[2023-06-05 18:05:10,746] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:05:10,748] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:05:10,748] [INFO] DQC Reference Directory: /var/lib/cwl/stg544d3433-e48d-49e6-9264-ff0cb1bd4af5/dqc_reference
[2023-06-05 18:05:11,811] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:05:11,811] [INFO] Task started: Prodigal
[2023-06-05 18:05:11,811] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c170553-c8a5-4252-aab6-66f19e6df53f/GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna.gz | prodigal -d GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/cds.fna -a GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:05:17,775] [INFO] Task succeeded: Prodigal
[2023-06-05 18:05:17,776] [INFO] Task started: HMMsearch
[2023-06-05 18:05:17,776] [INFO] Running command: hmmsearch --tblout GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg544d3433-e48d-49e6-9264-ff0cb1bd4af5/dqc_reference/reference_markers.hmm GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:05:17,992] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:05:17,993] [INFO] Found 6/6 markers.
[2023-06-05 18:05:18,028] [INFO] Query marker FASTA was written to GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/markers.fasta
[2023-06-05 18:05:18,028] [INFO] Task started: Blastn
[2023-06-05 18:05:18,028] [INFO] Running command: blastn -query GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/markers.fasta -db /var/lib/cwl/stg544d3433-e48d-49e6-9264-ff0cb1bd4af5/dqc_reference/reference_markers.fasta -out GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:05:18,649] [INFO] Task succeeded: Blastn
[2023-06-05 18:05:18,651] [INFO] Selected 26 target genomes.
[2023-06-05 18:05:18,652] [INFO] Target genome list was writen to GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/target_genomes.txt
[2023-06-05 18:05:18,658] [INFO] Task started: fastANI
[2023-06-05 18:05:18,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c170553-c8a5-4252-aab6-66f19e6df53f/GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna.gz --refList GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/target_genomes.txt --output GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:05:35,120] [INFO] Task succeeded: fastANI
[2023-06-05 18:05:35,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg544d3433-e48d-49e6-9264-ff0cb1bd4af5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:05:35,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg544d3433-e48d-49e6-9264-ff0cb1bd4af5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:05:35,124] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:05:35,124] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:05:35,124] [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
Clostridium vitabionis	strain=YH-T4B42	GCA_015351765.1	2784388	2784388	type	True	76.1199	55	787	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:05:35,127] [INFO] DFAST Taxonomy check result was written to GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/tc_result.tsv
[2023-06-05 18:05:35,127] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:05:35,127] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:05:35,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg544d3433-e48d-49e6-9264-ff0cb1bd4af5/dqc_reference/checkm_data
[2023-06-05 18:05:35,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:05:35,163] [INFO] Task started: CheckM
[2023-06-05 18:05:35,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/checkm_input GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/checkm_result
[2023-06-05 18:05:58,268] [INFO] Task succeeded: CheckM
[2023-06-05 18:05:58,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:05:58,285] [INFO] ===== Completeness check finished =====
[2023-06-05 18:05:58,285] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:05:58,286] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/markers.fasta)
[2023-06-05 18:05:58,286] [INFO] Task started: Blastn
[2023-06-05 18:05:58,286] [INFO] Running command: blastn -query GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/markers.fasta -db /var/lib/cwl/stg544d3433-e48d-49e6-9264-ff0cb1bd4af5/dqc_reference/reference_markers_gtdb.fasta -out GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:05:59,377] [INFO] Task succeeded: Blastn
[2023-06-05 18:05:59,392] [INFO] Selected 20 target genomes.
[2023-06-05 18:05:59,392] [INFO] Target genome list was writen to GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:05:59,442] [INFO] Task started: fastANI
[2023-06-05 18:05:59,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c170553-c8a5-4252-aab6-66f19e6df53f/GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna.gz --refList GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/target_genomes_gtdb.txt --output GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:06:07,913] [INFO] Task succeeded: fastANI
[2023-06-05 18:06:07,918] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:06:07,918] [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_900314255.1	s__UBA4285 sp900314255	99.2106	635	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA4285	95.0	99.23	99.23	0.85	0.85	2	conclusive
GCA_903789615.1	s__UBA4285 sp903789615	85.5514	600	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA4285	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002394965.1	s__UBA4285 sp002394965	83.6278	468	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA4285	95.0	98.87	98.87	0.86	0.86	2	-
GCA_900318405.1	s__Bilifractor sp900318405	76.2694	52	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	99.33	99.23	0.95	0.94	3	-
GCF_015351765.1	s__Clostridium_R vitabionis	76.0941	56	787	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_R	95.0	98.49	98.47	0.96	0.96	4	-
--------------------------------------------------------------------------------
[2023-06-05 18:06:07,930] [INFO] GTDB search result was written to GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/result_gtdb.tsv
[2023-06-05 18:06:07,931] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:06:07,948] [INFO] DFAST_QC result json was written to GCA_902781445.1_Rumen_uncultured_genome_RUG12668_genomic.fna/dqc_result.json
[2023-06-05 18:06:07,948] [INFO] DFAST_QC completed!
[2023-06-05 18:06:07,948] [INFO] Total running time: 0h0m57s