[2023-06-28 19:58:34,180] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:58:34,183] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:58:34,184] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0dc31f2-d4c3-4fee-b792-c8e9a38d2e20/dqc_reference
[2023-06-28 19:58:35,439] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:58:35,440] [INFO] Task started: Prodigal
[2023-06-28 19:58:35,440] [INFO] Running command: gunzip -c /var/lib/cwl/stgecce0cd0-79a4-4bab-96b2-d0cf8703626e/GCA_017467765.1_ASM1746776v1_genomic.fna.gz | prodigal -d GCA_017467765.1_ASM1746776v1_genomic.fna/cds.fna -a GCA_017467765.1_ASM1746776v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:58:40,211] [INFO] Task succeeded: Prodigal
[2023-06-28 19:58:40,211] [INFO] Task started: HMMsearch
[2023-06-28 19:58:40,211] [INFO] Running command: hmmsearch --tblout GCA_017467765.1_ASM1746776v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0dc31f2-d4c3-4fee-b792-c8e9a38d2e20/dqc_reference/reference_markers.hmm GCA_017467765.1_ASM1746776v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:58:40,385] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:58:40,386] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgecce0cd0-79a4-4bab-96b2-d0cf8703626e/GCA_017467765.1_ASM1746776v1_genomic.fna.gz]
[2023-06-28 19:58:40,410] [INFO] Query marker FASTA was written to GCA_017467765.1_ASM1746776v1_genomic.fna/markers.fasta
[2023-06-28 19:58:40,410] [INFO] Task started: Blastn
[2023-06-28 19:58:40,410] [INFO] Running command: blastn -query GCA_017467765.1_ASM1746776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0dc31f2-d4c3-4fee-b792-c8e9a38d2e20/dqc_reference/reference_markers.fasta -out GCA_017467765.1_ASM1746776v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:58:40,972] [INFO] Task succeeded: Blastn
[2023-06-28 19:58:40,978] [INFO] Selected 22 target genomes.
[2023-06-28 19:58:40,979] [INFO] Target genome list was writen to GCA_017467765.1_ASM1746776v1_genomic.fna/target_genomes.txt
[2023-06-28 19:58:40,983] [INFO] Task started: fastANI
[2023-06-28 19:58:40,983] [INFO] Running command: fastANI --query /var/lib/cwl/stgecce0cd0-79a4-4bab-96b2-d0cf8703626e/GCA_017467765.1_ASM1746776v1_genomic.fna.gz --refList GCA_017467765.1_ASM1746776v1_genomic.fna/target_genomes.txt --output GCA_017467765.1_ASM1746776v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:58:52,138] [INFO] Task succeeded: fastANI
[2023-06-28 19:58:52,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0dc31f2-d4c3-4fee-b792-c8e9a38d2e20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:58:52,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0dc31f2-d4c3-4fee-b792-c8e9a38d2e20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:58:52,141] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:58:52,141] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 19:58:52,141] [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 19:58:52,144] [INFO] DFAST Taxonomy check result was written to GCA_017467765.1_ASM1746776v1_genomic.fna/tc_result.tsv
[2023-06-28 19:58:52,144] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:58:52,145] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:58:52,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0dc31f2-d4c3-4fee-b792-c8e9a38d2e20/dqc_reference/checkm_data
[2023-06-28 19:58:52,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:58:52,174] [INFO] Task started: CheckM
[2023-06-28 19:58:52,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017467765.1_ASM1746776v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017467765.1_ASM1746776v1_genomic.fna/checkm_input GCA_017467765.1_ASM1746776v1_genomic.fna/checkm_result
[2023-06-28 19:59:12,335] [INFO] Task succeeded: CheckM
[2023-06-28 19:59:12,336] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:59:12,354] [INFO] ===== Completeness check finished =====
[2023-06-28 19:59:12,355] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:59:12,355] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017467765.1_ASM1746776v1_genomic.fna/markers.fasta)
[2023-06-28 19:59:12,355] [INFO] Task started: Blastn
[2023-06-28 19:59:12,355] [INFO] Running command: blastn -query GCA_017467765.1_ASM1746776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0dc31f2-d4c3-4fee-b792-c8e9a38d2e20/dqc_reference/reference_markers_gtdb.fasta -out GCA_017467765.1_ASM1746776v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:59:13,149] [INFO] Task succeeded: Blastn
[2023-06-28 19:59:13,153] [INFO] Selected 11 target genomes.
[2023-06-28 19:59:13,154] [INFO] Target genome list was writen to GCA_017467765.1_ASM1746776v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:59:13,156] [INFO] Task started: fastANI
[2023-06-28 19:59:13,156] [INFO] Running command: fastANI --query /var/lib/cwl/stgecce0cd0-79a4-4bab-96b2-d0cf8703626e/GCA_017467765.1_ASM1746776v1_genomic.fna.gz --refList GCA_017467765.1_ASM1746776v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017467765.1_ASM1746776v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:59:17,164] [INFO] Task succeeded: fastANI
[2023-06-28 19:59:17,170] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 19:59:17,171] [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_017624855.1	s__UBA3766 sp017624855	97.2522	417	629	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	97.27	97.27	0.66	0.66	2	conclusive
GCA_017473115.1	s__UBA3766 sp017473115	81.0544	333	629	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017622505.1	s__UBA3766 sp017622505	80.919	350	629	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057025.1	s__UBA3766 sp015057025	80.8347	366	629	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017473905.1	s__UBA3766 sp017473905	77.6251	132	629	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056945.1	s__UBA3766 sp015056945	76.981	108	629	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 19:59:17,172] [INFO] GTDB search result was written to GCA_017467765.1_ASM1746776v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:59:17,173] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:59:17,175] [INFO] DFAST_QC result json was written to GCA_017467765.1_ASM1746776v1_genomic.fna/dqc_result.json
[2023-06-28 19:59:17,175] [INFO] DFAST_QC completed!
[2023-06-28 19:59:17,176] [INFO] Total running time: 0h0m43s