[2024-01-24 12:13:54,698] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:54,702] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:54,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c3480c8-c5e4-4470-80dd-0be29ff1d32a/dqc_reference
[2024-01-24 12:13:57,516] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:57,517] [INFO] Task started: Prodigal
[2024-01-24 12:13:57,518] [INFO] Running command: gunzip -c /var/lib/cwl/stg70e2bc3a-ad4e-4940-9652-d840361c1253/GCF_000155955.1_ASM15595v1_genomic.fna.gz | prodigal -d GCF_000155955.1_ASM15595v1_genomic.fna/cds.fna -a GCF_000155955.1_ASM15595v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:05,408] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:05,408] [INFO] Task started: HMMsearch
[2024-01-24 12:14:05,409] [INFO] Running command: hmmsearch --tblout GCF_000155955.1_ASM15595v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c3480c8-c5e4-4470-80dd-0be29ff1d32a/dqc_reference/reference_markers.hmm GCF_000155955.1_ASM15595v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:05,702] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:05,703] [INFO] Found 6/6 markers.
[2024-01-24 12:14:05,731] [INFO] Query marker FASTA was written to GCF_000155955.1_ASM15595v1_genomic.fna/markers.fasta
[2024-01-24 12:14:05,731] [INFO] Task started: Blastn
[2024-01-24 12:14:05,731] [INFO] Running command: blastn -query GCF_000155955.1_ASM15595v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c3480c8-c5e4-4470-80dd-0be29ff1d32a/dqc_reference/reference_markers.fasta -out GCF_000155955.1_ASM15595v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:06,454] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:06,457] [INFO] Selected 12 target genomes.
[2024-01-24 12:14:06,458] [INFO] Target genome list was writen to GCF_000155955.1_ASM15595v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:06,473] [INFO] Task started: fastANI
[2024-01-24 12:14:06,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg70e2bc3a-ad4e-4940-9652-d840361c1253/GCF_000155955.1_ASM15595v1_genomic.fna.gz --refList GCF_000155955.1_ASM15595v1_genomic.fna/target_genomes.txt --output GCF_000155955.1_ASM15595v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:13,432] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:13,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c3480c8-c5e4-4470-80dd-0be29ff1d32a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:13,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c3480c8-c5e4-4470-80dd-0be29ff1d32a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:13,518] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:13,518] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:13,518] [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	100.0	856	856	95	conclusive
Mitsuokella jalaludinii	strain=DSM 13811	GCA_000702905.1	187979	187979	type	True	90.3672	664	856	95	below_threshold
Selenomonas montiformis	strain=WCA-380-WT-3B3	GCA_009697385.1	2652285	2652285	type	True	80.2853	207	856	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000208405.1	69823	69823	neotype	True	78.6012	239	856	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000160495.1	69823	69823	neotype	True	78.5375	241	856	95	below_threshold
Selenomonas ruminantium subsp. ruminantium	strain=ATCC 12561	GCA_000424065.1	114196	971	type	True	78.3182	128	856	95	below_threshold
Selenomonas infelix	strain=ATCC 43532	GCA_000234095.1	135082	135082	type	True	77.8169	118	856	95	below_threshold
Selenomonas timonae	strain=Marseille-Q3039	GCA_014250475.1	2754044	2754044	type	True	77.6513	181	856	95	below_threshold
Selenomonas felix	strain=Marseille-P3560	GCA_900186465.1	1944634	1944634	type	True	77.6033	166	856	95	below_threshold
Selenomonas artemidis	strain=DSM 19719	GCA_000426665.1	671224	671224	type	True	77.2493	129	856	95	below_threshold
Paenibacillus pasadenensis	strain=DSM 19293	GCA_000422485.1	217090	217090	type	True	76.2472	64	856	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:13,521] [INFO] DFAST Taxonomy check result was written to GCF_000155955.1_ASM15595v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:13,522] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:13,522] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:13,523] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c3480c8-c5e4-4470-80dd-0be29ff1d32a/dqc_reference/checkm_data
[2024-01-24 12:14:13,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:13,557] [INFO] Task started: CheckM
[2024-01-24 12:14:13,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000155955.1_ASM15595v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000155955.1_ASM15595v1_genomic.fna/checkm_input GCF_000155955.1_ASM15595v1_genomic.fna/checkm_result
[2024-01-24 12:14:41,557] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:41,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:41,583] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:41,583] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:41,583] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000155955.1_ASM15595v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:41,583] [INFO] Task started: Blastn
[2024-01-24 12:14:41,584] [INFO] Running command: blastn -query GCF_000155955.1_ASM15595v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c3480c8-c5e4-4470-80dd-0be29ff1d32a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000155955.1_ASM15595v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:42,683] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:42,688] [INFO] Selected 8 target genomes.
[2024-01-24 12:14:42,688] [INFO] Target genome list was writen to GCF_000155955.1_ASM15595v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:42,750] [INFO] Task started: fastANI
[2024-01-24 12:14:42,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg70e2bc3a-ad4e-4940-9652-d840361c1253/GCF_000155955.1_ASM15595v1_genomic.fna.gz --refList GCF_000155955.1_ASM15595v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000155955.1_ASM15595v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:47,855] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:47,867] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:47,867] [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_000155955.1	s__Mitsuokella multacida	100.0	856	856	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	97.52	96.22	0.92	0.87	5	conclusive
GCF_000702905.1	s__Mitsuokella jalaludinii	90.3492	665	856	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	98.12	97.46	0.90	0.85	11	-
GCA_902364065.1	s__Mitsuokella sp003458855	84.1088	546	856	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_900552565.1	s__Mitsuokella sp900552565	83.8196	461	856	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_900318215.1	s__Selenomonas_C sp900318215	80.9589	321	856	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	80.7008	372	856	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	-
GCF_000469545.1	s__Mitsuokella sp000469545	79.1606	286	856	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	98.87	98.87	0.89	0.89	2	-
GCA_900316275.1	s__UBA2897 sp900316275	79.0378	301	856	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__UBA2897	95.0	99.98	99.98	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:47,872] [INFO] GTDB search result was written to GCF_000155955.1_ASM15595v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:47,873] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:47,879] [INFO] DFAST_QC result json was written to GCF_000155955.1_ASM15595v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:47,880] [INFO] DFAST_QC completed!
[2024-01-24 12:14:47,880] [INFO] Total running time: 0h0m53s