[2023-06-28 17:21:03,563] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:21:03,565] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:21:03,565] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6603e75-bc99-4452-aaed-3f4d42163f1a/dqc_reference
[2023-06-28 17:21:04,806] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:21:04,807] [INFO] Task started: Prodigal
[2023-06-28 17:21:04,807] [INFO] Running command: gunzip -c /var/lib/cwl/stg83e9fb57-0515-4d05-910e-a8ea9ca4e83a/GCA_012522035.1_ASM1252203v1_genomic.fna.gz | prodigal -d GCA_012522035.1_ASM1252203v1_genomic.fna/cds.fna -a GCA_012522035.1_ASM1252203v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:21:11,145] [INFO] Task succeeded: Prodigal
[2023-06-28 17:21:11,146] [INFO] Task started: HMMsearch
[2023-06-28 17:21:11,146] [INFO] Running command: hmmsearch --tblout GCA_012522035.1_ASM1252203v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6603e75-bc99-4452-aaed-3f4d42163f1a/dqc_reference/reference_markers.hmm GCA_012522035.1_ASM1252203v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:21:11,410] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:21:11,412] [INFO] Found 6/6 markers.
[2023-06-28 17:21:11,448] [INFO] Query marker FASTA was written to GCA_012522035.1_ASM1252203v1_genomic.fna/markers.fasta
[2023-06-28 17:21:11,449] [INFO] Task started: Blastn
[2023-06-28 17:21:11,449] [INFO] Running command: blastn -query GCA_012522035.1_ASM1252203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6603e75-bc99-4452-aaed-3f4d42163f1a/dqc_reference/reference_markers.fasta -out GCA_012522035.1_ASM1252203v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:21:12,073] [INFO] Task succeeded: Blastn
[2023-06-28 17:21:12,078] [INFO] Selected 18 target genomes.
[2023-06-28 17:21:12,078] [INFO] Target genome list was writen to GCA_012522035.1_ASM1252203v1_genomic.fna/target_genomes.txt
[2023-06-28 17:21:12,082] [INFO] Task started: fastANI
[2023-06-28 17:21:12,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg83e9fb57-0515-4d05-910e-a8ea9ca4e83a/GCA_012522035.1_ASM1252203v1_genomic.fna.gz --refList GCA_012522035.1_ASM1252203v1_genomic.fna/target_genomes.txt --output GCA_012522035.1_ASM1252203v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:21:23,038] [INFO] Task succeeded: fastANI
[2023-06-28 17:21:23,039] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6603e75-bc99-4452-aaed-3f4d42163f1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:21:23,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6603e75-bc99-4452-aaed-3f4d42163f1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:21:23,041] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:21:23,042] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 17:21:23,042] [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
--------------------------------------------------------------------------------
[2023-06-28 17:21:23,044] [INFO] DFAST Taxonomy check result was written to GCA_012522035.1_ASM1252203v1_genomic.fna/tc_result.tsv
[2023-06-28 17:21:23,045] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:21:23,045] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:21:23,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6603e75-bc99-4452-aaed-3f4d42163f1a/dqc_reference/checkm_data
[2023-06-28 17:21:23,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:21:23,084] [INFO] Task started: CheckM
[2023-06-28 17:21:23,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012522035.1_ASM1252203v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012522035.1_ASM1252203v1_genomic.fna/checkm_input GCA_012522035.1_ASM1252203v1_genomic.fna/checkm_result
[2023-06-28 17:21:49,433] [INFO] Task succeeded: CheckM
[2023-06-28 17:21:49,434] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 17:21:49,462] [INFO] ===== Completeness check finished =====
[2023-06-28 17:21:49,462] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:21:49,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012522035.1_ASM1252203v1_genomic.fna/markers.fasta)
[2023-06-28 17:21:49,463] [INFO] Task started: Blastn
[2023-06-28 17:21:49,463] [INFO] Running command: blastn -query GCA_012522035.1_ASM1252203v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6603e75-bc99-4452-aaed-3f4d42163f1a/dqc_reference/reference_markers_gtdb.fasta -out GCA_012522035.1_ASM1252203v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:21:50,435] [INFO] Task succeeded: Blastn
[2023-06-28 17:21:50,441] [INFO] Selected 23 target genomes.
[2023-06-28 17:21:50,441] [INFO] Target genome list was writen to GCA_012522035.1_ASM1252203v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:21:50,459] [INFO] Task started: fastANI
[2023-06-28 17:21:50,459] [INFO] Running command: fastANI --query /var/lib/cwl/stg83e9fb57-0515-4d05-910e-a8ea9ca4e83a/GCA_012522035.1_ASM1252203v1_genomic.fna.gz --refList GCA_012522035.1_ASM1252203v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012522035.1_ASM1252203v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:22:00,897] [INFO] Task succeeded: fastANI
[2023-06-28 17:22:00,902] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 17:22:00,903] [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_012522035.1	s__DUPL01 sp012522035	100.0	710	720	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1212;f__UBA1257;g__DUPL01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012838385.1	s__DUPL01 sp012838385	89.6052	562	720	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UBA1212;f__UBA1257;g__DUPL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 17:22:00,963] [INFO] GTDB search result was written to GCA_012522035.1_ASM1252203v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:22:00,964] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:22:00,967] [INFO] DFAST_QC result json was written to GCA_012522035.1_ASM1252203v1_genomic.fna/dqc_result.json
[2023-06-28 17:22:00,967] [INFO] DFAST_QC completed!
[2023-06-28 17:22:00,967] [INFO] Total running time: 0h0m57s