive
GCA_017460025.1	s__Methanobrevibacter_A sp017460025	84.7558	309	711	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001477655.1	s__Methanobrevibacter_A millerae_A	84.2023	476	711	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_017447225.1	s__Methanobrevibacter_A sp017447225	83.7528	413	711	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_017553445.1	s__Methanobrevibacter_A sp017553445	82.6111	332	711	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_902777885.1	s__Methanobrevibacter_A sp902777885	82.3437	239	711	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_017409525.1	s__Methanobrevibacter_A sp017409525	79.7125	230	711	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 15:14:48,590] [INFO] GTDB search result was written to GCA_015063005.1_ASM1506300v1_genomic.fna/result_gtdb.tsv
[2023-06-28 15:14:48,591] [INFO] ===== GTDB Search completed =====
[2023-06-28 15:14:48,595] [INFO] DFAST_QC result json was written to GCA_015063005.1_ASM1506300v1_genomic.fna/dqc_result.json
[2023-06-28 15:14:48,595] [INFO] DFAST_QC completed!
[2023-06-28 15:14:48,595] [INFO] Total running time: 0h0m35s