[2023-06-27 04:41:03,544] [INFO] DFAST_QC pipeline started.
[2023-06-27 04:41:03,548] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 04:41:03,549] [INFO] DQC Reference Directory: /var/lib/cwl/stg88981fb9-8a09-4dab-8da4-b4c636e2d49e/dqc_reference
[2023-06-27 04:41:04,756] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 04:41:04,757] [INFO] Task started: Prodigal
[2023-06-27 04:41:04,758] [INFO] Running command: gunzip -c /var/lib/cwl/stga434139e-145d-4f81-a839-3a43bcd43b94/GCA_002686445.1_ASM268644v1_genomic.fna.gz | prodigal -d GCA_002686445.1_ASM268644v1_genomic.fna/cds.fna -a GCA_002686445.1_ASM268644v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 04:41:07,049] [INFO] Task succeeded: Prodigal
[2023-06-27 04:41:07,050] [INFO] Task started: HMMsearch
[2023-06-27 04:41:07,050] [INFO] Running command: hmmsearch --tblout GCA_002686445.1_ASM268644v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88981fb9-8a09-4dab-8da4-b4c636e2d49e/dqc_reference/reference_markers.hmm GCA_002686445.1_ASM268644v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 04:41:07,318] [INFO] Task succeeded: HMMsearch
[2023-06-27 04:41:07,320] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga434139e-145d-4f81-a839-3a43bcd43b94/GCA_002686445.1_ASM268644v1_genomic.fna.gz]
[2023-06-27 04:41:07,338] [INFO] Query marker FASTA was written to GCA_002686445.1_ASM268644v1_genomic.fna/markers.fasta
[2023-06-27 04:41:07,338] [INFO] Task started: Blastn
[2023-06-27 04:41:07,338] [INFO] Running command: blastn -query GCA_002686445.1_ASM268644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88981fb9-8a09-4dab-8da4-b4c636e2d49e/dqc_reference/reference_markers.fasta -out GCA_002686445.1_ASM268644v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:41:07,869] [INFO] Task succeeded: Blastn
[2023-06-27 04:41:07,874] [INFO] Selected 4 target genomes.
[2023-06-27 04:41:07,875] [INFO] Target genome list was writen to GCA_002686445.1_ASM268644v1_genomic.fna/target_genomes.txt
[2023-06-27 04:41:07,877] [INFO] Task started: fastANI
[2023-06-27 04:41:07,878] [INFO] Running command: fastANI --query /var/lib/cwl/stga434139e-145d-4f81-a839-3a43bcd43b94/GCA_002686445.1_ASM268644v1_genomic.fna.gz --refList GCA_002686445.1_ASM268644v1_genomic.fna/target_genomes.txt --output GCA_002686445.1_ASM268644v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 04:41:10,196] [INFO] Task succeeded: fastANI
[2023-06-27 04:41:10,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88981fb9-8a09-4dab-8da4-b4c636e2d49e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 04:41:10,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88981fb9-8a09-4dab-8da4-b4c636e2d49e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 04:41:10,201] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 04:41:10,201] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 04:41:10,202] [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
--------------------------------------------------------------------------------
[2023-06-27 04:41:10,217] [INFO] DFAST Taxonomy check result was written to GCA_002686445.1_ASM268644v1_genomic.fna/tc_result.tsv
[2023-06-27 04:41:10,218] [INFO] ===== Taxonomy check completed =====
[2023-06-27 04:41:10,218] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 04:41:10,219] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88981fb9-8a09-4dab-8da4-b4c636e2d49e/dqc_reference/checkm_data
[2023-06-27 04:41:10,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 04:41:10,236] [INFO] Task started: CheckM
[2023-06-27 04:41:10,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002686445.1_ASM268644v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002686445.1_ASM268644v1_genomic.fna/checkm_input GCA_002686445.1_ASM268644v1_genomic.fna/checkm_result
[2023-06-27 04:41:25,398] [INFO] Task succeeded: CheckM
[2023-06-27 04:41:25,400] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.97%
Contamintation: 6.25%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 04:41:25,442] [INFO] ===== Completeness check finished =====
[2023-06-27 04:41:25,442] [INFO] ===== Start GTDB Search =====
[2023-06-27 04:41:25,443] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002686445.1_ASM268644v1_genomic.fna/markers.fasta)
[2023-06-27 04:41:25,443] [INFO] Task started: Blastn
[2023-06-27 04:41:25,444] [INFO] Running command: blastn -query GCA_002686445.1_ASM268644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88981fb9-8a09-4dab-8da4-b4c636e2d49e/dqc_reference/reference_markers_gtdb.fasta -out GCA_002686445.1_ASM268644v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:41:26,084] [INFO] Task succeeded: Blastn
[2023-06-27 04:41:26,089] [INFO] Selected 9 target genomes.
[2023-06-27 04:41:26,089] [INFO] Target genome list was writen to GCA_002686445.1_ASM268644v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 04:41:26,097] [INFO] Task started: fastANI
[2023-06-27 04:41:26,098] [INFO] Running command: fastANI --query /var/lib/cwl/stga434139e-145d-4f81-a839-3a43bcd43b94/GCA_002686445.1_ASM268644v1_genomic.fna.gz --refList GCA_002686445.1_ASM268644v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002686445.1_ASM268644v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 04:41:28,298] [INFO] Task succeeded: fastANI
[2023-06-27 04:41:28,303] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 04:41:28,304] [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_002686445.1	s__GCA-2686445 sp002686445	100.0	276	279	d__Bacteria;p__Patescibacteria;c__Andersenbacteria;o__UBA10190;f__UBA10190;g__GCA-2686445	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-27 04:41:28,306] [INFO] GTDB search result was written to GCA_002686445.1_ASM268644v1_genomic.fna/result_gtdb.tsv
[2023-06-27 04:41:28,307] [INFO] ===== GTDB Search completed =====
[2023-06-27 04:41:28,310] [INFO] DFAST_QC result json was written to GCA_002686445.1_ASM268644v1_genomic.fna/dqc_result.json
[2023-06-27 04:41:28,311] [INFO] DFAST_QC completed!
[2023-06-27 04:41:28,311] [INFO] Total running time: 0h0m25s