[2023-06-28 04:51:28,354] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:51:28,356] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:51:28,356] [INFO] DQC Reference Directory: /var/lib/cwl/stg30be277b-955a-4802-b3ab-89ff7bac48dc/dqc_reference
[2023-06-28 04:51:29,498] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:51:29,499] [INFO] Task started: Prodigal
[2023-06-28 04:51:29,499] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b0a2f04-399c-41c0-b7d6-948271db8e15/GCA_019310865.1_ASM1931086v1_genomic.fna.gz | prodigal -d GCA_019310865.1_ASM1931086v1_genomic.fna/cds.fna -a GCA_019310865.1_ASM1931086v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:51:40,668] [INFO] Task succeeded: Prodigal
[2023-06-28 04:51:40,669] [INFO] Task started: HMMsearch
[2023-06-28 04:51:40,669] [INFO] Running command: hmmsearch --tblout GCA_019310865.1_ASM1931086v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30be277b-955a-4802-b3ab-89ff7bac48dc/dqc_reference/reference_markers.hmm GCA_019310865.1_ASM1931086v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:51:40,935] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:51:40,936] [INFO] Found 6/6 markers.
[2023-06-28 04:51:40,976] [INFO] Query marker FASTA was written to GCA_019310865.1_ASM1931086v1_genomic.fna/markers.fasta
[2023-06-28 04:51:40,976] [INFO] Task started: Blastn
[2023-06-28 04:51:40,976] [INFO] Running command: blastn -query GCA_019310865.1_ASM1931086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30be277b-955a-4802-b3ab-89ff7bac48dc/dqc_reference/reference_markers.fasta -out GCA_019310865.1_ASM1931086v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:51:41,539] [INFO] Task succeeded: Blastn
[2023-06-28 04:51:41,542] [INFO] Selected 26 target genomes.
[2023-06-28 04:51:41,543] [INFO] Target genome list was writen to GCA_019310865.1_ASM1931086v1_genomic.fna/target_genomes.txt
[2023-06-28 04:51:41,544] [INFO] Task started: fastANI
[2023-06-28 04:51:41,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b0a2f04-399c-41c0-b7d6-948271db8e15/GCA_019310865.1_ASM1931086v1_genomic.fna.gz --refList GCA_019310865.1_ASM1931086v1_genomic.fna/target_genomes.txt --output GCA_019310865.1_ASM1931086v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:51:57,167] [INFO] Task succeeded: fastANI
[2023-06-28 04:51:57,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30be277b-955a-4802-b3ab-89ff7bac48dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:51:57,168] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30be277b-955a-4802-b3ab-89ff7bac48dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:51:57,172] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:51:57,172] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 04:51:57,172] [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
Desulfosarcina ovata subsp. ovata	strain=oXyS1	GCA_009689005.1	2752305	83564	type	True	75.8407	57	1237	95	below_threshold
Desulfosarcina ovata subsp. sediminis	strain=28bB2T	GCA_009688985.1	885957	83564	type	True	75.7491	57	1237	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 04:51:57,174] [INFO] DFAST Taxonomy check result was written to GCA_019310865.1_ASM1931086v1_genomic.fna/tc_result.tsv
[2023-06-28 04:51:57,175] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:51:57,175] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:51:57,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30be277b-955a-4802-b3ab-89ff7bac48dc/dqc_reference/checkm_data
[2023-06-28 04:51:57,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:51:57,220] [INFO] Task started: CheckM
[2023-06-28 04:51:57,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310865.1_ASM1931086v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310865.1_ASM1931086v1_genomic.fna/checkm_input GCA_019310865.1_ASM1931086v1_genomic.fna/checkm_result
[2023-06-28 04:52:34,064] [INFO] Task succeeded: CheckM
[2023-06-28 04:52:34,065] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 04:52:34,080] [INFO] ===== Completeness check finished =====
[2023-06-28 04:52:34,081] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:52:34,081] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310865.1_ASM1931086v1_genomic.fna/markers.fasta)
[2023-06-28 04:52:34,081] [INFO] Task started: Blastn
[2023-06-28 04:52:34,081] [INFO] Running command: blastn -query GCA_019310865.1_ASM1931086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30be277b-955a-4802-b3ab-89ff7bac48dc/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310865.1_ASM1931086v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:52:34,805] [INFO] Task succeeded: Blastn
[2023-06-28 04:52:34,808] [INFO] Selected 27 target genomes.
[2023-06-28 04:52:34,808] [INFO] Target genome list was writen to GCA_019310865.1_ASM1931086v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:52:34,815] [INFO] Task started: fastANI
[2023-06-28 04:52:34,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b0a2f04-399c-41c0-b7d6-948271db8e15/GCA_019310865.1_ASM1931086v1_genomic.fna.gz --refList GCA_019310865.1_ASM1931086v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310865.1_ASM1931086v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:52:50,728] [INFO] Task succeeded: fastANI
[2023-06-28 04:52:50,730] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 04:52:50,730] [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
--------------------------------------------------------------------------------
[2023-06-28 04:52:50,732] [INFO] GTDB search result was written to GCA_019310865.1_ASM1931086v1_genomic.fna/result_gtdb.tsv
[2023-06-28 04:52:50,744] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:52:50,746] [INFO] DFAST_QC result json was written to GCA_019310865.1_ASM1931086v1_genomic.fna/dqc_result.json
[2023-06-28 04:52:50,746] [INFO] DFAST_QC completed!
[2023-06-28 04:52:50,746] [INFO] Total running time: 0h1m22s