[2023-06-28 18:27:03,451] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:27:03,454] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:27:03,455] [INFO] DQC Reference Directory: /var/lib/cwl/stg58f2c344-c8c3-428e-a5a7-fd11b23b99f7/dqc_reference
[2023-06-28 18:27:07,004] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:27:07,005] [INFO] Task started: Prodigal
[2023-06-28 18:27:07,006] [INFO] Running command: gunzip -c /var/lib/cwl/stge95e018d-5fc9-488d-9e55-0b26ec196c50/GCA_027044905.1_ASM2704490v1_genomic.fna.gz | prodigal -d GCA_027044905.1_ASM2704490v1_genomic.fna/cds.fna -a GCA_027044905.1_ASM2704490v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:27:09,857] [INFO] Task succeeded: Prodigal
[2023-06-28 18:27:09,858] [INFO] Task started: HMMsearch
[2023-06-28 18:27:09,858] [INFO] Running command: hmmsearch --tblout GCA_027044905.1_ASM2704490v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58f2c344-c8c3-428e-a5a7-fd11b23b99f7/dqc_reference/reference_markers.hmm GCA_027044905.1_ASM2704490v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:27:10,091] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:27:10,094] [INFO] Found 6/6 markers.
[2023-06-28 18:27:10,124] [INFO] Query marker FASTA was written to GCA_027044905.1_ASM2704490v1_genomic.fna/markers.fasta
[2023-06-28 18:27:10,125] [INFO] Task started: Blastn
[2023-06-28 18:27:10,125] [INFO] Running command: blastn -query GCA_027044905.1_ASM2704490v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58f2c344-c8c3-428e-a5a7-fd11b23b99f7/dqc_reference/reference_markers.fasta -out GCA_027044905.1_ASM2704490v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:27:13,348] [INFO] Task succeeded: Blastn
[2023-06-28 18:27:13,353] [INFO] Selected 26 target genomes.
[2023-06-28 18:27:13,353] [INFO] Target genome list was writen to GCA_027044905.1_ASM2704490v1_genomic.fna/target_genomes.txt
[2023-06-28 18:27:13,356] [INFO] Task started: fastANI
[2023-06-28 18:27:13,356] [INFO] Running command: fastANI --query /var/lib/cwl/stge95e018d-5fc9-488d-9e55-0b26ec196c50/GCA_027044905.1_ASM2704490v1_genomic.fna.gz --refList GCA_027044905.1_ASM2704490v1_genomic.fna/target_genomes.txt --output GCA_027044905.1_ASM2704490v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:27:20,419] [INFO] Task succeeded: fastANI
[2023-06-28 18:27:20,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58f2c344-c8c3-428e-a5a7-fd11b23b99f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:27:20,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58f2c344-c8c3-428e-a5a7-fd11b23b99f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:27:20,423] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:27:20,424] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:27:20,424] [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
Sulfurospirillum arcachonense	strain=DSM 9755	GCA_000597725.1	57666	57666	type	True	75.9548	57	429	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:27:20,425] [INFO] DFAST Taxonomy check result was written to GCA_027044905.1_ASM2704490v1_genomic.fna/tc_result.tsv
[2023-06-28 18:27:20,426] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:27:20,426] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:27:20,426] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58f2c344-c8c3-428e-a5a7-fd11b23b99f7/dqc_reference/checkm_data
[2023-06-28 18:27:20,427] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:27:20,457] [INFO] Task started: CheckM
[2023-06-28 18:27:20,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027044905.1_ASM2704490v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027044905.1_ASM2704490v1_genomic.fna/checkm_input GCA_027044905.1_ASM2704490v1_genomic.fna/checkm_result
[2023-06-28 18:27:37,822] [INFO] Task succeeded: CheckM
[2023-06-28 18:27:37,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:27:37,850] [INFO] ===== Completeness check finished =====
[2023-06-28 18:27:37,850] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:27:37,851] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027044905.1_ASM2704490v1_genomic.fna/markers.fasta)
[2023-06-28 18:27:37,851] [INFO] Task started: Blastn
[2023-06-28 18:27:37,852] [INFO] Running command: blastn -query GCA_027044905.1_ASM2704490v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58f2c344-c8c3-428e-a5a7-fd11b23b99f7/dqc_reference/reference_markers_gtdb.fasta -out GCA_027044905.1_ASM2704490v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:27:38,709] [INFO] Task succeeded: Blastn
[2023-06-28 18:27:38,714] [INFO] Selected 24 target genomes.
[2023-06-28 18:27:38,714] [INFO] Target genome list was writen to GCA_027044905.1_ASM2704490v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:27:38,724] [INFO] Task started: fastANI
[2023-06-28 18:27:38,725] [INFO] Running command: fastANI --query /var/lib/cwl/stge95e018d-5fc9-488d-9e55-0b26ec196c50/GCA_027044905.1_ASM2704490v1_genomic.fna.gz --refList GCA_027044905.1_ASM2704490v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027044905.1_ASM2704490v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:27:45,920] [INFO] Task succeeded: fastANI
[2023-06-28 18:27:45,925] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:27:45,926] [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_015488975.1	s__JAADDL01 sp015488975	98.0872	313	429	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__JAADDL01;g__JAADDL01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013153915.1	s__JAADDL01 sp013153915	76.3883	67	429	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__JAADDL01;g__JAADDL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:27:45,928] [INFO] GTDB search result was written to GCA_027044905.1_ASM2704490v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:27:45,929] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:27:45,932] [INFO] DFAST_QC result json was written to GCA_027044905.1_ASM2704490v1_genomic.fna/dqc_result.json
[2023-06-28 18:27:45,932] [INFO] DFAST_QC completed!
[2023-06-28 18:27:45,932] [INFO] Total running time: 0h0m42s