[2023-06-08 15:53:04,239] [INFO] DFAST_QC pipeline started.
[2023-06-08 15:53:04,244] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 15:53:04,244] [INFO] DQC Reference Directory: /var/lib/cwl/stga95f20a8-7bff-477e-9d7e-ee9570f181c0/dqc_reference
[2023-06-08 15:53:06,896] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 15:53:06,898] [INFO] Task started: Prodigal
[2023-06-08 15:53:06,899] [INFO] Running command: gunzip -c /var/lib/cwl/stg69f58af4-c7e5-4e8d-a703-037f7d026df6/GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna.gz | prodigal -d GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/cds.fna -a GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 15:53:13,405] [INFO] Task succeeded: Prodigal
[2023-06-08 15:53:13,405] [INFO] Task started: HMMsearch
[2023-06-08 15:53:13,405] [INFO] Running command: hmmsearch --tblout GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga95f20a8-7bff-477e-9d7e-ee9570f181c0/dqc_reference/reference_markers.hmm GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/protein.faa > /dev/null
[2023-06-08 15:53:13,722] [INFO] Task succeeded: HMMsearch
[2023-06-08 15:53:13,723] [INFO] Found 6/6 markers.
[2023-06-08 15:53:13,764] [INFO] Query marker FASTA was written to GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/markers.fasta
[2023-06-08 15:53:13,764] [INFO] Task started: Blastn
[2023-06-08 15:53:13,764] [INFO] Running command: blastn -query GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/markers.fasta -db /var/lib/cwl/stga95f20a8-7bff-477e-9d7e-ee9570f181c0/dqc_reference/reference_markers.fasta -out GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:53:14,385] [INFO] Task succeeded: Blastn
[2023-06-08 15:53:14,389] [INFO] Selected 25 target genomes.
[2023-06-08 15:53:14,390] [INFO] Target genome list was writen to GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/target_genomes.txt
[2023-06-08 15:53:14,392] [INFO] Task started: fastANI
[2023-06-08 15:53:14,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg69f58af4-c7e5-4e8d-a703-037f7d026df6/GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna.gz --refList GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/target_genomes.txt --output GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 15:53:30,154] [INFO] Task succeeded: fastANI
[2023-06-08 15:53:30,155] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga95f20a8-7bff-477e-9d7e-ee9570f181c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 15:53:30,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga95f20a8-7bff-477e-9d7e-ee9570f181c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 15:53:30,159] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 15:53:30,159] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 15:53:30,160] [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 15:53:30,162] [INFO] DFAST Taxonomy check result was written to GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/tc_result.tsv
[2023-06-08 15:53:30,162] [INFO] ===== Taxonomy check completed =====
[2023-06-08 15:53:30,163] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 15:53:30,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga95f20a8-7bff-477e-9d7e-ee9570f181c0/dqc_reference/checkm_data
[2023-06-08 15:53:30,168] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 15:53:30,196] [INFO] Task started: CheckM
[2023-06-08 15:53:30,196] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/checkm_input GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/checkm_result
[2023-06-08 15:53:54,448] [INFO] Task succeeded: CheckM
[2023-06-08 15:53:54,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 15:53:54,470] [INFO] ===== Completeness check finished =====
[2023-06-08 15:53:54,471] [INFO] ===== Start GTDB Search =====
[2023-06-08 15:53:54,471] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/markers.fasta)
[2023-06-08 15:53:54,472] [INFO] Task started: Blastn
[2023-06-08 15:53:54,472] [INFO] Running command: blastn -query GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/markers.fasta -db /var/lib/cwl/stga95f20a8-7bff-477e-9d7e-ee9570f181c0/dqc_reference/reference_markers_gtdb.fasta -out GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:53:55,236] [INFO] Task succeeded: Blastn
[2023-06-08 15:53:55,241] [INFO] Selected 14 target genomes.
[2023-06-08 15:53:55,241] [INFO] Target genome list was writen to GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 15:53:55,246] [INFO] Task started: fastANI
[2023-06-08 15:53:55,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg69f58af4-c7e5-4e8d-a703-037f7d026df6/GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna.gz --refList GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/target_genomes_gtdb.txt --output GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 15:54:00,143] [INFO] Task succeeded: fastANI
[2023-06-08 15:54:00,153] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 15:54:00,154] [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_900555925.1	s__Scatosoma sp900555925	98.7092	425	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	98.41	98.26	0.74	0.66	3	conclusive
GCA_904419075.1	s__Scatosoma sp904419075	94.37	556	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	97.64	97.64	0.92	0.92	2	-
GCA_900540805.1	s__Scatosoma sp003150575	80.8881	350	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	99.20	98.47	0.92	0.85	5	-
GCA_905209085.1	s__Scatosoma sp900552625	79.4986	307	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	99.19	98.78	0.94	0.91	5	-
GCA_018714725.1	s__Scatosoma pullistercoris	78.3343	181	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712725.1	s__Scatosoma pullicola	77.9525	203	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	99.20	98.54	0.90	0.87	3	-
GCA_017467275.1	s__Scatosoma sp017467275	77.346	97	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017471785.1	s__Scatosoma sp017471785	76.6697	99	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017504065.1	s__Scatosoma sp017504065	76.5494	64	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904373325.1	s__Gallimonas merdigallinarum	76.2853	78	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	98.69	97.92	0.89	0.88	4	-
GCA_900769545.1	s__Scatosoma sp900769545	76.2828	61	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 15:54:00,156] [INFO] GTDB search result was written to GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/result_gtdb.tsv
[2023-06-08 15:54:00,156] [INFO] ===== GTDB Search completed =====
[2023-06-08 15:54:00,159] [INFO] DFAST_QC result json was written to GCA_902461535.1_UHGG-TPA_MGYG-HGUT-00344_genomic.fna/dqc_result.json
[2023-06-08 15:54:00,160] [INFO] DFAST_QC completed!
[2023-06-08 15:54:00,160] [INFO] Total running time: 0h0m56s