[2023-06-29 13:50:26,747] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:50:26,750] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:50:26,750] [INFO] DQC Reference Directory: /var/lib/cwl/stg331dd92a-7f8e-4e84-8d30-8e2cc3a2be83/dqc_reference
[2023-06-29 13:50:28,045] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:50:28,046] [INFO] Task started: Prodigal
[2023-06-29 13:50:28,046] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4b6014f-57d4-48a3-8e8b-bb0b847919a1/GCA_021158285.1_ASM2115828v1_genomic.fna.gz | prodigal -d GCA_021158285.1_ASM2115828v1_genomic.fna/cds.fna -a GCA_021158285.1_ASM2115828v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:50:30,385] [INFO] Task succeeded: Prodigal
[2023-06-29 13:50:30,386] [INFO] Task started: HMMsearch
[2023-06-29 13:50:30,386] [INFO] Running command: hmmsearch --tblout GCA_021158285.1_ASM2115828v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg331dd92a-7f8e-4e84-8d30-8e2cc3a2be83/dqc_reference/reference_markers.hmm GCA_021158285.1_ASM2115828v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:50:30,593] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:50:30,595] [INFO] Found 6/6 markers.
[2023-06-29 13:50:30,612] [INFO] Query marker FASTA was written to GCA_021158285.1_ASM2115828v1_genomic.fna/markers.fasta
[2023-06-29 13:50:30,613] [INFO] Task started: Blastn
[2023-06-29 13:50:30,613] [INFO] Running command: blastn -query GCA_021158285.1_ASM2115828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg331dd92a-7f8e-4e84-8d30-8e2cc3a2be83/dqc_reference/reference_markers.fasta -out GCA_021158285.1_ASM2115828v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:50:31,196] [INFO] Task succeeded: Blastn
[2023-06-29 13:50:31,201] [INFO] Selected 10 target genomes.
[2023-06-29 13:50:31,202] [INFO] Target genome list was writen to GCA_021158285.1_ASM2115828v1_genomic.fna/target_genomes.txt
[2023-06-29 13:50:31,204] [INFO] Task started: fastANI
[2023-06-29 13:50:31,204] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4b6014f-57d4-48a3-8e8b-bb0b847919a1/GCA_021158285.1_ASM2115828v1_genomic.fna.gz --refList GCA_021158285.1_ASM2115828v1_genomic.fna/target_genomes.txt --output GCA_021158285.1_ASM2115828v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:50:35,501] [INFO] Task succeeded: fastANI
[2023-06-29 13:50:35,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg331dd92a-7f8e-4e84-8d30-8e2cc3a2be83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:50:35,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg331dd92a-7f8e-4e84-8d30-8e2cc3a2be83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:50:35,505] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:50:35,506] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 13:50:35,506] [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
--------------------------------------------------------------------------------
[2023-06-29 13:50:35,508] [INFO] DFAST Taxonomy check result was written to GCA_021158285.1_ASM2115828v1_genomic.fna/tc_result.tsv
[2023-06-29 13:50:35,509] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:50:35,509] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:50:35,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg331dd92a-7f8e-4e84-8d30-8e2cc3a2be83/dqc_reference/checkm_data
[2023-06-29 13:50:35,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:50:35,531] [INFO] Task started: CheckM
[2023-06-29 13:50:35,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021158285.1_ASM2115828v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021158285.1_ASM2115828v1_genomic.fna/checkm_input GCA_021158285.1_ASM2115828v1_genomic.fna/checkm_result
[2023-06-29 13:50:50,904] [INFO] Task succeeded: CheckM
[2023-06-29 13:50:50,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:50:50,930] [INFO] ===== Completeness check finished =====
[2023-06-29 13:50:50,930] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:50:50,931] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021158285.1_ASM2115828v1_genomic.fna/markers.fasta)
[2023-06-29 13:50:50,931] [INFO] Task started: Blastn
[2023-06-29 13:50:50,931] [INFO] Running command: blastn -query GCA_021158285.1_ASM2115828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg331dd92a-7f8e-4e84-8d30-8e2cc3a2be83/dqc_reference/reference_markers_gtdb.fasta -out GCA_021158285.1_ASM2115828v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:50:51,706] [INFO] Task succeeded: Blastn
[2023-06-29 13:50:51,710] [INFO] Selected 14 target genomes.
[2023-06-29 13:50:51,710] [INFO] Target genome list was writen to GCA_021158285.1_ASM2115828v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:50:51,726] [INFO] Task started: fastANI
[2023-06-29 13:50:51,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4b6014f-57d4-48a3-8e8b-bb0b847919a1/GCA_021158285.1_ASM2115828v1_genomic.fna.gz --refList GCA_021158285.1_ASM2115828v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021158285.1_ASM2115828v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:50:57,043] [INFO] Task succeeded: fastANI
[2023-06-29 13:50:57,046] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 13:50:57,047] [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_003650285.1	s__UBA646 sp003650285	98.6013	223	368	d__Bacteria;p__Caldisericota;c__Caldisericia;o__Caldisericales;f__Caldisericaceae;g__UBA646	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002299965.1	s__UBA646 sp002299965	91.0866	291	368	d__Bacteria;p__Caldisericota;c__Caldisericia;o__Caldisericales;f__Caldisericaceae;g__UBA646	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:50:57,049] [INFO] GTDB search result was written to GCA_021158285.1_ASM2115828v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:50:57,049] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:50:57,052] [INFO] DFAST_QC result json was written to GCA_021158285.1_ASM2115828v1_genomic.fna/dqc_result.json
[2023-06-29 13:50:57,052] [INFO] DFAST_QC completed!
[2023-06-29 13:50:57,052] [INFO] Total running time: 0h0m30s