[2023-06-17 01:45:18,709] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:45:18,711] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:45:18,712] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a3088d2-0221-48ad-8ea8-420ac7c2a8f2/dqc_reference
[2023-06-17 01:45:20,157] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:45:20,158] [INFO] Task started: Prodigal
[2023-06-17 01:45:20,159] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5a62690-add5-433b-9e3b-599e97f15aea/GCA_028708315.1_ASM2870831v1_genomic.fna.gz | prodigal -d GCA_028708315.1_ASM2870831v1_genomic.fna/cds.fna -a GCA_028708315.1_ASM2870831v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:45:23,276] [INFO] Task succeeded: Prodigal
[2023-06-17 01:45:23,276] [INFO] Task started: HMMsearch
[2023-06-17 01:45:23,277] [INFO] Running command: hmmsearch --tblout GCA_028708315.1_ASM2870831v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a3088d2-0221-48ad-8ea8-420ac7c2a8f2/dqc_reference/reference_markers.hmm GCA_028708315.1_ASM2870831v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:45:23,486] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:45:23,488] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc5a62690-add5-433b-9e3b-599e97f15aea/GCA_028708315.1_ASM2870831v1_genomic.fna.gz]
[2023-06-17 01:45:23,508] [INFO] Query marker FASTA was written to GCA_028708315.1_ASM2870831v1_genomic.fna/markers.fasta
[2023-06-17 01:45:23,508] [INFO] Task started: Blastn
[2023-06-17 01:45:23,509] [INFO] Running command: blastn -query GCA_028708315.1_ASM2870831v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a3088d2-0221-48ad-8ea8-420ac7c2a8f2/dqc_reference/reference_markers.fasta -out GCA_028708315.1_ASM2870831v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:45:23,995] [INFO] Task succeeded: Blastn
[2023-06-17 01:45:23,999] [INFO] Selected 5 target genomes.
[2023-06-17 01:45:24,000] [INFO] Target genome list was writen to GCA_028708315.1_ASM2870831v1_genomic.fna/target_genomes.txt
[2023-06-17 01:45:24,003] [INFO] Task started: fastANI
[2023-06-17 01:45:24,003] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5a62690-add5-433b-9e3b-599e97f15aea/GCA_028708315.1_ASM2870831v1_genomic.fna.gz --refList GCA_028708315.1_ASM2870831v1_genomic.fna/target_genomes.txt --output GCA_028708315.1_ASM2870831v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 01:45:26,331] [INFO] Task succeeded: fastANI
[2023-06-17 01:45:26,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a3088d2-0221-48ad-8ea8-420ac7c2a8f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 01:45:26,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a3088d2-0221-48ad-8ea8-420ac7c2a8f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 01:45:26,334] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 01:45:26,335] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 01:45:26,335] [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
--------------------------------------------------------------------------------
[2023-06-17 01:45:26,337] [INFO] DFAST Taxonomy check result was written to GCA_028708315.1_ASM2870831v1_genomic.fna/tc_result.tsv
[2023-06-17 01:45:26,337] [INFO] ===== Taxonomy check completed =====
[2023-06-17 01:45:26,338] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:45:26,338] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a3088d2-0221-48ad-8ea8-420ac7c2a8f2/dqc_reference/checkm_data
[2023-06-17 01:45:26,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:45:26,356] [INFO] Task started: CheckM
[2023-06-17 01:45:26,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028708315.1_ASM2870831v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028708315.1_ASM2870831v1_genomic.fna/checkm_input GCA_028708315.1_ASM2870831v1_genomic.fna/checkm_result
[2023-06-17 01:45:42,934] [INFO] Task succeeded: CheckM
[2023-06-17 01:45:42,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 01:45:42,957] [INFO] ===== Completeness check finished =====
[2023-06-17 01:45:42,958] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:45:42,958] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028708315.1_ASM2870831v1_genomic.fna/markers.fasta)
[2023-06-17 01:45:42,959] [INFO] Task started: Blastn
[2023-06-17 01:45:42,959] [INFO] Running command: blastn -query GCA_028708315.1_ASM2870831v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a3088d2-0221-48ad-8ea8-420ac7c2a8f2/dqc_reference/reference_markers_gtdb.fasta -out GCA_028708315.1_ASM2870831v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:45:43,411] [INFO] Task succeeded: Blastn
[2023-06-17 01:45:43,419] [INFO] Selected 6 target genomes.
[2023-06-17 01:45:43,419] [INFO] Target genome list was writen to GCA_028708315.1_ASM2870831v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:45:43,424] [INFO] Task started: fastANI
[2023-06-17 01:45:43,424] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5a62690-add5-433b-9e3b-599e97f15aea/GCA_028708315.1_ASM2870831v1_genomic.fna.gz --refList GCA_028708315.1_ASM2870831v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028708315.1_ASM2870831v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:45:45,201] [INFO] Task succeeded: fastANI
[2023-06-17 01:45:45,213] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 01:45:45,214] [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_002498365.1	s__VadinCA11 sp002498365	99.2367	349	356	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11	95.0	98.66	95.33	0.93	0.87	13	conclusive
GCA_002505345.1	s__VadinCA11 sp002505345	89.8109	339	356	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11	95.0	99.21	98.85	0.96	0.93	6	-
GCA_002509405.1	s__VadinCA11 sp002509405	88.2885	313	356	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620825.1	s__VadinCA11 sp011620825	81.9017	186	356	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905187815.1	s__UBA71 sp905187815	77.3944	95	356	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__UBA71	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461225.1	s__UBA71 sp017461225	77.1998	88	356	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__UBA71	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 01:45:45,216] [INFO] GTDB search result was written to GCA_028708315.1_ASM2870831v1_genomic.fna/result_gtdb.tsv
[2023-06-17 01:45:45,217] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:45:45,220] [INFO] DFAST_QC result json was written to GCA_028708315.1_ASM2870831v1_genomic.fna/dqc_result.json
[2023-06-17 01:45:45,220] [INFO] DFAST_QC completed!
[2023-06-17 01:45:45,220] [INFO] Total running time: 0h0m27s