[2023-06-05 18:57:35,281] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:57:35,284] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:57:35,284] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe1de085-0359-44a3-88b9-a5e7f8209576/dqc_reference
[2023-06-05 18:57:36,525] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:57:36,526] [INFO] Task started: Prodigal
[2023-06-05 18:57:36,526] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1edd517-fc01-4ae8-b10e-be7c5bf75bea/GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna.gz | prodigal -d GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/cds.fna -a GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:57:45,835] [INFO] Task succeeded: Prodigal
[2023-06-05 18:57:45,835] [INFO] Task started: HMMsearch
[2023-06-05 18:57:45,835] [INFO] Running command: hmmsearch --tblout GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe1de085-0359-44a3-88b9-a5e7f8209576/dqc_reference/reference_markers.hmm GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:57:46,114] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:57:46,115] [INFO] Found 6/6 markers.
[2023-06-05 18:57:46,150] [INFO] Query marker FASTA was written to GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/markers.fasta
[2023-06-05 18:57:46,150] [INFO] Task started: Blastn
[2023-06-05 18:57:46,150] [INFO] Running command: blastn -query GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe1de085-0359-44a3-88b9-a5e7f8209576/dqc_reference/reference_markers.fasta -out GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:57:46,831] [INFO] Task succeeded: Blastn
[2023-06-05 18:57:46,835] [INFO] Selected 31 target genomes.
[2023-06-05 18:57:46,835] [INFO] Target genome list was writen to GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/target_genomes.txt
[2023-06-05 18:57:46,859] [INFO] Task started: fastANI
[2023-06-05 18:57:46,859] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1edd517-fc01-4ae8-b10e-be7c5bf75bea/GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna.gz --refList GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/target_genomes.txt --output GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:58:09,802] [INFO] Task succeeded: fastANI
[2023-06-05 18:58:09,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe1de085-0359-44a3-88b9-a5e7f8209576/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:58:09,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe1de085-0359-44a3-88b9-a5e7f8209576/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:58:09,805] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:58:09,805] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:58:09,805] [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 18:58:09,809] [INFO] DFAST Taxonomy check result was written to GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/tc_result.tsv
[2023-06-05 18:58:09,810] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:58:09,810] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:58:09,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe1de085-0359-44a3-88b9-a5e7f8209576/dqc_reference/checkm_data
[2023-06-05 18:58:09,815] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:58:09,857] [INFO] Task started: CheckM
[2023-06-05 18:58:09,857] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/checkm_input GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/checkm_result
[2023-06-05 18:58:42,053] [INFO] Task succeeded: CheckM
[2023-06-05 18:58:42,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:58:42,072] [INFO] ===== Completeness check finished =====
[2023-06-05 18:58:42,073] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:58:42,074] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/markers.fasta)
[2023-06-05 18:58:42,074] [INFO] Task started: Blastn
[2023-06-05 18:58:42,074] [INFO] Running command: blastn -query GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe1de085-0359-44a3-88b9-a5e7f8209576/dqc_reference/reference_markers_gtdb.fasta -out GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:58:43,187] [INFO] Task succeeded: Blastn
[2023-06-05 18:58:43,192] [INFO] Selected 14 target genomes.
[2023-06-05 18:58:43,193] [INFO] Target genome list was writen to GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:58:43,209] [INFO] Task started: fastANI
[2023-06-05 18:58:43,209] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1edd517-fc01-4ae8-b10e-be7c5bf75bea/GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna.gz --refList GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/target_genomes_gtdb.txt --output GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:58:52,120] [INFO] Task succeeded: fastANI
[2023-06-05 18:58:52,139] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:58:52,139] [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_902764875.1	s__GCA-900199385 sp902764875	100.0	1053	1056	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	96.75	96.19	0.79	0.75	4	conclusive
GCA_017447185.1	s__GCA-900199385 sp017447185	81.1559	383	1056	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902793605.1	s__GCA-900199385 sp900320755	80.519	318	1056	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	98.77	98.33	0.88	0.86	8	-
GCA_017526525.1	s__GCA-900199385 sp017526525	80.2731	340	1056	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318145.1	s__GCA-900199385 sp900318145	80.2424	388	1056	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900315315.1	s__GCA-900199385 sp900315315	79.8142	356	1056	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017569285.1	s__GCA-900199385 sp017569285	79.7205	287	1056	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017569305.1	s__GCA-900199385 sp900322155	79.3227	292	1056	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	98.53	98.29	0.93	0.91	5	-
GCA_017404985.1	s__GCA-900199385 sp017404985	79.2749	273	1056	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017541105.1	s__GCA-900199385 sp017541105	78.9708	200	1056	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017431005.1	s__GCA-900199385 sp017431005	78.9067	210	1056	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017512985.1	s__GCA-900199385 sp017512985	78.8648	286	1056	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017652125.1	s__GCA-900199385 sp017652125	78.3927	225	1056	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017469265.1	s__RUG740 sp017469265	78.0644	219	1056	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:58:52,142] [INFO] GTDB search result was written to GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/result_gtdb.tsv
[2023-06-05 18:58:52,143] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:58:52,146] [INFO] DFAST_QC result json was written to GCA_902764875.1_Rumen_uncultured_genome_RUG10998_genomic.fna/dqc_result.json
[2023-06-05 18:58:52,146] [INFO] DFAST_QC completed!
[2023-06-05 18:58:52,146] [INFO] Total running time: 0h1m17s