[2023-06-08 10:29:33,140] [INFO] DFAST_QC pipeline started.
[2023-06-08 10:29:33,142] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 10:29:33,142] [INFO] DQC Reference Directory: /var/lib/cwl/stgd12bc0e8-87e0-43dd-a2d9-bcfeb73917aa/dqc_reference
[2023-06-08 10:29:34,296] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 10:29:34,297] [INFO] Task started: Prodigal
[2023-06-08 10:29:34,297] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b4e7624-31bd-4d29-9a03-f399d72e2af7/GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna.gz | prodigal -d GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/cds.fna -a GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 10:29:37,973] [INFO] Task succeeded: Prodigal
[2023-06-08 10:29:37,973] [INFO] Task started: HMMsearch
[2023-06-08 10:29:37,973] [INFO] Running command: hmmsearch --tblout GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd12bc0e8-87e0-43dd-a2d9-bcfeb73917aa/dqc_reference/reference_markers.hmm GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/protein.faa > /dev/null
[2023-06-08 10:29:38,199] [INFO] Task succeeded: HMMsearch
[2023-06-08 10:29:38,201] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0b4e7624-31bd-4d29-9a03-f399d72e2af7/GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna.gz]
[2023-06-08 10:29:38,223] [INFO] Query marker FASTA was written to GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/markers.fasta
[2023-06-08 10:29:38,223] [INFO] Task started: Blastn
[2023-06-08 10:29:38,223] [INFO] Running command: blastn -query GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/markers.fasta -db /var/lib/cwl/stgd12bc0e8-87e0-43dd-a2d9-bcfeb73917aa/dqc_reference/reference_markers.fasta -out GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:29:38,829] [INFO] Task succeeded: Blastn
[2023-06-08 10:29:38,833] [INFO] Selected 20 target genomes.
[2023-06-08 10:29:38,834] [INFO] Target genome list was writen to GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/target_genomes.txt
[2023-06-08 10:29:38,841] [INFO] Task started: fastANI
[2023-06-08 10:29:38,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b4e7624-31bd-4d29-9a03-f399d72e2af7/GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna.gz --refList GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/target_genomes.txt --output GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 10:29:53,642] [INFO] Task succeeded: fastANI
[2023-06-08 10:29:53,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd12bc0e8-87e0-43dd-a2d9-bcfeb73917aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 10:29:53,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd12bc0e8-87e0-43dd-a2d9-bcfeb73917aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 10:29:53,649] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 10:29:53,649] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 10:29:53,649] [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
Ruminococcus bromii	strain=ATCC 27255	GCA_002834225.1	40518	40518	suspected-type	True	77.4757	127	534	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 10:29:53,654] [INFO] DFAST Taxonomy check result was written to GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/tc_result.tsv
[2023-06-08 10:29:53,654] [INFO] ===== Taxonomy check completed =====
[2023-06-08 10:29:53,654] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 10:29:53,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd12bc0e8-87e0-43dd-a2d9-bcfeb73917aa/dqc_reference/checkm_data
[2023-06-08 10:29:53,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 10:29:53,680] [INFO] Task started: CheckM
[2023-06-08 10:29:53,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/checkm_input GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/checkm_result
[2023-06-08 10:30:12,242] [INFO] Task succeeded: CheckM
[2023-06-08 10:30:12,243] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 10:30:12,262] [INFO] ===== Completeness check finished =====
[2023-06-08 10:30:12,263] [INFO] ===== Start GTDB Search =====
[2023-06-08 10:30:12,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/markers.fasta)
[2023-06-08 10:30:12,264] [INFO] Task started: Blastn
[2023-06-08 10:30:12,264] [INFO] Running command: blastn -query GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/markers.fasta -db /var/lib/cwl/stgd12bc0e8-87e0-43dd-a2d9-bcfeb73917aa/dqc_reference/reference_markers_gtdb.fasta -out GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:30:13,234] [INFO] Task succeeded: Blastn
[2023-06-08 10:30:13,239] [INFO] Selected 15 target genomes.
[2023-06-08 10:30:13,239] [INFO] Target genome list was writen to GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 10:30:13,247] [INFO] Task started: fastANI
[2023-06-08 10:30:13,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b4e7624-31bd-4d29-9a03-f399d72e2af7/GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna.gz --refList GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/target_genomes_gtdb.txt --output GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 10:30:19,364] [INFO] Task succeeded: fastANI
[2023-06-08 10:30:19,380] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 10:30:19,380] [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_900319655.1	s__Ruminococcus_E sp900319655	96.6845	342	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.18	96.05	0.81	0.70	33	conclusive
GCA_905235295.1	s__Ruminococcus_E sp905235295	81.7788	312	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798605.1	s__Ruminococcus_E sp902798605	81.5015	331	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.91	97.91	0.86	0.86	2	-
GCA_902767845.1	s__Ruminococcus_E sp902767845	81.3225	304	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.96	98.96	0.86	0.86	2	-
GCA_900318495.1	s__Ruminococcus_E sp900318495	79.8957	235	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900315085.1	s__Ruminococcus_E sp900315085	79.4413	223	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.46	97.96	0.77	0.69	11	-
GCA_902765625.1	s__Ruminococcus_E sp902765625	79.3524	202	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.31	99.27	0.90	0.89	5	-
GCA_900316555.1	s__Ruminococcus_E sp900316555	79.3093	221	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.80	96.62	0.88	0.77	62	-
GCA_900315195.1	s__Ruminococcus_E sp900315195	78.9054	197	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.59	99.19	0.95	0.90	3	-
GCA_900317875.1	s__Ruminococcus_E sp900317875	78.7573	165	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.86	99.86	0.92	0.92	2	-
GCA_902766885.1	s__Ruminococcus_E sp902766885	78.7428	157	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003521625.1	s__Ruminococcus_E sp003521625	78.7202	155	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315605.1	s__Ruminococcus_E sp900315605	78.7123	177	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.58	96.04	0.85	0.75	11	-
GCA_902798365.1	s__Ruminococcus_E sp902798365	78.2491	196	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797525.1	s__Ruminococcus_E sp902797525	78.0558	152	534	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 10:30:19,382] [INFO] GTDB search result was written to GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/result_gtdb.tsv
[2023-06-08 10:30:19,385] [INFO] ===== GTDB Search completed =====
[2023-06-08 10:30:19,388] [INFO] DFAST_QC result json was written to GCA_902775705.1_Rumen_uncultured_genome_RUG12099_genomic.fna/dqc_result.json
[2023-06-08 10:30:19,388] [INFO] DFAST_QC completed!
[2023-06-08 10:30:19,389] [INFO] Total running time: 0h0m46s