[2023-06-05 02:46:50,222] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:46:50,225] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:46:50,225] [INFO] DQC Reference Directory: /var/lib/cwl/stge62b0ffb-b522-4905-b607-7c4c7d52d687/dqc_reference
[2023-06-05 02:46:52,899] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:46:52,900] [INFO] Task started: Prodigal
[2023-06-05 02:46:52,900] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e205100-1563-44ae-9506-05fdb0835f30/GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna.gz | prodigal -d GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/cds.fna -a GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:46:56,052] [INFO] Task succeeded: Prodigal
[2023-06-05 02:46:56,052] [INFO] Task started: HMMsearch
[2023-06-05 02:46:56,052] [INFO] Running command: hmmsearch --tblout GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge62b0ffb-b522-4905-b607-7c4c7d52d687/dqc_reference/reference_markers.hmm GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:46:56,271] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:46:56,272] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1e205100-1563-44ae-9506-05fdb0835f30/GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna.gz]
[2023-06-05 02:46:56,297] [INFO] Query marker FASTA was written to GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/markers.fasta
[2023-06-05 02:46:56,297] [INFO] Task started: Blastn
[2023-06-05 02:46:56,297] [INFO] Running command: blastn -query GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/markers.fasta -db /var/lib/cwl/stge62b0ffb-b522-4905-b607-7c4c7d52d687/dqc_reference/reference_markers.fasta -out GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:46:56,823] [INFO] Task succeeded: Blastn
[2023-06-05 02:46:56,827] [INFO] Selected 5 target genomes.
[2023-06-05 02:46:56,828] [INFO] Target genome list was writen to GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/target_genomes.txt
[2023-06-05 02:46:56,830] [INFO] Task started: fastANI
[2023-06-05 02:46:56,830] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e205100-1563-44ae-9506-05fdb0835f30/GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna.gz --refList GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/target_genomes.txt --output GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:46:58,417] [INFO] Task succeeded: fastANI
[2023-06-05 02:46:58,417] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge62b0ffb-b522-4905-b607-7c4c7d52d687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:46:58,418] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge62b0ffb-b522-4905-b607-7c4c7d52d687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:46:58,420] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:46:58,420] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 02:46:58,421] [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 02:46:58,423] [INFO] DFAST Taxonomy check result was written to GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/tc_result.tsv
[2023-06-05 02:46:58,424] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:46:58,424] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:46:58,424] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge62b0ffb-b522-4905-b607-7c4c7d52d687/dqc_reference/checkm_data
[2023-06-05 02:46:58,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:46:58,451] [INFO] Task started: CheckM
[2023-06-05 02:46:58,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/checkm_input GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/checkm_result
[2023-06-05 02:47:15,491] [INFO] Task succeeded: CheckM
[2023-06-05 02:47:15,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:47:15,512] [INFO] ===== Completeness check finished =====
[2023-06-05 02:47:15,512] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:47:15,513] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/markers.fasta)
[2023-06-05 02:47:15,513] [INFO] Task started: Blastn
[2023-06-05 02:47:15,513] [INFO] Running command: blastn -query GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/markers.fasta -db /var/lib/cwl/stge62b0ffb-b522-4905-b607-7c4c7d52d687/dqc_reference/reference_markers_gtdb.fasta -out GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:47:16,212] [INFO] Task succeeded: Blastn
[2023-06-05 02:47:16,217] [INFO] Selected 16 target genomes.
[2023-06-05 02:47:16,217] [INFO] Target genome list was writen to GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:47:16,251] [INFO] Task started: fastANI
[2023-06-05 02:47:16,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e205100-1563-44ae-9506-05fdb0835f30/GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna.gz --refList GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/target_genomes_gtdb.txt --output GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:47:21,500] [INFO] Task succeeded: fastANI
[2023-06-05 02:47:21,513] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:47:21,513] [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_900321905.1	s__Eubacterium_R sp900321905	96.9968	277	361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	97.58	96.21	0.81	0.71	7	conclusive
GCA_017446095.1	s__Eubacterium_R sp017446095	82.9092	283	361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015065445.1	s__Eubacterium_R sp015065445	79.7629	228	361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017514345.1	s__Eubacterium_R sp017514345	79.1103	194	361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017450645.1	s__Eubacterium_R sp017450645	78.5086	195	361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015066525.1	s__Eubacterium_R sp015066525	78.0756	150	361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017476375.1	s__Eubacterium_R sp017476375	77.3386	86	361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	97.26	97.26	0.85	0.84	3	-
GCA_905234495.1	s__Eubacterium_R sp905234495	77.3071	79	361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167205.1	s__Eubacterium_R coprostanoligenes	77.0454	73	361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.02	97.98	0.90	0.89	4	-
GCA_905234995.1	s__Eubacterium_R sp905234995	76.6854	69	361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900764665.1	s__Eubacterium_R sp900764665	76.6327	54	361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:47:21,515] [INFO] GTDB search result was written to GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/result_gtdb.tsv
[2023-06-05 02:47:21,516] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:47:21,519] [INFO] DFAST_QC result json was written to GCA_902767205.1_Rumen_uncultured_genome_RUG11239_genomic.fna/dqc_result.json
[2023-06-05 02:47:21,519] [INFO] DFAST_QC completed!
[2023-06-05 02:47:21,519] [INFO] Total running time: 0h0m31s