[2023-06-27 04:59:52,041] [INFO] DFAST_QC pipeline started.
[2023-06-27 04:59:52,043] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 04:59:52,043] [INFO] DQC Reference Directory: /var/lib/cwl/stg582aa542-4be2-48b9-ac60-26f8cc24a87e/dqc_reference
[2023-06-27 04:59:53,291] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 04:59:53,292] [INFO] Task started: Prodigal
[2023-06-27 04:59:53,292] [INFO] Running command: gunzip -c /var/lib/cwl/stg18ad79c8-dcf8-48c6-a65c-79b43023d8cc/GCA_027054565.1_ASM2705456v1_genomic.fna.gz | prodigal -d GCA_027054565.1_ASM2705456v1_genomic.fna/cds.fna -a GCA_027054565.1_ASM2705456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 04:59:58,465] [INFO] Task succeeded: Prodigal
[2023-06-27 04:59:58,466] [INFO] Task started: HMMsearch
[2023-06-27 04:59:58,466] [INFO] Running command: hmmsearch --tblout GCA_027054565.1_ASM2705456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg582aa542-4be2-48b9-ac60-26f8cc24a87e/dqc_reference/reference_markers.hmm GCA_027054565.1_ASM2705456v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 04:59:58,681] [INFO] Task succeeded: HMMsearch
[2023-06-27 04:59:58,683] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg18ad79c8-dcf8-48c6-a65c-79b43023d8cc/GCA_027054565.1_ASM2705456v1_genomic.fna.gz]
[2023-06-27 04:59:58,713] [INFO] Query marker FASTA was written to GCA_027054565.1_ASM2705456v1_genomic.fna/markers.fasta
[2023-06-27 04:59:58,714] [INFO] Task started: Blastn
[2023-06-27 04:59:58,714] [INFO] Running command: blastn -query GCA_027054565.1_ASM2705456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg582aa542-4be2-48b9-ac60-26f8cc24a87e/dqc_reference/reference_markers.fasta -out GCA_027054565.1_ASM2705456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:59:59,255] [INFO] Task succeeded: Blastn
[2023-06-27 04:59:59,260] [INFO] Selected 15 target genomes.
[2023-06-27 04:59:59,260] [INFO] Target genome list was writen to GCA_027054565.1_ASM2705456v1_genomic.fna/target_genomes.txt
[2023-06-27 04:59:59,266] [INFO] Task started: fastANI
[2023-06-27 04:59:59,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg18ad79c8-dcf8-48c6-a65c-79b43023d8cc/GCA_027054565.1_ASM2705456v1_genomic.fna.gz --refList GCA_027054565.1_ASM2705456v1_genomic.fna/target_genomes.txt --output GCA_027054565.1_ASM2705456v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:00:07,647] [INFO] Task succeeded: fastANI
[2023-06-27 05:00:07,648] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg582aa542-4be2-48b9-ac60-26f8cc24a87e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:00:07,648] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg582aa542-4be2-48b9-ac60-26f8cc24a87e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:00:07,652] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 05:00:07,653] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 05:00:07,653] [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 05:00:07,655] [INFO] DFAST Taxonomy check result was written to GCA_027054565.1_ASM2705456v1_genomic.fna/tc_result.tsv
[2023-06-27 05:00:07,656] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:00:07,656] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:00:07,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg582aa542-4be2-48b9-ac60-26f8cc24a87e/dqc_reference/checkm_data
[2023-06-27 05:00:07,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:00:07,694] [INFO] Task started: CheckM
[2023-06-27 05:00:07,694] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027054565.1_ASM2705456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027054565.1_ASM2705456v1_genomic.fna/checkm_input GCA_027054565.1_ASM2705456v1_genomic.fna/checkm_result
[2023-06-27 05:00:29,992] [INFO] Task succeeded: CheckM
[2023-06-27 05:00:29,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.04%
Contamintation: 7.29%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-27 05:00:30,019] [INFO] ===== Completeness check finished =====
[2023-06-27 05:00:30,020] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:00:30,020] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027054565.1_ASM2705456v1_genomic.fna/markers.fasta)
[2023-06-27 05:00:30,021] [INFO] Task started: Blastn
[2023-06-27 05:00:30,021] [INFO] Running command: blastn -query GCA_027054565.1_ASM2705456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg582aa542-4be2-48b9-ac60-26f8cc24a87e/dqc_reference/reference_markers_gtdb.fasta -out GCA_027054565.1_ASM2705456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:00:30,710] [INFO] Task succeeded: Blastn
[2023-06-27 05:00:30,715] [INFO] Selected 17 target genomes.
[2023-06-27 05:00:30,715] [INFO] Target genome list was writen to GCA_027054565.1_ASM2705456v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:00:30,728] [INFO] Task started: fastANI
[2023-06-27 05:00:30,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg18ad79c8-dcf8-48c6-a65c-79b43023d8cc/GCA_027054565.1_ASM2705456v1_genomic.fna.gz --refList GCA_027054565.1_ASM2705456v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027054565.1_ASM2705456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:00:40,063] [INFO] Task succeeded: fastANI
[2023-06-27 05:00:40,065] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 05:00:40,065] [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
--------------------------------------------------------------------------------
[2023-06-27 05:00:40,067] [INFO] GTDB search result was written to GCA_027054565.1_ASM2705456v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:00:40,068] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:00:40,071] [INFO] DFAST_QC result json was written to GCA_027054565.1_ASM2705456v1_genomic.fna/dqc_result.json
[2023-06-27 05:00:40,072] [INFO] DFAST_QC completed!
[2023-06-27 05:00:40,072] [INFO] Total running time: 0h0m48s