[2023-06-28 21:36:27,046] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:36:27,052] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:36:27,052] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ebc5b48-9464-47c5-aeaa-cc85f3a170f7/dqc_reference
[2023-06-28 21:36:29,133] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:36:29,134] [INFO] Task started: Prodigal
[2023-06-28 21:36:29,134] [INFO] Running command: gunzip -c /var/lib/cwl/stg83c96438-d2a0-474b-9a6d-11226bce30a6/GCA_017994155.1_ASM1799415v1_genomic.fna.gz | prodigal -d GCA_017994155.1_ASM1799415v1_genomic.fna/cds.fna -a GCA_017994155.1_ASM1799415v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:36:33,314] [INFO] Task succeeded: Prodigal
[2023-06-28 21:36:33,314] [INFO] Task started: HMMsearch
[2023-06-28 21:36:33,314] [INFO] Running command: hmmsearch --tblout GCA_017994155.1_ASM1799415v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ebc5b48-9464-47c5-aeaa-cc85f3a170f7/dqc_reference/reference_markers.hmm GCA_017994155.1_ASM1799415v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:36:33,468] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:36:33,469] [INFO] Found 6/6 markers.
[2023-06-28 21:36:33,481] [INFO] Query marker FASTA was written to GCA_017994155.1_ASM1799415v1_genomic.fna/markers.fasta
[2023-06-28 21:36:33,482] [INFO] Task started: Blastn
[2023-06-28 21:36:33,482] [INFO] Running command: blastn -query GCA_017994155.1_ASM1799415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ebc5b48-9464-47c5-aeaa-cc85f3a170f7/dqc_reference/reference_markers.fasta -out GCA_017994155.1_ASM1799415v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:36:34,038] [INFO] Task succeeded: Blastn
[2023-06-28 21:36:34,042] [INFO] Selected 15 target genomes.
[2023-06-28 21:36:34,043] [INFO] Target genome list was writen to GCA_017994155.1_ASM1799415v1_genomic.fna/target_genomes.txt
[2023-06-28 21:36:34,045] [INFO] Task started: fastANI
[2023-06-28 21:36:34,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg83c96438-d2a0-474b-9a6d-11226bce30a6/GCA_017994155.1_ASM1799415v1_genomic.fna.gz --refList GCA_017994155.1_ASM1799415v1_genomic.fna/target_genomes.txt --output GCA_017994155.1_ASM1799415v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:36:42,086] [INFO] Task succeeded: fastANI
[2023-06-28 21:36:42,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ebc5b48-9464-47c5-aeaa-cc85f3a170f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:36:42,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ebc5b48-9464-47c5-aeaa-cc85f3a170f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:36:42,088] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:36:42,088] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 21:36:42,088] [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 21:36:42,090] [INFO] DFAST Taxonomy check result was written to GCA_017994155.1_ASM1799415v1_genomic.fna/tc_result.tsv
[2023-06-28 21:36:42,091] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:36:42,091] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:36:42,091] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ebc5b48-9464-47c5-aeaa-cc85f3a170f7/dqc_reference/checkm_data
[2023-06-28 21:36:42,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:36:42,104] [INFO] Task started: CheckM
[2023-06-28 21:36:42,105] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017994155.1_ASM1799415v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017994155.1_ASM1799415v1_genomic.fna/checkm_input GCA_017994155.1_ASM1799415v1_genomic.fna/checkm_result
[2023-06-28 21:37:00,950] [INFO] Task succeeded: CheckM
[2023-06-28 21:37:00,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.70%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 21:37:00,970] [INFO] ===== Completeness check finished =====
[2023-06-28 21:37:00,970] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:37:00,971] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017994155.1_ASM1799415v1_genomic.fna/markers.fasta)
[2023-06-28 21:37:00,971] [INFO] Task started: Blastn
[2023-06-28 21:37:00,971] [INFO] Running command: blastn -query GCA_017994155.1_ASM1799415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ebc5b48-9464-47c5-aeaa-cc85f3a170f7/dqc_reference/reference_markers_gtdb.fasta -out GCA_017994155.1_ASM1799415v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:37:01,736] [INFO] Task succeeded: Blastn
[2023-06-28 21:37:01,740] [INFO] Selected 18 target genomes.
[2023-06-28 21:37:01,740] [INFO] Target genome list was writen to GCA_017994155.1_ASM1799415v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:37:01,750] [INFO] Task started: fastANI
[2023-06-28 21:37:01,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg83c96438-d2a0-474b-9a6d-11226bce30a6/GCA_017994155.1_ASM1799415v1_genomic.fna.gz --refList GCA_017994155.1_ASM1799415v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017994155.1_ASM1799415v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:37:05,647] [INFO] Task succeeded: fastANI
[2023-06-28 21:37:05,650] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 21:37:05,650] [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
--------------------------------------------------------------------------------
[2023-06-28 21:37:05,651] [INFO] GTDB search result was written to GCA_017994155.1_ASM1799415v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:37:05,652] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:37:05,654] [INFO] DFAST_QC result json was written to GCA_017994155.1_ASM1799415v1_genomic.fna/dqc_result.json
[2023-06-28 21:37:05,654] [INFO] DFAST_QC completed!
[2023-06-28 21:37:05,654] [INFO] Total running time: 0h0m39s