[2023-06-08 07:43:19,809] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:43:19,812] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:43:19,814] [INFO] DQC Reference Directory: /var/lib/cwl/stg35633bb7-4161-45ff-8219-361b2f2b3915/dqc_reference
[2023-06-08 07:43:21,049] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:43:21,050] [INFO] Task started: Prodigal
[2023-06-08 07:43:21,050] [INFO] Running command: gunzip -c /var/lib/cwl/stg424739d7-8a9c-49f2-a832-b125d9143bd4/GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna.gz | prodigal -d GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/cds.fna -a GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:43:24,168] [INFO] Task succeeded: Prodigal
[2023-06-08 07:43:24,169] [INFO] Task started: HMMsearch
[2023-06-08 07:43:24,169] [INFO] Running command: hmmsearch --tblout GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35633bb7-4161-45ff-8219-361b2f2b3915/dqc_reference/reference_markers.hmm GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:43:24,418] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:43:24,420] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg424739d7-8a9c-49f2-a832-b125d9143bd4/GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna.gz]
[2023-06-08 07:43:24,443] [INFO] Query marker FASTA was written to GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/markers.fasta
[2023-06-08 07:43:24,443] [INFO] Task started: Blastn
[2023-06-08 07:43:24,443] [INFO] Running command: blastn -query GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/markers.fasta -db /var/lib/cwl/stg35633bb7-4161-45ff-8219-361b2f2b3915/dqc_reference/reference_markers.fasta -out GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:43:25,038] [INFO] Task succeeded: Blastn
[2023-06-08 07:43:25,043] [INFO] Selected 17 target genomes.
[2023-06-08 07:43:25,044] [INFO] Target genome list was writen to GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/target_genomes.txt
[2023-06-08 07:43:25,046] [INFO] Task started: fastANI
[2023-06-08 07:43:25,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg424739d7-8a9c-49f2-a832-b125d9143bd4/GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna.gz --refList GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/target_genomes.txt --output GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:43:32,203] [INFO] Task succeeded: fastANI
[2023-06-08 07:43:32,204] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35633bb7-4161-45ff-8219-361b2f2b3915/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:43:32,205] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35633bb7-4161-45ff-8219-361b2f2b3915/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:43:32,212] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 07:43:32,212] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 07:43:32,212] [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
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	77.1962	71	478	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_000153885.1	39496	39496	suspected-type	True	77.085	69	478	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 07:43:32,215] [INFO] DFAST Taxonomy check result was written to GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/tc_result.tsv
[2023-06-08 07:43:32,216] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:43:32,216] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:43:32,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35633bb7-4161-45ff-8219-361b2f2b3915/dqc_reference/checkm_data
[2023-06-08 07:43:32,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:43:32,239] [INFO] Task started: CheckM
[2023-06-08 07:43:32,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/checkm_input GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/checkm_result
[2023-06-08 07:43:49,619] [INFO] Task succeeded: CheckM
[2023-06-08 07:43:49,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 07:43:49,646] [INFO] ===== Completeness check finished =====
[2023-06-08 07:43:49,647] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:43:49,647] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/markers.fasta)
[2023-06-08 07:43:49,647] [INFO] Task started: Blastn
[2023-06-08 07:43:49,647] [INFO] Running command: blastn -query GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/markers.fasta -db /var/lib/cwl/stg35633bb7-4161-45ff-8219-361b2f2b3915/dqc_reference/reference_markers_gtdb.fasta -out GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:43:50,529] [INFO] Task succeeded: Blastn
[2023-06-08 07:43:50,533] [INFO] Selected 7 target genomes.
[2023-06-08 07:43:50,534] [INFO] Target genome list was writen to GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:43:50,541] [INFO] Task started: fastANI
[2023-06-08 07:43:50,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg424739d7-8a9c-49f2-a832-b125d9143bd4/GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna.gz --refList GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/target_genomes_gtdb.txt --output GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:43:53,038] [INFO] Task succeeded: fastANI
[2023-06-08 07:43:53,049] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 07:43:53,049] [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_902793045.1	s__Eubacterium_G sp902793045	100.0	472	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002369135.1	s__Eubacterium_G sp002369135	94.0971	366	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	99.97	99.95	1.00	1.00	3	-
GCA_017514785.1	s__Eubacterium_G sp017514785	93.1123	312	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017965495.1	s__Eubacterium_G sp017965495	88.5461	323	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235555.1	s__Eubacterium_G sp905235555	87.8945	293	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017475235.1	s__Eubacterium_G sp017475235	87.6885	266	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774125.1	s__Eubacterium_G sp902774125	78.0941	99	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 07:43:53,051] [INFO] GTDB search result was written to GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/result_gtdb.tsv
[2023-06-08 07:43:53,052] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:43:53,056] [INFO] DFAST_QC result json was written to GCA_902793045.1_Rumen_uncultured_genome_RUG13824_genomic.fna/dqc_result.json
[2023-06-08 07:43:53,056] [INFO] DFAST_QC completed!
[2023-06-08 07:43:53,056] [INFO] Total running time: 0h0m33s