[2023-06-08 09:32:05,170] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:32:05,179] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:32:05,179] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3705584-2469-4f85-94d3-767780f19f61/dqc_reference
[2023-06-08 09:32:06,747] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:32:06,748] [INFO] Task started: Prodigal
[2023-06-08 09:32:06,748] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf8cc46a-8cd7-45cd-be53-8201c9a38a03/GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna.gz | prodigal -d GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/cds.fna -a GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:32:21,295] [INFO] Task succeeded: Prodigal
[2023-06-08 09:32:21,296] [INFO] Task started: HMMsearch
[2023-06-08 09:32:21,296] [INFO] Running command: hmmsearch --tblout GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3705584-2469-4f85-94d3-767780f19f61/dqc_reference/reference_markers.hmm GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:32:21,500] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:32:21,501] [INFO] Found 6/6 markers.
[2023-06-08 09:32:21,523] [INFO] Query marker FASTA was written to GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/markers.fasta
[2023-06-08 09:32:21,523] [INFO] Task started: Blastn
[2023-06-08 09:32:21,523] [INFO] Running command: blastn -query GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3705584-2469-4f85-94d3-767780f19f61/dqc_reference/reference_markers.fasta -out GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:32:22,124] [INFO] Task succeeded: Blastn
[2023-06-08 09:32:22,128] [INFO] Selected 36 target genomes.
[2023-06-08 09:32:22,128] [INFO] Target genome list was writen to GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/target_genomes.txt
[2023-06-08 09:32:22,132] [INFO] Task started: fastANI
[2023-06-08 09:32:22,133] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf8cc46a-8cd7-45cd-be53-8201c9a38a03/GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna.gz --refList GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/target_genomes.txt --output GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:32:44,474] [INFO] Task succeeded: fastANI
[2023-06-08 09:32:44,475] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3705584-2469-4f85-94d3-767780f19f61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:32:44,475] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3705584-2469-4f85-94d3-767780f19f61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:32:44,477] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:32:44,477] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 09:32:44,477] [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 09:32:44,479] [INFO] DFAST Taxonomy check result was written to GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/tc_result.tsv
[2023-06-08 09:32:44,479] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:32:44,479] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:32:44,479] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3705584-2469-4f85-94d3-767780f19f61/dqc_reference/checkm_data
[2023-06-08 09:32:44,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:32:44,506] [INFO] Task started: CheckM
[2023-06-08 09:32:44,506] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/checkm_input GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/checkm_result
[2023-06-08 09:33:26,388] [INFO] Task succeeded: CheckM
[2023-06-08 09:33:26,389] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:33:26,403] [INFO] ===== Completeness check finished =====
[2023-06-08 09:33:26,403] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:33:26,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/markers.fasta)
[2023-06-08 09:33:26,404] [INFO] Task started: Blastn
[2023-06-08 09:33:26,404] [INFO] Running command: blastn -query GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3705584-2469-4f85-94d3-767780f19f61/dqc_reference/reference_markers_gtdb.fasta -out GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:33:27,336] [INFO] Task succeeded: Blastn
[2023-06-08 09:33:27,339] [INFO] Selected 16 target genomes.
[2023-06-08 09:33:27,339] [INFO] Target genome list was writen to GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:33:27,343] [INFO] Task started: fastANI
[2023-06-08 09:33:27,343] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf8cc46a-8cd7-45cd-be53-8201c9a38a03/GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna.gz --refList GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/target_genomes_gtdb.txt --output GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:33:34,217] [INFO] Task succeeded: fastANI
[2023-06-08 09:33:34,228] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:33:34,228] [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_900318275.1	s__UBA1711 sp900318275	97.7878	635	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	98.21	97.13	0.91	0.87	7	conclusive
GCA_900314925.1	s__UBA1711 sp900314925	89.4736	615	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	97.65	96.66	0.91	0.86	9	-
GCA_017522105.1	s__UBA1711 sp017522105	85.113	508	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902777005.1	s__UBA1711 sp902777005	84.7266	506	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902791695.1	s__UBA1711 sp902791695	84.5784	494	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320975.1	s__UBA1711 sp900320975	83.6603	401	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	99.10	98.20	0.97	0.96	3	-
GCA_017542345.1	s__UBA1711 sp017542345	81.8711	257	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774395.1	s__UBA1711 sp902774395	81.8458	363	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551765.1	s__UBA1711 sp017551765	81.633	327	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	96.72	96.72	0.78	0.78	2	-
GCA_902771735.1	s__UBA1711 sp902771735	81.4256	341	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	97.93	97.68	0.89	0.88	5	-
GCA_017645585.1	s__UBA1711 sp017645585	81.4042	359	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002349055.1	s__UBA1711 sp002349055	81.3481	404	754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	99.90	99.90	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-08 09:33:34,230] [INFO] GTDB search result was written to GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/result_gtdb.tsv
[2023-06-08 09:33:34,231] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:33:34,233] [INFO] DFAST_QC result json was written to GCA_902775445.1_Rumen_uncultured_genome_RUG12075_genomic.fna/dqc_result.json
[2023-06-08 09:33:34,233] [INFO] DFAST_QC completed!
[2023-06-08 09:33:34,233] [INFO] Total running time: 0h1m29s