[2023-06-04 22:52:22,393] [INFO] DFAST_QC pipeline started.
[2023-06-04 22:52:22,396] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 22:52:22,396] [INFO] DQC Reference Directory: /var/lib/cwl/stg03f7fe25-2aab-4229-90a7-b4124dd528b4/dqc_reference
[2023-06-04 22:52:24,059] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 22:52:24,060] [INFO] Task started: Prodigal
[2023-06-04 22:52:24,060] [INFO] Running command: gunzip -c /var/lib/cwl/stga62f1e87-ad77-43b3-9cf3-55d077e6a5b8/GCA_934270445.1_ERR7745922_bin.194_genomic.fna.gz | prodigal -d GCA_934270445.1_ERR7745922_bin.194_genomic.fna/cds.fna -a GCA_934270445.1_ERR7745922_bin.194_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 22:52:26,815] [INFO] Task succeeded: Prodigal
[2023-06-04 22:52:26,815] [INFO] Task started: HMMsearch
[2023-06-04 22:52:26,815] [INFO] Running command: hmmsearch --tblout GCA_934270445.1_ERR7745922_bin.194_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03f7fe25-2aab-4229-90a7-b4124dd528b4/dqc_reference/reference_markers.hmm GCA_934270445.1_ERR7745922_bin.194_genomic.fna/protein.faa > /dev/null
[2023-06-04 22:52:27,045] [INFO] Task succeeded: HMMsearch
[2023-06-04 22:52:27,046] [INFO] Found 6/6 markers.
[2023-06-04 22:52:27,063] [INFO] Query marker FASTA was written to GCA_934270445.1_ERR7745922_bin.194_genomic.fna/markers.fasta
[2023-06-04 22:52:27,064] [INFO] Task started: Blastn
[2023-06-04 22:52:27,064] [INFO] Running command: blastn -query GCA_934270445.1_ERR7745922_bin.194_genomic.fna/markers.fasta -db /var/lib/cwl/stg03f7fe25-2aab-4229-90a7-b4124dd528b4/dqc_reference/reference_markers.fasta -out GCA_934270445.1_ERR7745922_bin.194_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:52:27,623] [INFO] Task succeeded: Blastn
[2023-06-04 22:52:27,627] [INFO] Selected 22 target genomes.
[2023-06-04 22:52:27,628] [INFO] Target genome list was writen to GCA_934270445.1_ERR7745922_bin.194_genomic.fna/target_genomes.txt
[2023-06-04 22:52:27,634] [INFO] Task started: fastANI
[2023-06-04 22:52:27,635] [INFO] Running command: fastANI --query /var/lib/cwl/stga62f1e87-ad77-43b3-9cf3-55d077e6a5b8/GCA_934270445.1_ERR7745922_bin.194_genomic.fna.gz --refList GCA_934270445.1_ERR7745922_bin.194_genomic.fna/target_genomes.txt --output GCA_934270445.1_ERR7745922_bin.194_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 22:52:44,913] [INFO] Task succeeded: fastANI
[2023-06-04 22:52:44,914] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03f7fe25-2aab-4229-90a7-b4124dd528b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 22:52:44,914] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03f7fe25-2aab-4229-90a7-b4124dd528b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 22:52:44,916] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 22:52:44,916] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 22:52:44,917] [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
--------------------------------------------------------------------------------
[2023-06-04 22:52:44,919] [INFO] DFAST Taxonomy check result was written to GCA_934270445.1_ERR7745922_bin.194_genomic.fna/tc_result.tsv
[2023-06-04 22:52:44,920] [INFO] ===== Taxonomy check completed =====
[2023-06-04 22:52:44,920] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 22:52:44,920] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03f7fe25-2aab-4229-90a7-b4124dd528b4/dqc_reference/checkm_data
[2023-06-04 22:52:44,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 22:52:44,947] [INFO] Task started: CheckM
[2023-06-04 22:52:44,947] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934270445.1_ERR7745922_bin.194_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934270445.1_ERR7745922_bin.194_genomic.fna/checkm_input GCA_934270445.1_ERR7745922_bin.194_genomic.fna/checkm_result
[2023-06-04 22:53:01,048] [INFO] Task succeeded: CheckM
[2023-06-04 22:53:01,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 22:53:01,075] [INFO] ===== Completeness check finished =====
[2023-06-04 22:53:01,076] [INFO] ===== Start GTDB Search =====
[2023-06-04 22:53:01,076] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934270445.1_ERR7745922_bin.194_genomic.fna/markers.fasta)
[2023-06-04 22:53:01,076] [INFO] Task started: Blastn
[2023-06-04 22:53:01,077] [INFO] Running command: blastn -query GCA_934270445.1_ERR7745922_bin.194_genomic.fna/markers.fasta -db /var/lib/cwl/stg03f7fe25-2aab-4229-90a7-b4124dd528b4/dqc_reference/reference_markers_gtdb.fasta -out GCA_934270445.1_ERR7745922_bin.194_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:53:01,862] [INFO] Task succeeded: Blastn
[2023-06-04 22:53:01,868] [INFO] Selected 21 target genomes.
[2023-06-04 22:53:01,868] [INFO] Target genome list was writen to GCA_934270445.1_ERR7745922_bin.194_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 22:53:01,882] [INFO] Task started: fastANI
[2023-06-04 22:53:01,883] [INFO] Running command: fastANI --query /var/lib/cwl/stga62f1e87-ad77-43b3-9cf3-55d077e6a5b8/GCA_934270445.1_ERR7745922_bin.194_genomic.fna.gz --refList GCA_934270445.1_ERR7745922_bin.194_genomic.fna/target_genomes_gtdb.txt --output GCA_934270445.1_ERR7745922_bin.194_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 22:53:07,800] [INFO] Task succeeded: fastANI
[2023-06-04 22:53:07,806] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 22:53:07,806] [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_003538975.1	s__UBA11475 sp003538975	97.9881	455	485	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__UBA11475	95.0	95.18	95.03	0.90	0.89	3	conclusive
--------------------------------------------------------------------------------
[2023-06-04 22:53:07,811] [INFO] GTDB search result was written to GCA_934270445.1_ERR7745922_bin.194_genomic.fna/result_gtdb.tsv
[2023-06-04 22:53:07,812] [INFO] ===== GTDB Search completed =====
[2023-06-04 22:53:07,814] [INFO] DFAST_QC result json was written to GCA_934270445.1_ERR7745922_bin.194_genomic.fna/dqc_result.json
[2023-06-04 22:53:07,814] [INFO] DFAST_QC completed!
[2023-06-04 22:53:07,815] [INFO] Total running time: 0h0m45s