[2023-06-08 08:48:50,243] [INFO] DFAST_QC pipeline started.
[2023-06-08 08:48:50,246] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 08:48:50,246] [INFO] DQC Reference Directory: /var/lib/cwl/stgd608794c-df8e-4fcf-a0e1-a1630d163b01/dqc_reference
[2023-06-08 08:48:51,472] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 08:48:51,473] [INFO] Task started: Prodigal
[2023-06-08 08:48:51,473] [INFO] Running command: gunzip -c /var/lib/cwl/stg72669be9-a86c-4c45-8e24-6b65ae11fe6c/GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna.gz | prodigal -d GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/cds.fna -a GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 08:49:05,710] [INFO] Task succeeded: Prodigal
[2023-06-08 08:49:05,710] [INFO] Task started: HMMsearch
[2023-06-08 08:49:05,710] [INFO] Running command: hmmsearch --tblout GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd608794c-df8e-4fcf-a0e1-a1630d163b01/dqc_reference/reference_markers.hmm GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/protein.faa > /dev/null
[2023-06-08 08:49:05,993] [INFO] Task succeeded: HMMsearch
[2023-06-08 08:49:05,994] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg72669be9-a86c-4c45-8e24-6b65ae11fe6c/GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna.gz]
[2023-06-08 08:49:06,036] [INFO] Query marker FASTA was written to GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/markers.fasta
[2023-06-08 08:49:06,037] [INFO] Task started: Blastn
[2023-06-08 08:49:06,037] [INFO] Running command: blastn -query GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/markers.fasta -db /var/lib/cwl/stgd608794c-df8e-4fcf-a0e1-a1630d163b01/dqc_reference/reference_markers.fasta -out GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:49:06,687] [INFO] Task succeeded: Blastn
[2023-06-08 08:49:06,691] [INFO] Selected 27 target genomes.
[2023-06-08 08:49:06,691] [INFO] Target genome list was writen to GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/target_genomes.txt
[2023-06-08 08:49:06,692] [INFO] Task started: fastANI
[2023-06-08 08:49:06,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg72669be9-a86c-4c45-8e24-6b65ae11fe6c/GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna.gz --refList GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/target_genomes.txt --output GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 08:49:20,552] [INFO] Task succeeded: fastANI
[2023-06-08 08:49:20,553] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd608794c-df8e-4fcf-a0e1-a1630d163b01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 08:49:20,553] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd608794c-df8e-4fcf-a0e1-a1630d163b01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 08:49:20,560] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 08:49:20,560] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 08:49:20,560] [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 dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.8019	104	731	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.7065	107	731	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.2889	56	731	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.2823	71	731	95	below_threshold
Paraprevotella xylaniphila	strain=YIT 11841	GCA_000205165.1	454155	454155	type	True	75.9869	51	731	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 08:49:20,563] [INFO] DFAST Taxonomy check result was written to GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/tc_result.tsv
[2023-06-08 08:49:20,564] [INFO] ===== Taxonomy check completed =====
[2023-06-08 08:49:20,564] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 08:49:20,564] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd608794c-df8e-4fcf-a0e1-a1630d163b01/dqc_reference/checkm_data
[2023-06-08 08:49:20,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 08:49:20,596] [INFO] Task started: CheckM
[2023-06-08 08:49:20,597] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/checkm_input GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/checkm_result
[2023-06-08 08:50:03,118] [INFO] Task succeeded: CheckM
[2023-06-08 08:50:03,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 08:50:03,152] [INFO] ===== Completeness check finished =====
[2023-06-08 08:50:03,153] [INFO] ===== Start GTDB Search =====
[2023-06-08 08:50:03,153] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/markers.fasta)
[2023-06-08 08:50:03,153] [INFO] Task started: Blastn
[2023-06-08 08:50:03,154] [INFO] Running command: blastn -query GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/markers.fasta -db /var/lib/cwl/stgd608794c-df8e-4fcf-a0e1-a1630d163b01/dqc_reference/reference_markers_gtdb.fasta -out GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:50:04,024] [INFO] Task succeeded: Blastn
[2023-06-08 08:50:04,029] [INFO] Selected 12 target genomes.
[2023-06-08 08:50:04,030] [INFO] Target genome list was writen to GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 08:50:04,034] [INFO] Task started: fastANI
[2023-06-08 08:50:04,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg72669be9-a86c-4c45-8e24-6b65ae11fe6c/GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna.gz --refList GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/target_genomes_gtdb.txt --output GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 08:50:09,525] [INFO] Task succeeded: fastANI
[2023-06-08 08:50:09,540] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 08:50:09,540] [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_900320435.1	s__UBA4372 sp900320435	97.3081	527	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	96.93	95.36	0.84	0.75	10	conclusive
GCA_902784475.1	s__UBA4372 sp902784475	94.7089	548	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902791295.1	s__UBA4372 sp902791295	89.1809	504	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902802815.1	s__UBA4372 sp902802815	80.8958	384	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016292045.1	s__UBA4372 sp016292045	80.5356	394	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017958545.1	s__UBA4372 sp017958545	80.0448	307	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016292545.1	s__UBA4372 sp016292545	77.5636	111	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017469525.1	s__UBA4372 sp017469525	77.436	126	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.07	96.85	0.89	0.86	4	-
GCA_018066225.1	s__Alloprevotella sp018066225	77.0795	52	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902787575.1	s__UBA4372 sp900320715	76.9974	97	731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.55	98.27	0.96	0.94	8	-
--------------------------------------------------------------------------------
[2023-06-08 08:50:09,558] [INFO] GTDB search result was written to GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/result_gtdb.tsv
[2023-06-08 08:50:09,559] [INFO] ===== GTDB Search completed =====
[2023-06-08 08:50:09,563] [INFO] DFAST_QC result json was written to GCA_902772045.1_Rumen_uncultured_genome_RUG11735_genomic.fna/dqc_result.json
[2023-06-08 08:50:09,563] [INFO] DFAST_QC completed!
[2023-06-08 08:50:09,563] [INFO] Total running time: 0h1m19s