[2023-06-05 00:14:19,767] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:14:19,770] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:14:19,770] [INFO] DQC Reference Directory: /var/lib/cwl/stg88a767a8-4304-4d27-b945-2c7a059f54d1/dqc_reference
[2023-06-05 00:14:22,390] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:14:22,392] [INFO] Task started: Prodigal
[2023-06-05 00:14:22,392] [INFO] Running command: gunzip -c /var/lib/cwl/stga65dcfde-a992-480c-b8f8-b92baa495c1f/GCA_934277975.1_ERR7745329_bin.96_genomic.fna.gz | prodigal -d GCA_934277975.1_ERR7745329_bin.96_genomic.fna/cds.fna -a GCA_934277975.1_ERR7745329_bin.96_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:14:25,451] [INFO] Task succeeded: Prodigal
[2023-06-05 00:14:25,451] [INFO] Task started: HMMsearch
[2023-06-05 00:14:25,451] [INFO] Running command: hmmsearch --tblout GCA_934277975.1_ERR7745329_bin.96_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88a767a8-4304-4d27-b945-2c7a059f54d1/dqc_reference/reference_markers.hmm GCA_934277975.1_ERR7745329_bin.96_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:14:25,631] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:14:25,633] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga65dcfde-a992-480c-b8f8-b92baa495c1f/GCA_934277975.1_ERR7745329_bin.96_genomic.fna.gz]
[2023-06-05 00:14:25,649] [INFO] Query marker FASTA was written to GCA_934277975.1_ERR7745329_bin.96_genomic.fna/markers.fasta
[2023-06-05 00:14:25,650] [INFO] Task started: Blastn
[2023-06-05 00:14:25,650] [INFO] Running command: blastn -query GCA_934277975.1_ERR7745329_bin.96_genomic.fna/markers.fasta -db /var/lib/cwl/stg88a767a8-4304-4d27-b945-2c7a059f54d1/dqc_reference/reference_markers.fasta -out GCA_934277975.1_ERR7745329_bin.96_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:14:26,198] [INFO] Task succeeded: Blastn
[2023-06-05 00:14:26,203] [INFO] Selected 9 target genomes.
[2023-06-05 00:14:26,204] [INFO] Target genome list was writen to GCA_934277975.1_ERR7745329_bin.96_genomic.fna/target_genomes.txt
[2023-06-05 00:14:26,207] [INFO] Task started: fastANI
[2023-06-05 00:14:26,207] [INFO] Running command: fastANI --query /var/lib/cwl/stga65dcfde-a992-480c-b8f8-b92baa495c1f/GCA_934277975.1_ERR7745329_bin.96_genomic.fna.gz --refList GCA_934277975.1_ERR7745329_bin.96_genomic.fna/target_genomes.txt --output GCA_934277975.1_ERR7745329_bin.96_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:14:28,886] [INFO] Task succeeded: fastANI
[2023-06-05 00:14:28,886] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88a767a8-4304-4d27-b945-2c7a059f54d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:14:28,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88a767a8-4304-4d27-b945-2c7a059f54d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:14:28,889] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:14:28,889] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 00:14:28,889] [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
--------------------------------------------------------------------------------
[2023-06-05 00:14:28,891] [INFO] DFAST Taxonomy check result was written to GCA_934277975.1_ERR7745329_bin.96_genomic.fna/tc_result.tsv
[2023-06-05 00:14:28,892] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:14:28,892] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:14:28,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88a767a8-4304-4d27-b945-2c7a059f54d1/dqc_reference/checkm_data
[2023-06-05 00:14:28,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:14:28,912] [INFO] Task started: CheckM
[2023-06-05 00:14:28,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934277975.1_ERR7745329_bin.96_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934277975.1_ERR7745329_bin.96_genomic.fna/checkm_input GCA_934277975.1_ERR7745329_bin.96_genomic.fna/checkm_result
[2023-06-05 00:14:45,802] [INFO] Task succeeded: CheckM
[2023-06-05 00:14:45,803] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:14:45,825] [INFO] ===== Completeness check finished =====
[2023-06-05 00:14:45,825] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:14:45,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934277975.1_ERR7745329_bin.96_genomic.fna/markers.fasta)
[2023-06-05 00:14:45,831] [INFO] Task started: Blastn
[2023-06-05 00:14:45,831] [INFO] Running command: blastn -query GCA_934277975.1_ERR7745329_bin.96_genomic.fna/markers.fasta -db /var/lib/cwl/stg88a767a8-4304-4d27-b945-2c7a059f54d1/dqc_reference/reference_markers_gtdb.fasta -out GCA_934277975.1_ERR7745329_bin.96_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:14:46,528] [INFO] Task succeeded: Blastn
[2023-06-05 00:14:46,533] [INFO] Selected 13 target genomes.
[2023-06-05 00:14:46,534] [INFO] Target genome list was writen to GCA_934277975.1_ERR7745329_bin.96_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:14:46,651] [INFO] Task started: fastANI
[2023-06-05 00:14:46,652] [INFO] Running command: fastANI --query /var/lib/cwl/stga65dcfde-a992-480c-b8f8-b92baa495c1f/GCA_934277975.1_ERR7745329_bin.96_genomic.fna.gz --refList GCA_934277975.1_ERR7745329_bin.96_genomic.fna/target_genomes_gtdb.txt --output GCA_934277975.1_ERR7745329_bin.96_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:14:50,473] [INFO] Task succeeded: fastANI
[2023-06-05 00:14:50,480] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 00:14:50,481] [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_001940825.1	s__UBA9732 sp001940825	87.1549	262	324	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA9732	95.0	96.97	96.95	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2023-06-05 00:14:50,483] [INFO] GTDB search result was written to GCA_934277975.1_ERR7745329_bin.96_genomic.fna/result_gtdb.tsv
[2023-06-05 00:14:50,483] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:14:50,486] [INFO] DFAST_QC result json was written to GCA_934277975.1_ERR7745329_bin.96_genomic.fna/dqc_result.json
[2023-06-05 00:14:50,487] [INFO] DFAST_QC completed!
[2023-06-05 00:14:50,487] [INFO] Total running time: 0h0m31s