[2024-01-24 13:49:40,197] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,199] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,199] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9d63629-2e65-4d6c-81df-93b9d91c3888/dqc_reference
[2024-01-24 13:49:41,525] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:41,526] [INFO] Task started: Prodigal
[2024-01-24 13:49:41,526] [INFO] Running command: gunzip -c /var/lib/cwl/stg439248e8-7ce4-4e50-8984-42ed9c5b5afb/GCF_902143385.2_3B_2_genomic.fna.gz | prodigal -d GCF_902143385.2_3B_2_genomic.fna/cds.fna -a GCF_902143385.2_3B_2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:47,329] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:47,329] [INFO] Task started: HMMsearch
[2024-01-24 13:49:47,330] [INFO] Running command: hmmsearch --tblout GCF_902143385.2_3B_2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9d63629-2e65-4d6c-81df-93b9d91c3888/dqc_reference/reference_markers.hmm GCF_902143385.2_3B_2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:47,542] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:47,543] [INFO] Found 6/6 markers.
[2024-01-24 13:49:47,566] [INFO] Query marker FASTA was written to GCF_902143385.2_3B_2_genomic.fna/markers.fasta
[2024-01-24 13:49:47,567] [INFO] Task started: Blastn
[2024-01-24 13:49:47,567] [INFO] Running command: blastn -query GCF_902143385.2_3B_2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9d63629-2e65-4d6c-81df-93b9d91c3888/dqc_reference/reference_markers.fasta -out GCF_902143385.2_3B_2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:48,172] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:48,178] [INFO] Selected 21 target genomes.
[2024-01-24 13:49:48,178] [INFO] Target genome list was writen to GCF_902143385.2_3B_2_genomic.fna/target_genomes.txt
[2024-01-24 13:49:48,187] [INFO] Task started: fastANI
[2024-01-24 13:49:48,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg439248e8-7ce4-4e50-8984-42ed9c5b5afb/GCF_902143385.2_3B_2_genomic.fna.gz --refList GCF_902143385.2_3B_2_genomic.fna/target_genomes.txt --output GCF_902143385.2_3B_2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:04,602] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:04,603] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9d63629-2e65-4d6c-81df-93b9d91c3888/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:04,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9d63629-2e65-4d6c-81df-93b9d91c3888/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:04,607] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:04,607] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:04,607] [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
Methylacidimicrobium cyclopophantes		GCA_902143385.2	1041766	1041766	type	True	100.0	625	628	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:50:04,609] [INFO] DFAST Taxonomy check result was written to GCF_902143385.2_3B_2_genomic.fna/tc_result.tsv
[2024-01-24 13:50:04,609] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:04,609] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:04,610] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9d63629-2e65-4d6c-81df-93b9d91c3888/dqc_reference/checkm_data
[2024-01-24 13:50:04,611] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:04,637] [INFO] Task started: CheckM
[2024-01-24 13:50:04,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902143385.2_3B_2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902143385.2_3B_2_genomic.fna/checkm_input GCF_902143385.2_3B_2_genomic.fna/checkm_result
[2024-01-24 13:50:27,812] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:27,813] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:27,828] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:27,828] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:27,829] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902143385.2_3B_2_genomic.fna/markers.fasta)
[2024-01-24 13:50:27,829] [INFO] Task started: Blastn
[2024-01-24 13:50:27,829] [INFO] Running command: blastn -query GCF_902143385.2_3B_2_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9d63629-2e65-4d6c-81df-93b9d91c3888/dqc_reference/reference_markers_gtdb.fasta -out GCF_902143385.2_3B_2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:28,789] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:28,793] [INFO] Selected 9 target genomes.
[2024-01-24 13:50:28,793] [INFO] Target genome list was writen to GCF_902143385.2_3B_2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:28,809] [INFO] Task started: fastANI
[2024-01-24 13:50:28,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg439248e8-7ce4-4e50-8984-42ed9c5b5afb/GCF_902143385.2_3B_2_genomic.fna.gz --refList GCF_902143385.2_3B_2_genomic.fna/target_genomes_gtdb.txt --output GCF_902143385.2_3B_2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:35,485] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:35,494] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:35,494] [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_902143385.2	s__Methylacidimicrobium cyclopophantes	100.0	625	628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__Methylacidiphilaceae;g__Methylacidimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017310545.1	s__Methylacidimicrobium sp017310545	79.0114	364	628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__Methylacidiphilaceae;g__Methylacidimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902143375.2	s__Methylacidimicrobium tartarophylax	78.9847	357	628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__Methylacidiphilaceae;g__Methylacidimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000526255.1	s__Methylacidimicrobium sp000526255	78.8573	354	628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__Methylacidiphilaceae;g__Methylacidimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379365.1	s__Methylacidimicrobium sp000379365	78.6501	361	628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__Methylacidiphilaceae;g__Methylacidimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903064525.1	s__Methylacidimicrobium sp903064525	77.9442	291	628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Methylacidiphilales;f__Methylacidiphilaceae;g__Methylacidimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:35,502] [INFO] GTDB search result was written to GCF_902143385.2_3B_2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:35,502] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:35,506] [INFO] DFAST_QC result json was written to GCF_902143385.2_3B_2_genomic.fna/dqc_result.json
[2024-01-24 13:50:35,507] [INFO] DFAST_QC completed!
[2024-01-24 13:50:35,507] [INFO] Total running time: 0h0m55s