[2023-06-08 11:46:45,119] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:46:45,122] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:46:45,123] [INFO] DQC Reference Directory: /var/lib/cwl/stga8307a9a-3aa2-456d-865d-65081baac81b/dqc_reference
[2023-06-08 11:46:46,462] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:46:46,463] [INFO] Task started: Prodigal
[2023-06-08 11:46:46,463] [INFO] Running command: gunzip -c /var/lib/cwl/stg64ab38d3-c44d-48d3-9559-e91ca79a1ec1/GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna.gz | prodigal -d GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/cds.fna -a GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:46:52,279] [INFO] Task succeeded: Prodigal
[2023-06-08 11:46:52,279] [INFO] Task started: HMMsearch
[2023-06-08 11:46:52,279] [INFO] Running command: hmmsearch --tblout GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8307a9a-3aa2-456d-865d-65081baac81b/dqc_reference/reference_markers.hmm GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:46:52,592] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:46:52,593] [INFO] Found 6/6 markers.
[2023-06-08 11:46:52,644] [INFO] Query marker FASTA was written to GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/markers.fasta
[2023-06-08 11:46:52,644] [INFO] Task started: Blastn
[2023-06-08 11:46:52,645] [INFO] Running command: blastn -query GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/markers.fasta -db /var/lib/cwl/stga8307a9a-3aa2-456d-865d-65081baac81b/dqc_reference/reference_markers.fasta -out GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:46:53,310] [INFO] Task succeeded: Blastn
[2023-06-08 11:46:53,314] [INFO] Selected 18 target genomes.
[2023-06-08 11:46:53,315] [INFO] Target genome list was writen to GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/target_genomes.txt
[2023-06-08 11:46:53,317] [INFO] Task started: fastANI
[2023-06-08 11:46:53,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg64ab38d3-c44d-48d3-9559-e91ca79a1ec1/GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna.gz --refList GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/target_genomes.txt --output GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:47:02,457] [INFO] Task succeeded: fastANI
[2023-06-08 11:47:02,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8307a9a-3aa2-456d-865d-65081baac81b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:47:02,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8307a9a-3aa2-456d-865d-65081baac81b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:47:02,459] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:47:02,459] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 11:47:02,460] [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
--------------------------------------------------------------------------------
[2023-06-08 11:47:02,462] [INFO] DFAST Taxonomy check result was written to GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/tc_result.tsv
[2023-06-08 11:47:02,462] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:47:02,463] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:47:02,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8307a9a-3aa2-456d-865d-65081baac81b/dqc_reference/checkm_data
[2023-06-08 11:47:02,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:47:02,497] [INFO] Task started: CheckM
[2023-06-08 11:47:02,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/checkm_input GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/checkm_result
[2023-06-08 11:47:27,669] [INFO] Task succeeded: CheckM
[2023-06-08 11:47:27,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:47:27,692] [INFO] ===== Completeness check finished =====
[2023-06-08 11:47:27,692] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:47:27,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/markers.fasta)
[2023-06-08 11:47:27,693] [INFO] Task started: Blastn
[2023-06-08 11:47:27,693] [INFO] Running command: blastn -query GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/markers.fasta -db /var/lib/cwl/stga8307a9a-3aa2-456d-865d-65081baac81b/dqc_reference/reference_markers_gtdb.fasta -out GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:47:28,721] [INFO] Task succeeded: Blastn
[2023-06-08 11:47:28,726] [INFO] Selected 16 target genomes.
[2023-06-08 11:47:28,726] [INFO] Target genome list was writen to GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:47:28,730] [INFO] Task started: fastANI
[2023-06-08 11:47:28,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg64ab38d3-c44d-48d3-9559-e91ca79a1ec1/GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna.gz --refList GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/target_genomes_gtdb.txt --output GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:47:37,102] [INFO] Task succeeded: fastANI
[2023-06-08 11:47:37,115] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:47:37,115] [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_902778175.1	s__UBA1213 sp902778175	100.0	826	833	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	98.60	98.60	0.84	0.84	2	conclusive
GCA_902801055.1	s__UBA1213 sp902801055	83.3116	391	833	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902763365.1	s__UBA1213 sp902763365	80.1342	223	833	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902764235.1	s__UBA1213 sp902764235	79.4249	252	833	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766585.1	s__UBA1213 sp902766585	78.462	168	833	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315875.1	s__UBA1213 sp900315875	78.3005	180	833	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	99.46	99.46	0.95	0.95	2	-
GCA_017475765.1	s__UBA1213 sp017475765	78.1594	178	833	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902773025.1	s__UBA1213 sp902773025	77.5818	186	833	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316485.1	s__UBA1213 sp900316485	77.5209	162	833	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	99.79	99.79	0.96	0.96	2	-
GCA_900320235.1	s__UBA1213 sp900320235	77.3962	126	833	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	99.73	99.73	0.83	0.83	2	-
GCA_900317395.1	s__UBA1213 sp900317395	77.2555	119	833	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	99.75	99.75	0.88	0.88	2	-
GCA_902766305.1	s__UBA1213 sp902766305	76.57	109	833	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1213	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 11:47:37,117] [INFO] GTDB search result was written to GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/result_gtdb.tsv
[2023-06-08 11:47:37,118] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:47:37,125] [INFO] DFAST_QC result json was written to GCA_902778175.1_Rumen_uncultured_genome_RUG12347_genomic.fna/dqc_result.json
[2023-06-08 11:47:37,125] [INFO] DFAST_QC completed!
[2023-06-08 11:47:37,125] [INFO] Total running time: 0h0m52s