[2023-06-17 14:42:40,372] [INFO] DFAST_QC pipeline started.
[2023-06-17 14:42:40,374] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 14:42:40,374] [INFO] DQC Reference Directory: /var/lib/cwl/stg935897a6-2034-4e91-85e7-f365323d7d7e/dqc_reference
[2023-06-17 14:42:41,577] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 14:42:41,578] [INFO] Task started: Prodigal
[2023-06-17 14:42:41,578] [INFO] Running command: gunzip -c /var/lib/cwl/stg293327b8-db1c-4c40-9dc6-c501d4fa99d2/GCA_009693165.1_ASM969316v1_genomic.fna.gz | prodigal -d GCA_009693165.1_ASM969316v1_genomic.fna/cds.fna -a GCA_009693165.1_ASM969316v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 14:42:48,709] [INFO] Task succeeded: Prodigal
[2023-06-17 14:42:48,710] [INFO] Task started: HMMsearch
[2023-06-17 14:42:48,710] [INFO] Running command: hmmsearch --tblout GCA_009693165.1_ASM969316v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg935897a6-2034-4e91-85e7-f365323d7d7e/dqc_reference/reference_markers.hmm GCA_009693165.1_ASM969316v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 14:42:49,020] [INFO] Task succeeded: HMMsearch
[2023-06-17 14:42:49,021] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg293327b8-db1c-4c40-9dc6-c501d4fa99d2/GCA_009693165.1_ASM969316v1_genomic.fna.gz]
[2023-06-17 14:42:49,043] [INFO] Query marker FASTA was written to GCA_009693165.1_ASM969316v1_genomic.fna/markers.fasta
[2023-06-17 14:42:49,043] [INFO] Task started: Blastn
[2023-06-17 14:42:49,044] [INFO] Running command: blastn -query GCA_009693165.1_ASM969316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg935897a6-2034-4e91-85e7-f365323d7d7e/dqc_reference/reference_markers.fasta -out GCA_009693165.1_ASM969316v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:42:49,624] [INFO] Task succeeded: Blastn
[2023-06-17 14:42:49,629] [INFO] Selected 29 target genomes.
[2023-06-17 14:42:49,629] [INFO] Target genome list was writen to GCA_009693165.1_ASM969316v1_genomic.fna/target_genomes.txt
[2023-06-17 14:42:49,640] [INFO] Task started: fastANI
[2023-06-17 14:42:49,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg293327b8-db1c-4c40-9dc6-c501d4fa99d2/GCA_009693165.1_ASM969316v1_genomic.fna.gz --refList GCA_009693165.1_ASM969316v1_genomic.fna/target_genomes.txt --output GCA_009693165.1_ASM969316v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 14:43:12,230] [INFO] Task succeeded: fastANI
[2023-06-17 14:43:12,231] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg935897a6-2034-4e91-85e7-f365323d7d7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 14:43:12,231] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg935897a6-2034-4e91-85e7-f365323d7d7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 14:43:12,234] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 14:43:12,234] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 14:43:12,234] [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 14:43:12,237] [INFO] DFAST Taxonomy check result was written to GCA_009693165.1_ASM969316v1_genomic.fna/tc_result.tsv
[2023-06-17 14:43:12,237] [INFO] ===== Taxonomy check completed =====
[2023-06-17 14:43:12,238] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 14:43:12,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg935897a6-2034-4e91-85e7-f365323d7d7e/dqc_reference/checkm_data
[2023-06-17 14:43:12,243] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 14:43:12,269] [INFO] Task started: CheckM
[2023-06-17 14:43:12,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009693165.1_ASM969316v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009693165.1_ASM969316v1_genomic.fna/checkm_input GCA_009693165.1_ASM969316v1_genomic.fna/checkm_result
[2023-06-17 14:43:39,282] [INFO] Task succeeded: CheckM
[2023-06-17 14:43:39,284] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 14:43:39,305] [INFO] ===== Completeness check finished =====
[2023-06-17 14:43:39,306] [INFO] ===== Start GTDB Search =====
[2023-06-17 14:43:39,306] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009693165.1_ASM969316v1_genomic.fna/markers.fasta)
[2023-06-17 14:43:39,306] [INFO] Task started: Blastn
[2023-06-17 14:43:39,307] [INFO] Running command: blastn -query GCA_009693165.1_ASM969316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg935897a6-2034-4e91-85e7-f365323d7d7e/dqc_reference/reference_markers_gtdb.fasta -out GCA_009693165.1_ASM969316v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:43:40,073] [INFO] Task succeeded: Blastn
[2023-06-17 14:43:40,077] [INFO] Selected 20 target genomes.
[2023-06-17 14:43:40,077] [INFO] Target genome list was writen to GCA_009693165.1_ASM969316v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 14:43:40,114] [INFO] Task started: fastANI
[2023-06-17 14:43:40,114] [INFO] Running command: fastANI --query /var/lib/cwl/stg293327b8-db1c-4c40-9dc6-c501d4fa99d2/GCA_009693165.1_ASM969316v1_genomic.fna.gz --refList GCA_009693165.1_ASM969316v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009693165.1_ASM969316v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 14:43:54,755] [INFO] Task succeeded: fastANI
[2023-06-17 14:43:54,763] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 14:43:54,764] [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_009693165.1	s__UBA12225 sp009693165	100.0	680	683	d__Bacteria;p__Chloroflexota;c__UBA2235;o__UBA12225;f__UBA12225;g__UBA12225	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002347925.1	s__UBA12225 sp002347925	84.6424	525	683	d__Bacteria;p__Chloroflexota;c__UBA2235;o__UBA12225;f__UBA12225;g__UBA12225	95.0	98.21	95.05	0.90	0.85	18	-
GCA_903836285.1	s__CAILQO01 sp903836285	77.1493	91	683	d__Bacteria;p__Chloroflexota;c__UBA2235;o__UBA12225;f__UBA12225;g__CAILQO01	95.0	98.79	98.57	0.84	0.81	6	-
--------------------------------------------------------------------------------
[2023-06-17 14:43:54,766] [INFO] GTDB search result was written to GCA_009693165.1_ASM969316v1_genomic.fna/result_gtdb.tsv
[2023-06-17 14:43:54,767] [INFO] ===== GTDB Search completed =====
[2023-06-17 14:43:54,770] [INFO] DFAST_QC result json was written to GCA_009693165.1_ASM969316v1_genomic.fna/dqc_result.json
[2023-06-17 14:43:54,770] [INFO] DFAST_QC completed!
[2023-06-17 14:43:54,771] [INFO] Total running time: 0h1m14s