[2023-06-30 00:55:57,979] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:55:57,981] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:55:57,981] [INFO] DQC Reference Directory: /var/lib/cwl/stg916e2925-73e6-4364-b8d4-70e40f770d42/dqc_reference
[2023-06-30 00:55:59,238] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:55:59,239] [INFO] Task started: Prodigal
[2023-06-30 00:55:59,239] [INFO] Running command: gunzip -c /var/lib/cwl/stgad35f398-16ee-4aef-9f8c-bb129a8c9b59/GCA_019747895.1_ASM1974789v1_genomic.fna.gz | prodigal -d GCA_019747895.1_ASM1974789v1_genomic.fna/cds.fna -a GCA_019747895.1_ASM1974789v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:56:09,140] [INFO] Task succeeded: Prodigal
[2023-06-30 00:56:09,140] [INFO] Task started: HMMsearch
[2023-06-30 00:56:09,140] [INFO] Running command: hmmsearch --tblout GCA_019747895.1_ASM1974789v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg916e2925-73e6-4364-b8d4-70e40f770d42/dqc_reference/reference_markers.hmm GCA_019747895.1_ASM1974789v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:56:09,361] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:56:09,362] [INFO] Found 6/6 markers.
[2023-06-30 00:56:09,385] [INFO] Query marker FASTA was written to GCA_019747895.1_ASM1974789v1_genomic.fna/markers.fasta
[2023-06-30 00:56:09,386] [INFO] Task started: Blastn
[2023-06-30 00:56:09,386] [INFO] Running command: blastn -query GCA_019747895.1_ASM1974789v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg916e2925-73e6-4364-b8d4-70e40f770d42/dqc_reference/reference_markers.fasta -out GCA_019747895.1_ASM1974789v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:56:10,002] [INFO] Task succeeded: Blastn
[2023-06-30 00:56:10,006] [INFO] Selected 11 target genomes.
[2023-06-30 00:56:10,007] [INFO] Target genome list was writen to GCA_019747895.1_ASM1974789v1_genomic.fna/target_genomes.txt
[2023-06-30 00:56:10,010] [INFO] Task started: fastANI
[2023-06-30 00:56:10,010] [INFO] Running command: fastANI --query /var/lib/cwl/stgad35f398-16ee-4aef-9f8c-bb129a8c9b59/GCA_019747895.1_ASM1974789v1_genomic.fna.gz --refList GCA_019747895.1_ASM1974789v1_genomic.fna/target_genomes.txt --output GCA_019747895.1_ASM1974789v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:56:16,563] [INFO] Task succeeded: fastANI
[2023-06-30 00:56:16,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg916e2925-73e6-4364-b8d4-70e40f770d42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:56:16,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg916e2925-73e6-4364-b8d4-70e40f770d42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:56:16,566] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:56:16,566] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 00:56:16,567] [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
--------------------------------------------------------------------------------
[2023-06-30 00:56:16,569] [INFO] DFAST Taxonomy check result was written to GCA_019747895.1_ASM1974789v1_genomic.fna/tc_result.tsv
[2023-06-30 00:56:16,570] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:56:16,570] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:56:16,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg916e2925-73e6-4364-b8d4-70e40f770d42/dqc_reference/checkm_data
[2023-06-30 00:56:16,575] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:56:16,598] [INFO] Task started: CheckM
[2023-06-30 00:56:16,598] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019747895.1_ASM1974789v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019747895.1_ASM1974789v1_genomic.fna/checkm_input GCA_019747895.1_ASM1974789v1_genomic.fna/checkm_result
[2023-06-30 00:56:50,820] [INFO] Task succeeded: CheckM
[2023-06-30 00:56:50,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 00:56:50,842] [INFO] ===== Completeness check finished =====
[2023-06-30 00:56:50,842] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:56:50,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019747895.1_ASM1974789v1_genomic.fna/markers.fasta)
[2023-06-30 00:56:50,843] [INFO] Task started: Blastn
[2023-06-30 00:56:50,844] [INFO] Running command: blastn -query GCA_019747895.1_ASM1974789v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg916e2925-73e6-4364-b8d4-70e40f770d42/dqc_reference/reference_markers_gtdb.fasta -out GCA_019747895.1_ASM1974789v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:56:51,691] [INFO] Task succeeded: Blastn
[2023-06-30 00:56:51,697] [INFO] Selected 19 target genomes.
[2023-06-30 00:56:51,697] [INFO] Target genome list was writen to GCA_019747895.1_ASM1974789v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:56:51,708] [INFO] Task started: fastANI
[2023-06-30 00:56:51,709] [INFO] Running command: fastANI --query /var/lib/cwl/stgad35f398-16ee-4aef-9f8c-bb129a8c9b59/GCA_019747895.1_ASM1974789v1_genomic.fna.gz --refList GCA_019747895.1_ASM1974789v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019747895.1_ASM1974789v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:57:00,695] [INFO] Task succeeded: fastANI
[2023-06-30 00:57:00,702] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 00:57:00,702] [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_016871655.1	s__CAIWMF01 sp016871655	78.6071	243	657	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA6821;g__CAIWMF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008932965.1	s__CAIWMF01 sp008932965	76.5753	69	657	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__UBA6821;g__CAIWMF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 00:57:00,705] [INFO] GTDB search result was written to GCA_019747895.1_ASM1974789v1_genomic.fna/result_gtdb.tsv
[2023-06-30 00:57:00,705] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:57:00,707] [INFO] DFAST_QC result json was written to GCA_019747895.1_ASM1974789v1_genomic.fna/dqc_result.json
[2023-06-30 00:57:00,708] [INFO] DFAST_QC completed!
[2023-06-30 00:57:00,708] [INFO] Total running time: 0h1m3s