[2023-06-08 00:03:33,635] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:03:33,641] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:03:33,641] [INFO] DQC Reference Directory: /var/lib/cwl/stg0919d3e4-b7e0-4717-8288-f5434f42e906/dqc_reference
[2023-06-08 00:03:35,222] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:03:35,223] [INFO] Task started: Prodigal
[2023-06-08 00:03:35,223] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f0dedec-c8b3-48ce-b9c9-cdc0bd7d5336/GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna.gz | prodigal -d GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/cds.fna -a GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:03:46,030] [INFO] Task succeeded: Prodigal
[2023-06-08 00:03:46,030] [INFO] Task started: HMMsearch
[2023-06-08 00:03:46,030] [INFO] Running command: hmmsearch --tblout GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0919d3e4-b7e0-4717-8288-f5434f42e906/dqc_reference/reference_markers.hmm GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:03:46,256] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:03:46,262] [INFO] Found 6/6 markers.
[2023-06-08 00:03:46,290] [INFO] Query marker FASTA was written to GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/markers.fasta
[2023-06-08 00:03:46,290] [INFO] Task started: Blastn
[2023-06-08 00:03:46,290] [INFO] Running command: blastn -query GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/markers.fasta -db /var/lib/cwl/stg0919d3e4-b7e0-4717-8288-f5434f42e906/dqc_reference/reference_markers.fasta -out GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:03:46,933] [INFO] Task succeeded: Blastn
[2023-06-08 00:03:46,959] [INFO] Selected 35 target genomes.
[2023-06-08 00:03:46,960] [INFO] Target genome list was writen to GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/target_genomes.txt
[2023-06-08 00:03:46,963] [INFO] Task started: fastANI
[2023-06-08 00:03:46,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f0dedec-c8b3-48ce-b9c9-cdc0bd7d5336/GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna.gz --refList GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/target_genomes.txt --output GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:04:04,894] [INFO] Task succeeded: fastANI
[2023-06-08 00:04:04,894] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0919d3e4-b7e0-4717-8288-f5434f42e906/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:04:04,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0919d3e4-b7e0-4717-8288-f5434f42e906/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:04:04,901] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 00:04:04,901] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 00:04:04,901] [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
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	76.8968	58	664	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	76.6394	56	664	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 00:04:04,903] [INFO] DFAST Taxonomy check result was written to GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/tc_result.tsv
[2023-06-08 00:04:04,904] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:04:04,904] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:04:04,905] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0919d3e4-b7e0-4717-8288-f5434f42e906/dqc_reference/checkm_data
[2023-06-08 00:04:04,907] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:04:04,964] [INFO] Task started: CheckM
[2023-06-08 00:04:04,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/checkm_input GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/checkm_result
[2023-06-08 00:04:41,049] [INFO] Task succeeded: CheckM
[2023-06-08 00:04:41,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 00:04:41,071] [INFO] ===== Completeness check finished =====
[2023-06-08 00:04:41,071] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:04:41,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/markers.fasta)
[2023-06-08 00:04:41,072] [INFO] Task started: Blastn
[2023-06-08 00:04:41,072] [INFO] Running command: blastn -query GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/markers.fasta -db /var/lib/cwl/stg0919d3e4-b7e0-4717-8288-f5434f42e906/dqc_reference/reference_markers_gtdb.fasta -out GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:04:42,078] [INFO] Task succeeded: Blastn
[2023-06-08 00:04:42,081] [INFO] Selected 13 target genomes.
[2023-06-08 00:04:42,082] [INFO] Target genome list was writen to GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:04:42,083] [INFO] Task started: fastANI
[2023-06-08 00:04:42,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f0dedec-c8b3-48ce-b9c9-cdc0bd7d5336/GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna.gz --refList GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/target_genomes_gtdb.txt --output GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:04:48,577] [INFO] Task succeeded: fastANI
[2023-06-08 00:04:48,591] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 00:04:48,592] [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_902774005.1	s__UBA4334 sp902774005	100.0	656	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.45	96.72	0.82	0.82	3	conclusive
GCA_905233285.1	s__UBA4334 sp905233285	87.9712	478	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342585.1	s__UBA4334 sp002342585	79.7464	301	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.26	96.88	0.84	0.78	5	-
GCA_002353215.1	s__UBA4334 sp002353215	79.6196	203	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002353575.1	s__UBA4334 sp002353575	79.2012	300	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	99.97	99.97	0.90	0.85	5	-
GCA_017540585.1	s__UBA4334 sp017540585	77.6942	92	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	96.33	96.33	0.78	0.78	2	-
GCA_017617575.1	s__UBA4334 sp017617575	77.4631	100	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017453465.1	s__UBA4334 sp017453465	77.4037	150	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905236065.1	s__UBA4334 sp905236065	77.2532	124	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902802265.1	s__UBA4334 sp902802265	77.2347	133	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	97.98	97.98	0.87	0.87	2	-
GCA_905234125.1	s__UBA4334 sp905234125	77.2312	110	664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4334	95.0	98.16	98.16	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-08 00:04:48,594] [INFO] GTDB search result was written to GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/result_gtdb.tsv
[2023-06-08 00:04:48,594] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:04:48,597] [INFO] DFAST_QC result json was written to GCA_902774005.1_Rumen_uncultured_genome_RUG11924_genomic.fna/dqc_result.json
[2023-06-08 00:04:48,598] [INFO] DFAST_QC completed!
[2023-06-08 00:04:48,598] [INFO] Total running time: 0h1m15s