[2023-07-01 07:29:54,384] [INFO] DFAST_QC pipeline started.
[2023-07-01 07:29:54,388] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 07:29:54,388] [INFO] DQC Reference Directory: /var/lib/cwl/stg816b9c2d-021e-4a5f-a211-ee5e8ddc3d56/dqc_reference
[2023-07-01 07:29:55,613] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 07:29:55,614] [INFO] Task started: Prodigal
[2023-07-01 07:29:55,614] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a08bf3c-a1c4-4292-923e-8baffcaa41ae/GCA_024690935.1_ASM2469093v1_genomic.fna.gz | prodigal -d GCA_024690935.1_ASM2469093v1_genomic.fna/cds.fna -a GCA_024690935.1_ASM2469093v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 07:30:00,564] [INFO] Task succeeded: Prodigal
[2023-07-01 07:30:00,565] [INFO] Task started: HMMsearch
[2023-07-01 07:30:00,565] [INFO] Running command: hmmsearch --tblout GCA_024690935.1_ASM2469093v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg816b9c2d-021e-4a5f-a211-ee5e8ddc3d56/dqc_reference/reference_markers.hmm GCA_024690935.1_ASM2469093v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 07:30:00,818] [INFO] Task succeeded: HMMsearch
[2023-07-01 07:30:00,820] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0a08bf3c-a1c4-4292-923e-8baffcaa41ae/GCA_024690935.1_ASM2469093v1_genomic.fna.gz]
[2023-07-01 07:30:00,888] [INFO] Query marker FASTA was written to GCA_024690935.1_ASM2469093v1_genomic.fna/markers.fasta
[2023-07-01 07:30:00,889] [INFO] Task started: Blastn
[2023-07-01 07:30:00,889] [INFO] Running command: blastn -query GCA_024690935.1_ASM2469093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg816b9c2d-021e-4a5f-a211-ee5e8ddc3d56/dqc_reference/reference_markers.fasta -out GCA_024690935.1_ASM2469093v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 07:30:01,449] [INFO] Task succeeded: Blastn
[2023-07-01 07:30:01,469] [INFO] Selected 27 target genomes.
[2023-07-01 07:30:01,470] [INFO] Target genome list was writen to GCA_024690935.1_ASM2469093v1_genomic.fna/target_genomes.txt
[2023-07-01 07:30:01,474] [INFO] Task started: fastANI
[2023-07-01 07:30:01,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a08bf3c-a1c4-4292-923e-8baffcaa41ae/GCA_024690935.1_ASM2469093v1_genomic.fna.gz --refList GCA_024690935.1_ASM2469093v1_genomic.fna/target_genomes.txt --output GCA_024690935.1_ASM2469093v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 07:30:12,714] [INFO] Task succeeded: fastANI
[2023-07-01 07:30:12,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg816b9c2d-021e-4a5f-a211-ee5e8ddc3d56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 07:30:12,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg816b9c2d-021e-4a5f-a211-ee5e8ddc3d56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 07:30:12,718] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 07:30:12,718] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 07:30:12,718] [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
--------------------------------------------------------------------------------
[2023-07-01 07:30:12,720] [INFO] DFAST Taxonomy check result was written to GCA_024690935.1_ASM2469093v1_genomic.fna/tc_result.tsv
[2023-07-01 07:30:12,721] [INFO] ===== Taxonomy check completed =====
[2023-07-01 07:30:12,721] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 07:30:12,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg816b9c2d-021e-4a5f-a211-ee5e8ddc3d56/dqc_reference/checkm_data
[2023-07-01 07:30:12,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 07:30:12,771] [INFO] Task started: CheckM
[2023-07-01 07:30:12,771] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024690935.1_ASM2469093v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024690935.1_ASM2469093v1_genomic.fna/checkm_input GCA_024690935.1_ASM2469093v1_genomic.fna/checkm_result
[2023-07-01 07:30:35,846] [INFO] Task succeeded: CheckM
[2023-07-01 07:30:35,848] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 14.77%
Strain heterogeneity: 10.53%
--------------------------------------------------------------------------------
[2023-07-01 07:30:35,878] [INFO] ===== Completeness check finished =====
[2023-07-01 07:30:35,878] [INFO] ===== Start GTDB Search =====
[2023-07-01 07:30:35,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024690935.1_ASM2469093v1_genomic.fna/markers.fasta)
[2023-07-01 07:30:35,879] [INFO] Task started: Blastn
[2023-07-01 07:30:35,879] [INFO] Running command: blastn -query GCA_024690935.1_ASM2469093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg816b9c2d-021e-4a5f-a211-ee5e8ddc3d56/dqc_reference/reference_markers_gtdb.fasta -out GCA_024690935.1_ASM2469093v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 07:30:36,668] [INFO] Task succeeded: Blastn
[2023-07-01 07:30:36,673] [INFO] Selected 25 target genomes.
[2023-07-01 07:30:36,674] [INFO] Target genome list was writen to GCA_024690935.1_ASM2469093v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 07:30:36,687] [INFO] Task started: fastANI
[2023-07-01 07:30:36,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a08bf3c-a1c4-4292-923e-8baffcaa41ae/GCA_024690935.1_ASM2469093v1_genomic.fna.gz --refList GCA_024690935.1_ASM2469093v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024690935.1_ASM2469093v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 07:30:47,875] [INFO] Task succeeded: fastANI
[2023-07-01 07:30:47,882] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 07:30:47,882] [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_900315015.1	s__UBA9722 sp900315015	96.635	669	842	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9722	95.0	98.75	97.45	0.95	0.91	6	conclusive
GCF_000420825.1	s__Butyrivibrio sp000420825	77.1661	52	842	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 07:30:47,884] [INFO] GTDB search result was written to GCA_024690935.1_ASM2469093v1_genomic.fna/result_gtdb.tsv
[2023-07-01 07:30:47,885] [INFO] ===== GTDB Search completed =====
[2023-07-01 07:30:47,887] [INFO] DFAST_QC result json was written to GCA_024690935.1_ASM2469093v1_genomic.fna/dqc_result.json
[2023-07-01 07:30:47,887] [INFO] DFAST_QC completed!
[2023-07-01 07:30:47,888] [INFO] Total running time: 0h0m54s