[2024-01-25 19:00:05,774] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:00:05,777] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:00:05,777] [INFO] DQC Reference Directory: /var/lib/cwl/stg86cce8fc-4c6f-4927-ae41-c3aed085de46/dqc_reference
[2024-01-25 19:00:07,000] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:00:07,001] [INFO] Task started: Prodigal
[2024-01-25 19:00:07,002] [INFO] Running command: gunzip -c /var/lib/cwl/stg672a7d25-0709-487e-9b17-0ee3467ccd6c/GCF_000381005.1_ASM38100v1_genomic.fna.gz | prodigal -d GCF_000381005.1_ASM38100v1_genomic.fna/cds.fna -a GCF_000381005.1_ASM38100v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:00:13,623] [INFO] Task succeeded: Prodigal
[2024-01-25 19:00:13,623] [INFO] Task started: HMMsearch
[2024-01-25 19:00:13,624] [INFO] Running command: hmmsearch --tblout GCF_000381005.1_ASM38100v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86cce8fc-4c6f-4927-ae41-c3aed085de46/dqc_reference/reference_markers.hmm GCF_000381005.1_ASM38100v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:00:13,834] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:00:13,835] [INFO] Found 6/6 markers.
[2024-01-25 19:00:13,859] [INFO] Query marker FASTA was written to GCF_000381005.1_ASM38100v1_genomic.fna/markers.fasta
[2024-01-25 19:00:13,860] [INFO] Task started: Blastn
[2024-01-25 19:00:13,860] [INFO] Running command: blastn -query GCF_000381005.1_ASM38100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86cce8fc-4c6f-4927-ae41-c3aed085de46/dqc_reference/reference_markers.fasta -out GCF_000381005.1_ASM38100v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:14,477] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:14,479] [INFO] Selected 10 target genomes.
[2024-01-25 19:00:14,479] [INFO] Target genome list was writen to GCF_000381005.1_ASM38100v1_genomic.fna/target_genomes.txt
[2024-01-25 19:00:14,487] [INFO] Task started: fastANI
[2024-01-25 19:00:14,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg672a7d25-0709-487e-9b17-0ee3467ccd6c/GCF_000381005.1_ASM38100v1_genomic.fna.gz --refList GCF_000381005.1_ASM38100v1_genomic.fna/target_genomes.txt --output GCF_000381005.1_ASM38100v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:00:19,153] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:19,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86cce8fc-4c6f-4927-ae41-c3aed085de46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:00:19,154] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86cce8fc-4c6f-4927-ae41-c3aed085de46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:00:19,160] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:00:19,161] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:00:19,161] [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	80.9649	374	857	95	below_threshold
Mitsuokella jalaludinii	strain=DSM 13811	GCA_000702905.1	187979	187979	type	True	80.9277	362	857	95	below_threshold
Selenomonas montiformis	strain=WCA-380-WT-3B3	GCA_009697385.1	2652285	2652285	type	True	78.8122	172	857	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000160495.1	69823	69823	neotype	True	78.3426	253	857	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000208405.1	69823	69823	neotype	True	78.2974	255	857	95	below_threshold
Selenomonas timonae	strain=Marseille-Q3039	GCA_014250475.1	2754044	2754044	type	True	77.9044	173	857	95	below_threshold
Selenomonas felix	strain=Marseille-P3560	GCA_900186465.1	1944634	1944634	type	True	77.7169	158	857	95	below_threshold
Selenomonas infelix	strain=ATCC 43532	GCA_000234095.1	135082	135082	type	True	77.3871	155	857	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:00:19,162] [INFO] DFAST Taxonomy check result was written to GCF_000381005.1_ASM38100v1_genomic.fna/tc_result.tsv
[2024-01-25 19:00:19,162] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:00:19,163] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:00:19,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86cce8fc-4c6f-4927-ae41-c3aed085de46/dqc_reference/checkm_data
[2024-01-25 19:00:19,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:00:19,191] [INFO] Task started: CheckM
[2024-01-25 19:00:19,191] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000381005.1_ASM38100v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000381005.1_ASM38100v1_genomic.fna/checkm_input GCF_000381005.1_ASM38100v1_genomic.fna/checkm_result
[2024-01-25 19:00:42,349] [INFO] Task succeeded: CheckM
[2024-01-25 19:00:42,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:00:42,368] [INFO] ===== Completeness check finished =====
[2024-01-25 19:00:42,368] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:00:42,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000381005.1_ASM38100v1_genomic.fna/markers.fasta)
[2024-01-25 19:00:42,369] [INFO] Task started: Blastn
[2024-01-25 19:00:42,369] [INFO] Running command: blastn -query GCF_000381005.1_ASM38100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86cce8fc-4c6f-4927-ae41-c3aed085de46/dqc_reference/reference_markers_gtdb.fasta -out GCF_000381005.1_ASM38100v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:43,337] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:43,340] [INFO] Selected 9 target genomes.
[2024-01-25 19:00:43,340] [INFO] Target genome list was writen to GCF_000381005.1_ASM38100v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:00:43,374] [INFO] Task started: fastANI
[2024-01-25 19:00:43,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg672a7d25-0709-487e-9b17-0ee3467ccd6c/GCF_000381005.1_ASM38100v1_genomic.fna.gz --refList GCF_000381005.1_ASM38100v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000381005.1_ASM38100v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:00:49,325] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:49,332] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:00:49,333] [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_000381005.1	s__Selenomonas_C bovis	100.0	854	857	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	conclusive
GCA_902763085.1	s__Selenomonas_C sp002351185	87.532	521	857	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_902780535.1	s__Selenomonas_C sp902780535	82.0254	417	857	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_900318215.1	s__Selenomonas_C sp900318215	82.0044	380	857	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	81.9091	427	857	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	81.3428	441	857	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_000155955.1	s__Mitsuokella multacida	80.9689	374	857	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	97.52	96.22	0.92	0.87	5	-
GCF_000702905.1	s__Mitsuokella jalaludinii	80.8859	366	857	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	98.12	97.46	0.90	0.85	11	-
GCF_000469545.1	s__Mitsuokella sp000469545	79.4186	246	857	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella	95.0	98.87	98.87	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:00:49,334] [INFO] GTDB search result was written to GCF_000381005.1_ASM38100v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:00:49,335] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:00:49,337] [INFO] DFAST_QC result json was written to GCF_000381005.1_ASM38100v1_genomic.fna/dqc_result.json
[2024-01-25 19:00:49,338] [INFO] DFAST_QC completed!
[2024-01-25 19:00:49,338] [INFO] Total running time: 0h0m44s