[2023-06-08 13:52:15,393] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:52:15,398] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:52:15,398] [INFO] DQC Reference Directory: /var/lib/cwl/stg4912356b-9d0b-454e-bc77-3961309f7fb8/dqc_reference
[2023-06-08 13:52:17,684] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:52:17,685] [INFO] Task started: Prodigal
[2023-06-08 13:52:17,686] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc7fed70-73a0-44de-ae05-2cdd4ef69974/GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna.gz | prodigal -d GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/cds.fna -a GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:52:23,568] [INFO] Task succeeded: Prodigal
[2023-06-08 13:52:23,568] [INFO] Task started: HMMsearch
[2023-06-08 13:52:23,569] [INFO] Running command: hmmsearch --tblout GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4912356b-9d0b-454e-bc77-3961309f7fb8/dqc_reference/reference_markers.hmm GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:52:23,815] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:52:23,817] [INFO] Found 6/6 markers.
[2023-06-08 13:52:23,843] [INFO] Query marker FASTA was written to GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/markers.fasta
[2023-06-08 13:52:23,844] [INFO] Task started: Blastn
[2023-06-08 13:52:23,844] [INFO] Running command: blastn -query GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/markers.fasta -db /var/lib/cwl/stg4912356b-9d0b-454e-bc77-3961309f7fb8/dqc_reference/reference_markers.fasta -out GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:52:24,524] [INFO] Task succeeded: Blastn
[2023-06-08 13:52:24,528] [INFO] Selected 13 target genomes.
[2023-06-08 13:52:24,528] [INFO] Target genome list was writen to GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/target_genomes.txt
[2023-06-08 13:52:24,529] [INFO] Task started: fastANI
[2023-06-08 13:52:24,530] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc7fed70-73a0-44de-ae05-2cdd4ef69974/GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna.gz --refList GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/target_genomes.txt --output GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:52:30,071] [INFO] Task succeeded: fastANI
[2023-06-08 13:52:30,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4912356b-9d0b-454e-bc77-3961309f7fb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:52:30,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4912356b-9d0b-454e-bc77-3961309f7fb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:52:30,088] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 13:52:30,089] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 13:52:30,089] [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 jalaludinii	strain=DSM 13811	GCA_000702905.1	187979	187979	type	True	98.5623	614	655	95	conclusive
Mitsuokella multacida	strain=DSM 20544	GCA_000155955.1	52226	52226	type	True	90.1472	589	655	95	below_threshold
Selenomonas montiformis	strain=WCA-380-WT-3B3	GCA_009697385.1	2652285	2652285	type	True	79.7102	177	655	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000208405.1	69823	69823	neotype	True	77.9786	202	655	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000160495.1	69823	69823	neotype	True	77.9365	210	655	95	below_threshold
Selenomonas timonae	strain=Marseille-Q3039	GCA_014250475.1	2754044	2754044	type	True	77.7434	157	655	95	below_threshold
Selenomonas felix	strain=Marseille-P3560	GCA_900186465.1	1944634	1944634	type	True	77.6954	138	655	95	below_threshold
Selenomonas flueggei	strain=ATCC 43531	GCA_000160695.1	135080	135080	type	True	77.2205	116	655	95	below_threshold
Selenomonas artemidis	strain=DSM 19719	GCA_000426665.1	671224	671224	type	True	77.1287	139	655	95	below_threshold
Selenomonas infelix	strain=ATCC 43532	GCA_000234095.1	135082	135082	type	True	77.0273	122	655	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 13:52:30,091] [INFO] DFAST Taxonomy check result was written to GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/tc_result.tsv
[2023-06-08 13:52:30,091] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:52:30,092] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:52:30,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4912356b-9d0b-454e-bc77-3961309f7fb8/dqc_reference/checkm_data
[2023-06-08 13:52:30,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:52:30,129] [INFO] Task started: CheckM
[2023-06-08 13:52:30,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/checkm_input GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/checkm_result
[2023-06-08 13:52:53,388] [INFO] Task succeeded: CheckM
[2023-06-08 13:52:53,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:52:53,408] [INFO] ===== Completeness check finished =====
[2023-06-08 13:52:53,408] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:52:53,409] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/markers.fasta)
[2023-06-08 13:52:53,409] [INFO] Task started: Blastn
[2023-06-08 13:52:53,409] [INFO] Running command: blastn -query GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/markers.fasta -db /var/lib/cwl/stg4912356b-9d0b-454e-bc77-3961309f7fb8/dqc_reference/reference_markers_gtdb.fasta -out GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:52:54,394] [INFO] Task succeeded: Blastn
[2023-06-08 13:52:54,398] [INFO] Selected 9 target genomes.
[2023-06-08 13:52:54,398] [INFO] Target genome list was writen to GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:52:54,400] [INFO] Task started: fastANI
[2023-06-08 13:52:54,400] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc7fed70-73a0-44de-ae05-2cdd4ef69974/GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna.gz --refList GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/target_genomes_gtdb.txt --output GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:52:59,214] [INFO] Task succeeded: fastANI
[2023-06-08 13:52:59,231] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 13:52:59,231] [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
GCF_000702905.1	s__Mitsuokella jalaludinii	98.5301	615	655	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	98.12	97.46	0.90	0.85	11	conclusive
GCF_000155955.1	s__Mitsuokella multacida	90.1348	590	655	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	97.52	96.22	0.92	0.87	5	-
GCA_900552565.1	s__Mitsuokella sp900552565	84.2639	416	655	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	99.02	98.08	0.93	0.92	3	-
GCA_902364065.1	s__Mitsuokella sp003458855	83.399	468	655	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	97.62	95.79	0.87	0.62	6	-
GCA_902763085.1	s__Selenomonas_C sp002351185	80.7805	307	655	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	-
GCA_900315575.1	s__Selenomonas_C sp900315575	80.6229	339	655	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_900318215.1	s__Selenomonas_C sp900318215	80.5085	304	655	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	-
GCA_902780535.1	s__Selenomonas_C sp902780535	80.5074	332	655	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	-
GCF_000469545.1	s__Mitsuokella sp000469545	79.0922	260	655	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	98.87	98.87	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-08 13:52:59,234] [INFO] GTDB search result was written to GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/result_gtdb.tsv
[2023-06-08 13:52:59,234] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:52:59,239] [INFO] DFAST_QC result json was written to GCA_902763045.1_Rumen_uncultured_genome_RUG10819_genomic.fna/dqc_result.json
[2023-06-08 13:52:59,239] [INFO] DFAST_QC completed!
[2023-06-08 13:52:59,239] [INFO] Total running time: 0h0m44s