[2023-06-13 15:44:50,225] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:44:50,239] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:44:50,239] [INFO] DQC Reference Directory: /var/lib/cwl/stg834d85f6-c405-4046-9f1c-c77fffb83645/dqc_reference
[2023-06-13 15:44:51,485] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:44:51,486] [INFO] Task started: Prodigal
[2023-06-13 15:44:51,486] [INFO] Running command: gunzip -c /var/lib/cwl/stg077f35e1-cbde-43af-bf73-2b1de8facb20/GCA_022771645.1_ASM2277164v1_genomic.fna.gz | prodigal -d GCA_022771645.1_ASM2277164v1_genomic.fna/cds.fna -a GCA_022771645.1_ASM2277164v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:44:59,091] [INFO] Task succeeded: Prodigal
[2023-06-13 15:44:59,092] [INFO] Task started: HMMsearch
[2023-06-13 15:44:59,092] [INFO] Running command: hmmsearch --tblout GCA_022771645.1_ASM2277164v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg834d85f6-c405-4046-9f1c-c77fffb83645/dqc_reference/reference_markers.hmm GCA_022771645.1_ASM2277164v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:44:59,289] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:44:59,291] [INFO] Found 6/6 markers.
[2023-06-13 15:44:59,317] [INFO] Query marker FASTA was written to GCA_022771645.1_ASM2277164v1_genomic.fna/markers.fasta
[2023-06-13 15:44:59,317] [INFO] Task started: Blastn
[2023-06-13 15:44:59,317] [INFO] Running command: blastn -query GCA_022771645.1_ASM2277164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg834d85f6-c405-4046-9f1c-c77fffb83645/dqc_reference/reference_markers.fasta -out GCA_022771645.1_ASM2277164v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:45:00,019] [INFO] Task succeeded: Blastn
[2023-06-13 15:45:00,024] [INFO] Selected 12 target genomes.
[2023-06-13 15:45:00,024] [INFO] Target genome list was writen to GCA_022771645.1_ASM2277164v1_genomic.fna/target_genomes.txt
[2023-06-13 15:45:00,026] [INFO] Task started: fastANI
[2023-06-13 15:45:00,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg077f35e1-cbde-43af-bf73-2b1de8facb20/GCA_022771645.1_ASM2277164v1_genomic.fna.gz --refList GCA_022771645.1_ASM2277164v1_genomic.fna/target_genomes.txt --output GCA_022771645.1_ASM2277164v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:45:07,136] [INFO] Task succeeded: fastANI
[2023-06-13 15:45:07,137] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg834d85f6-c405-4046-9f1c-c77fffb83645/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:45:07,137] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg834d85f6-c405-4046-9f1c-c77fffb83645/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:45:07,146] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:45:07,147] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 15:45:07,147] [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	80.7517	356	857	95	below_threshold
Mitsuokella jalaludinii	strain=DSM 13811	GCA_000702905.1	187979	187979	type	True	80.4511	345	857	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000208405.1	69823	69823	neotype	True	77.9918	212	857	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000160495.1	69823	69823	neotype	True	77.9613	216	857	95	below_threshold
Selenomonas infelix	strain=ATCC 43532	GCA_000234095.1	135082	135082	type	True	77.1455	139	857	95	below_threshold
Selenomonas artemidis	strain=DSM 19719	GCA_000426665.1	671224	671224	type	True	77.1281	147	857	95	below_threshold
Selenomonas noxia	strain=ATCC 43541	GCA_000160555.1	135083	135083	type	True	76.9545	111	857	95	below_threshold
Selenomonas ruminantium subsp. ruminantium	strain=ATCC 12561	GCA_000424065.1	114196	971	type	True	76.864	81	857	95	below_threshold
Actinoplanes tereljensis	strain=NBRC 105297	GCA_016862435.1	571912	571912	type	True	74.8471	58	857	95	below_threshold
Streptomyces varsoviensis	strain=NRRL B-3589	GCA_000719255.1	67373	67373	type	True	74.6784	71	857	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 15:45:07,149] [INFO] DFAST Taxonomy check result was written to GCA_022771645.1_ASM2277164v1_genomic.fna/tc_result.tsv
[2023-06-13 15:45:07,149] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:45:07,149] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:45:07,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg834d85f6-c405-4046-9f1c-c77fffb83645/dqc_reference/checkm_data
[2023-06-13 15:45:07,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:45:07,179] [INFO] Task started: CheckM
[2023-06-13 15:45:07,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022771645.1_ASM2277164v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022771645.1_ASM2277164v1_genomic.fna/checkm_input GCA_022771645.1_ASM2277164v1_genomic.fna/checkm_result
[2023-06-13 15:45:34,229] [INFO] Task succeeded: CheckM
[2023-06-13 15:45:34,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:45:34,253] [INFO] ===== Completeness check finished =====
[2023-06-13 15:45:34,254] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:45:34,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022771645.1_ASM2277164v1_genomic.fna/markers.fasta)
[2023-06-13 15:45:34,254] [INFO] Task started: Blastn
[2023-06-13 15:45:34,254] [INFO] Running command: blastn -query GCA_022771645.1_ASM2277164v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg834d85f6-c405-4046-9f1c-c77fffb83645/dqc_reference/reference_markers_gtdb.fasta -out GCA_022771645.1_ASM2277164v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:45:35,293] [INFO] Task succeeded: Blastn
[2023-06-13 15:45:35,297] [INFO] Selected 6 target genomes.
[2023-06-13 15:45:35,297] [INFO] Target genome list was writen to GCA_022771645.1_ASM2277164v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:45:35,301] [INFO] Task started: fastANI
[2023-06-13 15:45:35,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg077f35e1-cbde-43af-bf73-2b1de8facb20/GCA_022771645.1_ASM2277164v1_genomic.fna.gz --refList GCA_022771645.1_ASM2277164v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022771645.1_ASM2277164v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:45:39,660] [INFO] Task succeeded: fastANI
[2023-06-13 15:45:39,669] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 15:45:39,669] [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_900314825.1	s__Selenomonas_C sp900314825	87.5427	630	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	-
GCA_900318215.1	s__Selenomonas_C sp900318215	84.6322	476	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	84.6119	540	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_902780535.1	s__Selenomonas_C sp902780535	84.5394	537	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_902763085.1	s__Selenomonas_C sp002351185	81.8331	393	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	-
GCF_000381005.1	s__Selenomonas_C bovis	81.6634	434	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	-
--------------------------------------------------------------------------------
[2023-06-13 15:45:39,671] [INFO] GTDB search result was written to GCA_022771645.1_ASM2277164v1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:45:39,673] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:45:39,677] [INFO] DFAST_QC result json was written to GCA_022771645.1_ASM2277164v1_genomic.fna/dqc_result.json
[2023-06-13 15:45:39,677] [INFO] DFAST_QC completed!
[2023-06-13 15:45:39,677] [INFO] Total running time: 0h0m49s