[2023-06-07 23:37:29,795] [INFO] DFAST_QC pipeline started.
[2023-06-07 23:37:29,798] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 23:37:29,798] [INFO] DQC Reference Directory: /var/lib/cwl/stgebbbdb63-09be-4268-865b-d9b55015c862/dqc_reference
[2023-06-07 23:37:31,278] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 23:37:31,279] [INFO] Task started: Prodigal
[2023-06-07 23:37:31,279] [INFO] Running command: gunzip -c /var/lib/cwl/stg93312bb0-b926-4590-b00b-a2851f999579/GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna.gz | prodigal -d GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/cds.fna -a GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 23:37:36,062] [INFO] Task succeeded: Prodigal
[2023-06-07 23:37:36,062] [INFO] Task started: HMMsearch
[2023-06-07 23:37:36,062] [INFO] Running command: hmmsearch --tblout GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebbbdb63-09be-4268-865b-d9b55015c862/dqc_reference/reference_markers.hmm GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/protein.faa > /dev/null
[2023-06-07 23:37:36,267] [INFO] Task succeeded: HMMsearch
[2023-06-07 23:37:36,268] [INFO] Found 6/6 markers.
[2023-06-07 23:37:36,292] [INFO] Query marker FASTA was written to GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/markers.fasta
[2023-06-07 23:37:36,292] [INFO] Task started: Blastn
[2023-06-07 23:37:36,292] [INFO] Running command: blastn -query GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/markers.fasta -db /var/lib/cwl/stgebbbdb63-09be-4268-865b-d9b55015c862/dqc_reference/reference_markers.fasta -out GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:37:36,938] [INFO] Task succeeded: Blastn
[2023-06-07 23:37:36,942] [INFO] Selected 29 target genomes.
[2023-06-07 23:37:36,943] [INFO] Target genome list was writen to GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/target_genomes.txt
[2023-06-07 23:37:36,947] [INFO] Task started: fastANI
[2023-06-07 23:37:36,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg93312bb0-b926-4590-b00b-a2851f999579/GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna.gz --refList GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/target_genomes.txt --output GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 23:37:56,399] [INFO] Task succeeded: fastANI
[2023-06-07 23:37:56,399] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebbbdb63-09be-4268-865b-d9b55015c862/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 23:37:56,399] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebbbdb63-09be-4268-865b-d9b55015c862/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 23:37:56,401] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 23:37:56,401] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 23:37:56,401] [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
--------------------------------------------------------------------------------
[2023-06-07 23:37:56,403] [INFO] DFAST Taxonomy check result was written to GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/tc_result.tsv
[2023-06-07 23:37:56,404] [INFO] ===== Taxonomy check completed =====
[2023-06-07 23:37:56,404] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 23:37:56,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebbbdb63-09be-4268-865b-d9b55015c862/dqc_reference/checkm_data
[2023-06-07 23:37:56,407] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 23:37:56,430] [INFO] Task started: CheckM
[2023-06-07 23:37:56,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/checkm_input GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/checkm_result
[2023-06-07 23:38:16,525] [INFO] Task succeeded: CheckM
[2023-06-07 23:38:16,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 1.85%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 23:38:16,545] [INFO] ===== Completeness check finished =====
[2023-06-07 23:38:16,545] [INFO] ===== Start GTDB Search =====
[2023-06-07 23:38:16,545] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/markers.fasta)
[2023-06-07 23:38:16,545] [INFO] Task started: Blastn
[2023-06-07 23:38:16,546] [INFO] Running command: blastn -query GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/markers.fasta -db /var/lib/cwl/stgebbbdb63-09be-4268-865b-d9b55015c862/dqc_reference/reference_markers_gtdb.fasta -out GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:38:17,622] [INFO] Task succeeded: Blastn
[2023-06-07 23:38:17,626] [INFO] Selected 19 target genomes.
[2023-06-07 23:38:17,626] [INFO] Target genome list was writen to GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 23:38:17,634] [INFO] Task started: fastANI
[2023-06-07 23:38:17,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg93312bb0-b926-4590-b00b-a2851f999579/GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna.gz --refList GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/target_genomes_gtdb.txt --output GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 23:38:25,284] [INFO] Task succeeded: fastANI
[2023-06-07 23:38:25,296] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 23:38:25,296] [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_902766175.1	s__Stomatobaculum sp902766175	100.0	623	633	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Stomatobaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902793685.1	s__Stomatobaculum sp902793685	77.6462	154	633	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Stomatobaculum	95.0	97.67	97.61	0.89	0.87	3	-
GCA_017449925.1	s__Stomatobaculum sp017449925	77.5406	97	633	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Stomatobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766415.1	s__Stomatobaculum sp902766415	77.4348	119	633	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Stomatobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000242235.1	s__Stomatobaculum longum	77.4344	112	633	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Stomatobaculum	95.0	97.78	97.78	0.96	0.96	2	-
GCA_902780465.1	s__Stomatobaculum sp902780465	77.4119	124	633	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Stomatobaculum	95.0	97.77	97.33	0.79	0.76	4	-
GCF_003014445.1	s__Stomatobaculum naviforme	77.2688	117	633	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Stomatobaculum	95.0	100.00	100.00	0.99	0.99	3	-
GCA_905370385.1	s__Stomatobaculum longum_A	77.0786	93	633	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Stomatobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114845.1	s__Lachnoclostridium_A stercoripullorum	76.5495	51	633	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.44	98.44	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-06-07 23:38:25,298] [INFO] GTDB search result was written to GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/result_gtdb.tsv
[2023-06-07 23:38:25,302] [INFO] ===== GTDB Search completed =====
[2023-06-07 23:38:25,304] [INFO] DFAST_QC result json was written to GCA_902766175.1_Rumen_uncultured_genome_RUG11135_genomic.fna/dqc_result.json
[2023-06-07 23:38:25,305] [INFO] DFAST_QC completed!
[2023-06-07 23:38:25,305] [INFO] Total running time: 0h0m56s