[2023-06-08 09:35:05,655] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:35:05,659] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:35:05,660] [INFO] DQC Reference Directory: /var/lib/cwl/stge5ab7a3c-2a89-4bca-9cd4-cf6ef31f23e9/dqc_reference
[2023-06-08 09:35:07,694] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:35:07,695] [INFO] Task started: Prodigal
[2023-06-08 09:35:07,696] [INFO] Running command: gunzip -c /var/lib/cwl/stg77327af2-00bf-40ec-86fe-63490d459ff8/GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna.gz | prodigal -d GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/cds.fna -a GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:35:15,688] [INFO] Task succeeded: Prodigal
[2023-06-08 09:35:15,689] [INFO] Task started: HMMsearch
[2023-06-08 09:35:15,689] [INFO] Running command: hmmsearch --tblout GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5ab7a3c-2a89-4bca-9cd4-cf6ef31f23e9/dqc_reference/reference_markers.hmm GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:35:15,954] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:35:15,955] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg77327af2-00bf-40ec-86fe-63490d459ff8/GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna.gz]
[2023-06-08 09:35:15,982] [INFO] Query marker FASTA was written to GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/markers.fasta
[2023-06-08 09:35:15,982] [INFO] Task started: Blastn
[2023-06-08 09:35:15,982] [INFO] Running command: blastn -query GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/markers.fasta -db /var/lib/cwl/stge5ab7a3c-2a89-4bca-9cd4-cf6ef31f23e9/dqc_reference/reference_markers.fasta -out GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:35:16,632] [INFO] Task succeeded: Blastn
[2023-06-08 09:35:16,636] [INFO] Selected 8 target genomes.
[2023-06-08 09:35:16,637] [INFO] Target genome list was writen to GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/target_genomes.txt
[2023-06-08 09:35:16,637] [INFO] Task started: fastANI
[2023-06-08 09:35:16,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg77327af2-00bf-40ec-86fe-63490d459ff8/GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna.gz --refList GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/target_genomes.txt --output GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:35:20,204] [INFO] Task succeeded: fastANI
[2023-06-08 09:35:20,205] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5ab7a3c-2a89-4bca-9cd4-cf6ef31f23e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:35:20,205] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5ab7a3c-2a89-4bca-9cd4-cf6ef31f23e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:35:20,216] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:35:20,216] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 09:35:20,216] [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
Mitsuokella multacida	strain=DSM 20544	GCA_000155955.1	52226	52226	type	True	80.8328	372	881	95	below_threshold
Mitsuokella jalaludinii	strain=DSM 13811	GCA_000702905.1	187979	187979	type	True	80.398	364	881	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000160495.1	69823	69823	neotype	True	77.9384	204	881	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000208405.1	69823	69823	neotype	True	77.8865	204	881	95	below_threshold
Selenomonas montiformis	strain=WCA-380-WT-3B3	GCA_009697385.1	2652285	2652285	type	True	77.6908	141	881	95	below_threshold
Selenomonas felix	strain=Marseille-P3560	GCA_900186465.1	1944634	1944634	type	True	77.3156	142	881	95	below_threshold
Selenomonas artemidis	strain=DSM 19719	GCA_000426665.1	671224	671224	type	True	77.2935	116	881	95	below_threshold
Selenomonas ruminantium subsp. ruminantium	strain=ATCC 12561	GCA_000424065.1	114196	971	type	True	77.0833	100	881	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 09:35:20,218] [INFO] DFAST Taxonomy check result was written to GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/tc_result.tsv
[2023-06-08 09:35:20,218] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:35:20,218] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:35:20,219] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5ab7a3c-2a89-4bca-9cd4-cf6ef31f23e9/dqc_reference/checkm_data
[2023-06-08 09:35:20,220] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:35:20,248] [INFO] Task started: CheckM
[2023-06-08 09:35:20,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/checkm_input GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/checkm_result
[2023-06-08 09:35:48,835] [INFO] Task succeeded: CheckM
[2023-06-08 09:35:48,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:35:48,856] [INFO] ===== Completeness check finished =====
[2023-06-08 09:35:48,856] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:35:48,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/markers.fasta)
[2023-06-08 09:35:48,857] [INFO] Task started: Blastn
[2023-06-08 09:35:48,857] [INFO] Running command: blastn -query GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/markers.fasta -db /var/lib/cwl/stge5ab7a3c-2a89-4bca-9cd4-cf6ef31f23e9/dqc_reference/reference_markers_gtdb.fasta -out GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:35:49,831] [INFO] Task succeeded: Blastn
[2023-06-08 09:35:49,835] [INFO] Selected 9 target genomes.
[2023-06-08 09:35:49,835] [INFO] Target genome list was writen to GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:35:49,839] [INFO] Task started: fastANI
[2023-06-08 09:35:49,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg77327af2-00bf-40ec-86fe-63490d459ff8/GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna.gz --refList GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/target_genomes_gtdb.txt --output GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:35:55,224] [INFO] Task succeeded: fastANI
[2023-06-08 09:35:55,235] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:35:55,235] [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_900318215.1	s__Selenomonas_C sp900318215	98.0365	611	881	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	98.35	97.85	0.83	0.79	6	conclusive
GCA_902780535.1	s__Selenomonas_C sp902780535	94.0672	628	881	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	97.25	96.14	0.82	0.79	5	-
GCA_900315575.1	s__Selenomonas_C sp900315575	92.9928	646	881	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	98.35	97.63	0.83	0.78	4	-
GCA_900314825.1	s__Selenomonas_C sp900314825	83.9853	573	881	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	99.95	99.95	0.95	0.95	2	-
GCA_902763085.1	s__Selenomonas_C sp002351185	81.6297	415	881	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	98.44	97.41	0.83	0.79	3	-
GCF_000381005.1	s__Selenomonas_C bovis	81.5095	453	881	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_C	95.0	97.36	95.92	0.90	0.82	11	-
GCA_017444295.1	s__UBA3796 sp017444295	76.7634	97	881	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__UBA3796	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 09:35:55,237] [INFO] GTDB search result was written to GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/result_gtdb.tsv
[2023-06-08 09:35:55,237] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:35:55,240] [INFO] DFAST_QC result json was written to GCA_902795175.1_Rumen_uncultured_genome_RUG14048_genomic.fna/dqc_result.json
[2023-06-08 09:35:55,241] [INFO] DFAST_QC completed!
[2023-06-08 09:35:55,241] [INFO] Total running time: 0h0m50s