[2023-06-05 18:33:28,293] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:33:28,295] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:33:28,295] [INFO] DQC Reference Directory: /var/lib/cwl/stg741b9b98-2d34-4d6e-8468-63a6ec218f3a/dqc_reference
[2023-06-05 18:33:29,435] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:33:29,436] [INFO] Task started: Prodigal
[2023-06-05 18:33:29,436] [INFO] Running command: gunzip -c /var/lib/cwl/stg364e8c51-1e13-4edf-88bb-80d7fc8ae381/GCA_902836645.1_MGYG-HGUT-04840_genomic.fna.gz | prodigal -d GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/cds.fna -a GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:33:31,605] [INFO] Task succeeded: Prodigal
[2023-06-05 18:33:31,605] [INFO] Task started: HMMsearch
[2023-06-05 18:33:31,605] [INFO] Running command: hmmsearch --tblout GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg741b9b98-2d34-4d6e-8468-63a6ec218f3a/dqc_reference/reference_markers.hmm GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:33:31,777] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:33:31,778] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg364e8c51-1e13-4edf-88bb-80d7fc8ae381/GCA_902836645.1_MGYG-HGUT-04840_genomic.fna.gz]
[2023-06-05 18:33:31,807] [INFO] Query marker FASTA was written to GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/markers.fasta
[2023-06-05 18:33:31,807] [INFO] Task started: Blastn
[2023-06-05 18:33:31,807] [INFO] Running command: blastn -query GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/markers.fasta -db /var/lib/cwl/stg741b9b98-2d34-4d6e-8468-63a6ec218f3a/dqc_reference/reference_markers.fasta -out GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:33:32,322] [INFO] Task succeeded: Blastn
[2023-06-05 18:33:32,326] [INFO] Selected 20 target genomes.
[2023-06-05 18:33:32,326] [INFO] Target genome list was writen to GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/target_genomes.txt
[2023-06-05 18:33:32,332] [INFO] Task started: fastANI
[2023-06-05 18:33:32,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg364e8c51-1e13-4edf-88bb-80d7fc8ae381/GCA_902836645.1_MGYG-HGUT-04840_genomic.fna.gz --refList GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/target_genomes.txt --output GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:33:40,962] [INFO] Task succeeded: fastANI
[2023-06-05 18:33:40,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg741b9b98-2d34-4d6e-8468-63a6ec218f3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:33:40,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg741b9b98-2d34-4d6e-8468-63a6ec218f3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:33:40,967] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:33:40,967] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:33:40,967] [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
--------------------------------------------------------------------------------
[2023-06-05 18:33:40,973] [INFO] DFAST Taxonomy check result was written to GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/tc_result.tsv
[2023-06-05 18:33:40,974] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:33:40,974] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:33:40,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg741b9b98-2d34-4d6e-8468-63a6ec218f3a/dqc_reference/checkm_data
[2023-06-05 18:33:40,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:33:40,992] [INFO] Task started: CheckM
[2023-06-05 18:33:40,993] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/checkm_input GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/checkm_result
[2023-06-05 18:33:54,303] [INFO] Task succeeded: CheckM
[2023-06-05 18:33:54,304] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.45%
Contamintation: 1.30%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-05 18:33:54,323] [INFO] ===== Completeness check finished =====
[2023-06-05 18:33:54,324] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:33:54,324] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/markers.fasta)
[2023-06-05 18:33:54,324] [INFO] Task started: Blastn
[2023-06-05 18:33:54,324] [INFO] Running command: blastn -query GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/markers.fasta -db /var/lib/cwl/stg741b9b98-2d34-4d6e-8468-63a6ec218f3a/dqc_reference/reference_markers_gtdb.fasta -out GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:33:55,035] [INFO] Task succeeded: Blastn
[2023-06-05 18:33:55,038] [INFO] Selected 12 target genomes.
[2023-06-05 18:33:55,038] [INFO] Target genome list was writen to GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:33:55,053] [INFO] Task started: fastANI
[2023-06-05 18:33:55,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg364e8c51-1e13-4edf-88bb-80d7fc8ae381/GCA_902836645.1_MGYG-HGUT-04840_genomic.fna.gz --refList GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/target_genomes_gtdb.txt --output GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:33:59,667] [INFO] Task succeeded: fastANI
[2023-06-05 18:33:59,670] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:33:59,670] [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_900553085.1	s__QALR01 sp900553085	90.2211	54	56	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__QALR01	95.0	99.77	99.67	0.93	0.89	4	-
--------------------------------------------------------------------------------
[2023-06-05 18:33:59,672] [INFO] GTDB search result was written to GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/result_gtdb.tsv
[2023-06-05 18:33:59,672] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:33:59,674] [INFO] DFAST_QC result json was written to GCA_902836645.1_MGYG-HGUT-04840_genomic.fna/dqc_result.json
[2023-06-05 18:33:59,674] [INFO] DFAST_QC completed!
[2023-06-05 18:33:59,674] [INFO] Total running time: 0h0m31s