[2023-06-05 10:47:22,142] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:47:22,144] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:47:22,144] [INFO] DQC Reference Directory: /var/lib/cwl/stg49a6be18-7ece-4c82-8e49-325bc7b106ff/dqc_reference
[2023-06-05 10:47:23,415] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:47:23,416] [INFO] Task started: Prodigal
[2023-06-05 10:47:23,417] [INFO] Running command: gunzip -c /var/lib/cwl/stgfdb62490-b966-4ad6-a47b-064e24476eac/GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna.gz | prodigal -d GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/cds.fna -a GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:47:39,897] [INFO] Task succeeded: Prodigal
[2023-06-05 10:47:39,898] [INFO] Task started: HMMsearch
[2023-06-05 10:47:39,898] [INFO] Running command: hmmsearch --tblout GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49a6be18-7ece-4c82-8e49-325bc7b106ff/dqc_reference/reference_markers.hmm GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:47:40,171] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:47:40,173] [INFO] Found 6/6 markers.
[2023-06-05 10:47:40,200] [INFO] Query marker FASTA was written to GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/markers.fasta
[2023-06-05 10:47:40,201] [INFO] Task started: Blastn
[2023-06-05 10:47:40,201] [INFO] Running command: blastn -query GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/markers.fasta -db /var/lib/cwl/stg49a6be18-7ece-4c82-8e49-325bc7b106ff/dqc_reference/reference_markers.fasta -out GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:47:40,823] [INFO] Task succeeded: Blastn
[2023-06-05 10:47:40,828] [INFO] Selected 31 target genomes.
[2023-06-05 10:47:40,828] [INFO] Target genome list was writen to GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/target_genomes.txt
[2023-06-05 10:47:40,834] [INFO] Task started: fastANI
[2023-06-05 10:47:40,835] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdb62490-b966-4ad6-a47b-064e24476eac/GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna.gz --refList GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/target_genomes.txt --output GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:47:58,191] [INFO] Task succeeded: fastANI
[2023-06-05 10:47:58,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49a6be18-7ece-4c82-8e49-325bc7b106ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:47:58,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49a6be18-7ece-4c82-8e49-325bc7b106ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:47:58,199] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:47:58,199] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 10:47:58,199] [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
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	77.6715	188	796	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009676955.1	2606626	2606626	type	True	77.6307	191	796	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 10:47:58,202] [INFO] DFAST Taxonomy check result was written to GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/tc_result.tsv
[2023-06-05 10:47:58,202] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:47:58,202] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:47:58,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49a6be18-7ece-4c82-8e49-325bc7b106ff/dqc_reference/checkm_data
[2023-06-05 10:47:58,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:47:58,236] [INFO] Task started: CheckM
[2023-06-05 10:47:58,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/checkm_input GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/checkm_result
[2023-06-05 10:48:47,072] [INFO] Task succeeded: CheckM
[2023-06-05 10:48:47,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 10:48:47,095] [INFO] ===== Completeness check finished =====
[2023-06-05 10:48:47,095] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:48:47,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/markers.fasta)
[2023-06-05 10:48:47,096] [INFO] Task started: Blastn
[2023-06-05 10:48:47,096] [INFO] Running command: blastn -query GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/markers.fasta -db /var/lib/cwl/stg49a6be18-7ece-4c82-8e49-325bc7b106ff/dqc_reference/reference_markers_gtdb.fasta -out GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:48:48,001] [INFO] Task succeeded: Blastn
[2023-06-05 10:48:48,006] [INFO] Selected 15 target genomes.
[2023-06-05 10:48:48,006] [INFO] Target genome list was writen to GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:48:48,009] [INFO] Task started: fastANI
[2023-06-05 10:48:48,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdb62490-b966-4ad6-a47b-064e24476eac/GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna.gz --refList GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/target_genomes_gtdb.txt --output GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:48:56,929] [INFO] Task succeeded: fastANI
[2023-06-05 10:48:56,946] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 10:48:56,946] [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_900318065.1	s__Sodaliphilus sp900318065	98.4717	731	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.54	97.91	0.91	0.84	24	conclusive
GCA_002353285.1	s__Sodaliphilus sp002353285	81.9882	415	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.36	97.36	0.78	0.78	2	-
GCA_900318255.1	s__Sodaliphilus sp900318255	81.8539	518	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.43	97.80	0.91	0.84	5	-
GCA_902792435.1	s__Sodaliphilus sp902792435	81.5419	462	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	96.75	96.43	0.87	0.84	5	-
GCA_902762385.1	s__Sodaliphilus sp902762385	81.3396	471	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.01	95.72	0.89	0.77	6	-
GCA_902785925.1	s__Sodaliphilus sp902785925	81.2002	469	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.61	97.00	0.89	0.87	5	-
GCA_902777835.1	s__Sodaliphilus sp902777835	80.7501	430	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.18	97.18	0.83	0.83	2	-
GCA_905233845.1	s__Sodaliphilus sp905233845	80.5699	459	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017451225.1	s__Sodaliphilus sp017451225	80.5232	350	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002396125.1	s__Sodaliphilus sp002396125	80.4517	357	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017618355.1	s__Sodaliphilus sp017618355	80.3755	413	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017557625.1	s__Sodaliphilus sp017557625	80.2905	420	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017964485.1	s__Sodaliphilus sp017964485	80.1034	430	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	96.79	96.79	0.86	0.86	2	-
GCA_017548365.1	s__Sodaliphilus sp017548365	79.8674	410	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017557665.1	s__Sodaliphilus sp017557665	78.3215	206	796	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 10:48:56,948] [INFO] GTDB search result was written to GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/result_gtdb.tsv
[2023-06-05 10:48:56,949] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:48:56,952] [INFO] DFAST_QC result json was written to GCA_902759425.1_Rumen_uncultured_genome_RUG10462_genomic.fna/dqc_result.json
[2023-06-05 10:48:56,952] [INFO] DFAST_QC completed!
[2023-06-05 10:48:56,952] [INFO] Total running time: 0h1m35s