[2023-06-04 17:34:33,569] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:34:33,574] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:34:33,575] [INFO] DQC Reference Directory: /var/lib/cwl/stgb32330e7-ec43-40fe-95a8-454d804a83db/dqc_reference
[2023-06-04 17:34:36,657] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:34:36,683] [INFO] Task started: Prodigal
[2023-06-04 17:34:36,684] [INFO] Running command: gunzip -c /var/lib/cwl/stg44f420c2-a60a-4b8e-83ec-c6b0ec567b95/GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna.gz | prodigal -d GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/cds.fna -a GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:34:40,253] [INFO] Task succeeded: Prodigal
[2023-06-04 17:34:40,254] [INFO] Task started: HMMsearch
[2023-06-04 17:34:40,254] [INFO] Running command: hmmsearch --tblout GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb32330e7-ec43-40fe-95a8-454d804a83db/dqc_reference/reference_markers.hmm GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:34:40,475] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:34:40,477] [INFO] Found 6/6 markers.
[2023-06-04 17:34:40,504] [INFO] Query marker FASTA was written to GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/markers.fasta
[2023-06-04 17:34:40,504] [INFO] Task started: Blastn
[2023-06-04 17:34:40,505] [INFO] Running command: blastn -query GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/markers.fasta -db /var/lib/cwl/stgb32330e7-ec43-40fe-95a8-454d804a83db/dqc_reference/reference_markers.fasta -out GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:34:42,129] [INFO] Task succeeded: Blastn
[2023-06-04 17:34:42,134] [INFO] Selected 13 target genomes.
[2023-06-04 17:34:42,134] [INFO] Target genome list was writen to GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/target_genomes.txt
[2023-06-04 17:34:43,745] [INFO] Task started: fastANI
[2023-06-04 17:34:43,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg44f420c2-a60a-4b8e-83ec-c6b0ec567b95/GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna.gz --refList GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/target_genomes.txt --output GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:34:50,933] [INFO] Task succeeded: fastANI
[2023-06-04 17:34:50,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb32330e7-ec43-40fe-95a8-454d804a83db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:34:50,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb32330e7-ec43-40fe-95a8-454d804a83db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:34:50,942] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 17:34:50,942] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 17:34:50,942] [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
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	84.6678	287	361	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	80.054	217	361	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.7292	115	361	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.6799	129	361	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.4584	73	361	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	77.293	66	361	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.1769	83	361	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 17:34:50,944] [INFO] DFAST Taxonomy check result was written to GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/tc_result.tsv
[2023-06-04 17:34:50,945] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:34:50,945] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:34:50,945] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb32330e7-ec43-40fe-95a8-454d804a83db/dqc_reference/checkm_data
[2023-06-04 17:34:50,946] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:34:50,968] [INFO] Task started: CheckM
[2023-06-04 17:34:50,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/checkm_input GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/checkm_result
[2023-06-04 17:35:08,983] [INFO] Task succeeded: CheckM
[2023-06-04 17:35:08,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.43%
Contamintation: 5.56%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-04 17:35:09,007] [INFO] ===== Completeness check finished =====
[2023-06-04 17:35:09,008] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:35:09,008] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/markers.fasta)
[2023-06-04 17:35:09,008] [INFO] Task started: Blastn
[2023-06-04 17:35:09,009] [INFO] Running command: blastn -query GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/markers.fasta -db /var/lib/cwl/stgb32330e7-ec43-40fe-95a8-454d804a83db/dqc_reference/reference_markers_gtdb.fasta -out GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:35:10,309] [INFO] Task succeeded: Blastn
[2023-06-04 17:35:10,317] [INFO] Selected 7 target genomes.
[2023-06-04 17:35:10,318] [INFO] Target genome list was writen to GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:35:10,391] [INFO] Task started: fastANI
[2023-06-04 17:35:10,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg44f420c2-a60a-4b8e-83ec-c6b0ec567b95/GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna.gz --refList GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/target_genomes_gtdb.txt --output GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:35:13,214] [INFO] Task succeeded: fastANI
[2023-06-04 17:35:13,223] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 17:35:13,224] [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_900313295.1	s__CAG-83 sp900313295	99.0786	284	361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.79	96.38	0.88	0.79	5	conclusive
GCA_902388735.1	s__CAG-83 sp902388735	85.4334	274	361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.86	98.86	0.87	0.87	2	-
GCF_018326305.1	s__CAG-83 sp900549395	84.648	288	361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.26	97.06	0.85	0.74	6	-
GCA_004557655.1	s__CAG-83 sp004557655	84.5325	280	361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550615.1	s__CAG-83 sp900550615	84.4147	253	361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.53	97.53	0.77	0.77	2	-
GCA_003539495.1	s__CAG-83 sp003539495	84.2721	291	361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.87	97.47	0.86	0.82	8	-
GCF_018408575.1	s__CAG-83 sp000431575	80.054	217	361	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	97.84	97.37	0.92	0.86	9	-
--------------------------------------------------------------------------------
[2023-06-04 17:35:13,226] [INFO] GTDB search result was written to GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/result_gtdb.tsv
[2023-06-04 17:35:13,226] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:35:13,229] [INFO] DFAST_QC result json was written to GCA_902797465.1_Rumen_uncultured_genome_RUG14269_genomic.fna/dqc_result.json
[2023-06-04 17:35:13,229] [INFO] DFAST_QC completed!
[2023-06-04 17:35:13,229] [INFO] Total running time: 0h0m40s