[2024-01-24 14:47:08,933] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:08,936] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:08,936] [INFO] DQC Reference Directory: /var/lib/cwl/stg03cf6796-7d1a-4ce1-8994-5a94080c6668/dqc_reference
[2024-01-24 14:47:10,255] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:10,256] [INFO] Task started: Prodigal
[2024-01-24 14:47:10,256] [INFO] Running command: gunzip -c /var/lib/cwl/stgb084e6f8-70b9-4114-a879-ea89c6453b3f/GCF_007475525.1_ASM747552v1_genomic.fna.gz | prodigal -d GCF_007475525.1_ASM747552v1_genomic.fna/cds.fna -a GCF_007475525.1_ASM747552v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:15,182] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:15,183] [INFO] Task started: HMMsearch
[2024-01-24 14:47:15,183] [INFO] Running command: hmmsearch --tblout GCF_007475525.1_ASM747552v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03cf6796-7d1a-4ce1-8994-5a94080c6668/dqc_reference/reference_markers.hmm GCF_007475525.1_ASM747552v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:15,404] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:15,406] [INFO] Found 6/6 markers.
[2024-01-24 14:47:15,427] [INFO] Query marker FASTA was written to GCF_007475525.1_ASM747552v1_genomic.fna/markers.fasta
[2024-01-24 14:47:15,427] [INFO] Task started: Blastn
[2024-01-24 14:47:15,427] [INFO] Running command: blastn -query GCF_007475525.1_ASM747552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03cf6796-7d1a-4ce1-8994-5a94080c6668/dqc_reference/reference_markers.fasta -out GCF_007475525.1_ASM747552v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:16,008] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:16,012] [INFO] Selected 19 target genomes.
[2024-01-24 14:47:16,013] [INFO] Target genome list was writen to GCF_007475525.1_ASM747552v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:16,026] [INFO] Task started: fastANI
[2024-01-24 14:47:16,026] [INFO] Running command: fastANI --query /var/lib/cwl/stgb084e6f8-70b9-4114-a879-ea89c6453b3f/GCF_007475525.1_ASM747552v1_genomic.fna.gz --refList GCF_007475525.1_ASM747552v1_genomic.fna/target_genomes.txt --output GCF_007475525.1_ASM747552v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:25,657] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:25,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03cf6796-7d1a-4ce1-8994-5a94080c6668/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:25,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03cf6796-7d1a-4ce1-8994-5a94080c6668/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:25,660] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:47:25,660] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-24 14:47:25,660] [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
--------------------------------------------------------------------------------
[2024-01-24 14:47:25,662] [INFO] DFAST Taxonomy check result was written to GCF_007475525.1_ASM747552v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:25,662] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:25,663] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:25,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03cf6796-7d1a-4ce1-8994-5a94080c6668/dqc_reference/checkm_data
[2024-01-24 14:47:25,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:25,692] [INFO] Task started: CheckM
[2024-01-24 14:47:25,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007475525.1_ASM747552v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007475525.1_ASM747552v1_genomic.fna/checkm_input GCF_007475525.1_ASM747552v1_genomic.fna/checkm_result
[2024-01-24 14:47:48,500] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:48,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:48,520] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:48,520] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:48,521] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007475525.1_ASM747552v1_genomic.fna/markers.fasta)
[2024-01-24 14:47:48,521] [INFO] Task started: Blastn
[2024-01-24 14:47:48,521] [INFO] Running command: blastn -query GCF_007475525.1_ASM747552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03cf6796-7d1a-4ce1-8994-5a94080c6668/dqc_reference/reference_markers_gtdb.fasta -out GCF_007475525.1_ASM747552v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:49,344] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:49,348] [INFO] Selected 12 target genomes.
[2024-01-24 14:47:49,348] [INFO] Target genome list was writen to GCF_007475525.1_ASM747552v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:49,358] [INFO] Task started: fastANI
[2024-01-24 14:47:49,358] [INFO] Running command: fastANI --query /var/lib/cwl/stgb084e6f8-70b9-4114-a879-ea89c6453b3f/GCF_007475525.1_ASM747552v1_genomic.fna.gz --refList GCF_007475525.1_ASM747552v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007475525.1_ASM747552v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:47:54,086] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:54,091] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:47:54,091] [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_007475525.1	s__Methylacidiphilum kamchatkense	100.0	734	734	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__Methylacidiphilaceae;g__Methylacidiphilum	95.0	99.97	99.97	1.00	1.00	2	conclusive
GCF_004421185.1	s__Methylacidiphilum sp004421185	92.9557	643	734	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__Methylacidiphilaceae;g__Methylacidiphilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000953475.1	s__Methylacidiphilum fumariolicum	92.5855	684	734	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__Methylacidiphilaceae;g__Methylacidiphilum	95.0	99.98	99.97	1.00	1.00	6	-
GCF_000019665.1	s__Methylacidiphilum infernorum	76.4941	148	734	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__Methylacidiphilaceae;g__Methylacidiphilum	95.0	96.14	96.14	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:47:54,095] [INFO] GTDB search result was written to GCF_007475525.1_ASM747552v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:47:54,095] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:47:54,097] [INFO] DFAST_QC result json was written to GCF_007475525.1_ASM747552v1_genomic.fna/dqc_result.json
[2024-01-24 14:47:54,098] [INFO] DFAST_QC completed!
[2024-01-24 14:47:54,098] [INFO] Total running time: 0h0m45s