[2023-06-05 18:01:56,891] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:01:56,893] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:01:56,893] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b661fbb-e112-4e34-89a9-20fc57038b00/dqc_reference
[2023-06-05 18:01:59,890] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:01:59,894] [INFO] Task started: Prodigal
[2023-06-05 18:01:59,894] [INFO] Running command: gunzip -c /var/lib/cwl/stg3dd42560-79f6-4273-ab9a-af800c16cea3/GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna.gz | prodigal -d GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/cds.fna -a GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:02:10,318] [INFO] Task succeeded: Prodigal
[2023-06-05 18:02:10,318] [INFO] Task started: HMMsearch
[2023-06-05 18:02:10,318] [INFO] Running command: hmmsearch --tblout GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b661fbb-e112-4e34-89a9-20fc57038b00/dqc_reference/reference_markers.hmm GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:02:10,597] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:02:10,598] [INFO] Found 6/6 markers.
[2023-06-05 18:02:10,646] [INFO] Query marker FASTA was written to GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/markers.fasta
[2023-06-05 18:02:10,646] [INFO] Task started: Blastn
[2023-06-05 18:02:10,647] [INFO] Running command: blastn -query GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b661fbb-e112-4e34-89a9-20fc57038b00/dqc_reference/reference_markers.fasta -out GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:02:11,518] [INFO] Task succeeded: Blastn
[2023-06-05 18:02:11,523] [INFO] Selected 13 target genomes.
[2023-06-05 18:02:11,523] [INFO] Target genome list was writen to GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/target_genomes.txt
[2023-06-05 18:02:11,526] [INFO] Task started: fastANI
[2023-06-05 18:02:11,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dd42560-79f6-4273-ab9a-af800c16cea3/GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna.gz --refList GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/target_genomes.txt --output GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:02:19,045] [INFO] Task succeeded: fastANI
[2023-06-05 18:02:19,045] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b661fbb-e112-4e34-89a9-20fc57038b00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:02:19,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b661fbb-e112-4e34-89a9-20fc57038b00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:02:19,056] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:02:19,056] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:02:19,057] [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	80.957	348	817	95	below_threshold
Mitsuokella jalaludinii	strain=DSM 13811	GCA_000702905.1	187979	187979	type	True	80.7819	340	817	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000208405.1	69823	69823	neotype	True	77.8141	215	817	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000160495.1	69823	69823	neotype	True	77.7344	217	817	95	below_threshold
Selenomonas montiformis	strain=WCA-380-WT-3B3	GCA_009697385.1	2652285	2652285	type	True	77.4527	139	817	95	below_threshold
Selenomonas artemidis	strain=DSM 19719	GCA_000426665.1	671224	671224	type	True	77.447	133	817	95	below_threshold
Selenomonas ruminantium subsp. ruminantium	strain=ATCC 12561	GCA_000424065.1	114196	971	type	True	77.2785	93	817	95	below_threshold
Selenomonas flueggei	strain=ATCC 43531	GCA_000160695.1	135080	135080	type	True	77.2001	125	817	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	75.1049	54	817	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:02:19,059] [INFO] DFAST Taxonomy check result was written to GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/tc_result.tsv
[2023-06-05 18:02:19,059] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:02:19,059] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:02:19,060] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b661fbb-e112-4e34-89a9-20fc57038b00/dqc_reference/checkm_data
[2023-06-05 18:02:19,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:02:19,118] [INFO] Task started: CheckM
[2023-06-05 18:02:19,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/checkm_input GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/checkm_result
[2023-06-05 18:02:50,352] [INFO] Task succeeded: CheckM
[2023-06-05 18:02:50,353] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:02:50,395] [INFO] ===== Completeness check finished =====
[2023-06-05 18:02:50,395] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:02:50,396] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/markers.fasta)
[2023-06-05 18:02:50,396] [INFO] Task started: Blastn
[2023-06-05 18:02:50,396] [INFO] Running command: blastn -query GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b661fbb-e112-4e34-89a9-20fc57038b00/dqc_reference/reference_markers_gtdb.fasta -out GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:02:51,415] [INFO] Task succeeded: Blastn
[2023-06-05 18:02:51,437] [INFO] Selected 7 target genomes.
[2023-06-05 18:02:51,438] [INFO] Target genome list was writen to GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:02:51,444] [INFO] Task started: fastANI
[2023-06-05 18:02:51,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dd42560-79f6-4273-ab9a-af800c16cea3/GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna.gz --refList GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/target_genomes_gtdb.txt --output GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:02:57,523] [INFO] Task succeeded: fastANI
[2023-06-05 18:02:57,531] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:02:57,531] [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_902780535.1	s__Selenomonas_C sp902780535	97.1803	665	817	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	conclusive
GCA_900318215.1	s__Selenomonas_C sp900318215	93.9543	538	817	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_900315575.1	s__Selenomonas_C sp900315575	92.6224	601	817	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	84.0126	543	817	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	-
GCF_000381005.1	s__Selenomonas_C bovis	81.7448	417	817	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_902763085.1	s__Selenomonas_C sp002351185	81.6155	380	817	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_000702905.1	s__Mitsuokella jalaludinii	80.8181	338	817	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	98.12	97.46	0.90	0.85	11	-
--------------------------------------------------------------------------------
[2023-06-05 18:02:57,535] [INFO] GTDB search result was written to GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/result_gtdb.tsv
[2023-06-05 18:02:57,536] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:02:57,540] [INFO] DFAST_QC result json was written to GCA_902781695.1_Rumen_uncultured_genome_RUG12704_genomic.fna/dqc_result.json
[2023-06-05 18:02:57,540] [INFO] DFAST_QC completed!
[2023-06-05 18:02:57,540] [INFO] Total running time: 0h1m1s