[2023-06-28 21:36:40,510] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:36:40,512] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:36:40,512] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf6a2b0d-dffc-4b7d-82fd-d9197313d62b/dqc_reference
[2023-06-28 21:36:41,744] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:36:41,745] [INFO] Task started: Prodigal
[2023-06-28 21:36:41,745] [INFO] Running command: gunzip -c /var/lib/cwl/stg94202b57-101e-4464-b715-290657803a84/GCA_017962825.1_ASM1796282v1_genomic.fna.gz | prodigal -d GCA_017962825.1_ASM1796282v1_genomic.fna/cds.fna -a GCA_017962825.1_ASM1796282v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:36:48,203] [INFO] Task succeeded: Prodigal
[2023-06-28 21:36:48,204] [INFO] Task started: HMMsearch
[2023-06-28 21:36:48,204] [INFO] Running command: hmmsearch --tblout GCA_017962825.1_ASM1796282v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf6a2b0d-dffc-4b7d-82fd-d9197313d62b/dqc_reference/reference_markers.hmm GCA_017962825.1_ASM1796282v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:36:48,480] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:36:48,482] [INFO] Found 6/6 markers.
[2023-06-28 21:36:48,520] [INFO] Query marker FASTA was written to GCA_017962825.1_ASM1796282v1_genomic.fna/markers.fasta
[2023-06-28 21:36:48,521] [INFO] Task started: Blastn
[2023-06-28 21:36:48,521] [INFO] Running command: blastn -query GCA_017962825.1_ASM1796282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf6a2b0d-dffc-4b7d-82fd-d9197313d62b/dqc_reference/reference_markers.fasta -out GCA_017962825.1_ASM1796282v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:36:49,161] [INFO] Task succeeded: Blastn
[2023-06-28 21:36:49,165] [INFO] Selected 29 target genomes.
[2023-06-28 21:36:49,165] [INFO] Target genome list was writen to GCA_017962825.1_ASM1796282v1_genomic.fna/target_genomes.txt
[2023-06-28 21:36:49,166] [INFO] Task started: fastANI
[2023-06-28 21:36:49,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg94202b57-101e-4464-b715-290657803a84/GCA_017962825.1_ASM1796282v1_genomic.fna.gz --refList GCA_017962825.1_ASM1796282v1_genomic.fna/target_genomes.txt --output GCA_017962825.1_ASM1796282v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:37:03,992] [INFO] Task succeeded: fastANI
[2023-06-28 21:37:03,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf6a2b0d-dffc-4b7d-82fd-d9197313d62b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:37:03,993] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf6a2b0d-dffc-4b7d-82fd-d9197313d62b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:37:03,995] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:37:03,995] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 21:37:03,996] [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
--------------------------------------------------------------------------------
[2023-06-28 21:37:03,998] [INFO] DFAST Taxonomy check result was written to GCA_017962825.1_ASM1796282v1_genomic.fna/tc_result.tsv
[2023-06-28 21:37:03,999] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:37:03,999] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:37:03,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf6a2b0d-dffc-4b7d-82fd-d9197313d62b/dqc_reference/checkm_data
[2023-06-28 21:37:04,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:37:04,037] [INFO] Task started: CheckM
[2023-06-28 21:37:04,038] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017962825.1_ASM1796282v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017962825.1_ASM1796282v1_genomic.fna/checkm_input GCA_017962825.1_ASM1796282v1_genomic.fna/checkm_result
[2023-06-28 21:37:29,885] [INFO] Task succeeded: CheckM
[2023-06-28 21:37:29,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 21:37:29,907] [INFO] ===== Completeness check finished =====
[2023-06-28 21:37:29,908] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:37:29,908] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017962825.1_ASM1796282v1_genomic.fna/markers.fasta)
[2023-06-28 21:37:29,908] [INFO] Task started: Blastn
[2023-06-28 21:37:29,908] [INFO] Running command: blastn -query GCA_017962825.1_ASM1796282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf6a2b0d-dffc-4b7d-82fd-d9197313d62b/dqc_reference/reference_markers_gtdb.fasta -out GCA_017962825.1_ASM1796282v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:37:30,916] [INFO] Task succeeded: Blastn
[2023-06-28 21:37:30,921] [INFO] Selected 10 target genomes.
[2023-06-28 21:37:30,921] [INFO] Target genome list was writen to GCA_017962825.1_ASM1796282v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:37:30,924] [INFO] Task started: fastANI
[2023-06-28 21:37:30,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg94202b57-101e-4464-b715-290657803a84/GCA_017962825.1_ASM1796282v1_genomic.fna.gz --refList GCA_017962825.1_ASM1796282v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017962825.1_ASM1796282v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:37:36,205] [INFO] Task succeeded: fastANI
[2023-06-28 21:37:36,216] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:37:36,217] [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_017962825.1	s__AC2028 sp017962825	100.0	898	906	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__AC2028	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016291475.1	s__AC2028 sp016291475	90.0425	661	906	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__AC2028	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017940415.1	s__AC2028 sp017940415	85.7468	593	906	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__AC2028	95.0	96.51	96.51	0.85	0.85	2	-
GCA_018056425.1	s__AC2028 sp018056425	84.891	519	906	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__AC2028	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902794095.1	s__AC2028 sp902794095	84.6025	484	906	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__AC2028	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000702085.1	s__AC2028 sp000702085	84.2598	581	906	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__AC2028	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 21:37:36,219] [INFO] GTDB search result was written to GCA_017962825.1_ASM1796282v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:37:36,220] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:37:36,223] [INFO] DFAST_QC result json was written to GCA_017962825.1_ASM1796282v1_genomic.fna/dqc_result.json
[2023-06-28 21:37:36,223] [INFO] DFAST_QC completed!
[2023-06-28 21:37:36,223] [INFO] Total running time: 0h0m56s