[2024-01-24 12:30:52,771] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:52,773] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:52,773] [INFO] DQC Reference Directory: /var/lib/cwl/stgccb5e19f-edf6-4747-8238-bec094476b0b/dqc_reference
[2024-01-24 12:30:54,097] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:54,103] [INFO] Task started: Prodigal
[2024-01-24 12:30:54,103] [INFO] Running command: gunzip -c /var/lib/cwl/stge046a79a-b84d-4027-b469-6c863eed35c0/GCF_008271345.1_ASM827134v1_genomic.fna.gz | prodigal -d GCF_008271345.1_ASM827134v1_genomic.fna/cds.fna -a GCF_008271345.1_ASM827134v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:02,873] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:02,873] [INFO] Task started: HMMsearch
[2024-01-24 12:31:02,873] [INFO] Running command: hmmsearch --tblout GCF_008271345.1_ASM827134v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccb5e19f-edf6-4747-8238-bec094476b0b/dqc_reference/reference_markers.hmm GCF_008271345.1_ASM827134v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:03,157] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:03,159] [INFO] Found 6/6 markers.
[2024-01-24 12:31:03,197] [INFO] Query marker FASTA was written to GCF_008271345.1_ASM827134v1_genomic.fna/markers.fasta
[2024-01-24 12:31:03,198] [INFO] Task started: Blastn
[2024-01-24 12:31:03,198] [INFO] Running command: blastn -query GCF_008271345.1_ASM827134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccb5e19f-edf6-4747-8238-bec094476b0b/dqc_reference/reference_markers.fasta -out GCF_008271345.1_ASM827134v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:03,885] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:03,889] [INFO] Selected 14 target genomes.
[2024-01-24 12:31:03,889] [INFO] Target genome list was writen to GCF_008271345.1_ASM827134v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:03,899] [INFO] Task started: fastANI
[2024-01-24 12:31:03,899] [INFO] Running command: fastANI --query /var/lib/cwl/stge046a79a-b84d-4027-b469-6c863eed35c0/GCF_008271345.1_ASM827134v1_genomic.fna.gz --refList GCF_008271345.1_ASM827134v1_genomic.fna/target_genomes.txt --output GCF_008271345.1_ASM827134v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:12,592] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:12,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccb5e19f-edf6-4747-8238-bec094476b0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:12,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccb5e19f-edf6-4747-8238-bec094476b0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:12,604] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:31:12,604] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:31:12,604] [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
Selenomonas montiformis	strain=WCA-380-WT-3B3	GCA_009697385.1	2652285	2652285	type	True	79.6202	313	977	95	below_threshold
Mitsuokella jalaludinii	strain=DSM 13811	GCA_000702905.1	187979	187979	type	True	79.6039	317	977	95	below_threshold
Mitsuokella multacida	strain=DSM 20544	GCA_000155955.1	52226	52226	type	True	79.5001	331	977	95	below_threshold
Selenomonas ruminantium subsp. ruminantium	strain=ATCC 12561	GCA_000424065.1	114196	971	type	True	79.3802	296	977	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000160495.1	69823	69823	neotype	True	76.8241	120	977	95	below_threshold
Selenomonas felix	strain=Marseille-P3560	GCA_900186465.1	1944634	1944634	type	True	76.7915	108	977	95	below_threshold
Selenomonas artemidis	strain=DSM 19719	GCA_000426665.1	671224	671224	type	True	76.7029	75	977	95	below_threshold
Selenomonas timonae	strain=Marseille-Q3039	GCA_014250475.1	2754044	2754044	type	True	76.5573	103	977	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:12,605] [INFO] DFAST Taxonomy check result was written to GCF_008271345.1_ASM827134v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:12,606] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:12,606] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:12,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccb5e19f-edf6-4747-8238-bec094476b0b/dqc_reference/checkm_data
[2024-01-24 12:31:12,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:12,638] [INFO] Task started: CheckM
[2024-01-24 12:31:12,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008271345.1_ASM827134v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008271345.1_ASM827134v1_genomic.fna/checkm_input GCF_008271345.1_ASM827134v1_genomic.fna/checkm_result
[2024-01-24 12:31:43,352] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:43,355] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:43,372] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:43,372] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:43,373] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008271345.1_ASM827134v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:43,373] [INFO] Task started: Blastn
[2024-01-24 12:31:43,373] [INFO] Running command: blastn -query GCF_008271345.1_ASM827134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccb5e19f-edf6-4747-8238-bec094476b0b/dqc_reference/reference_markers_gtdb.fasta -out GCF_008271345.1_ASM827134v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:44,355] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:44,359] [INFO] Selected 7 target genomes.
[2024-01-24 12:31:44,359] [INFO] Target genome list was writen to GCF_008271345.1_ASM827134v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:44,559] [INFO] Task started: fastANI
[2024-01-24 12:31:44,559] [INFO] Running command: fastANI --query /var/lib/cwl/stge046a79a-b84d-4027-b469-6c863eed35c0/GCF_008271345.1_ASM827134v1_genomic.fna.gz --refList GCF_008271345.1_ASM827134v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008271345.1_ASM827134v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:49,583] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:49,590] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:49,590] [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_900113715.1	s__Selenomonas_A ruminantium_F	97.4056	818	977	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	97.92	97.43	0.89	0.84	3	conclusive
GCA_015058575.1	s__Selenomonas_A ruminantium_O	91.5354	755	977	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116485.1	s__Selenomonas_A ruminantium_G	88.826	726	977	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702005.1	s__Selenomonas_A sp000702005	83.0085	523	977	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	98.34	98.34	0.89	0.89	2	-
GCF_900100835.1	s__Selenomonas_A ruminantium_E	82.6101	515	977	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271295.1	s__Selenomonas_A sp008271295	82.2182	539	977	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	98.50	98.50	0.96	0.96	2	-
GCA_018052705.1	s__Selenomonas_A sp018052705	79.013	253	977	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:49,592] [INFO] GTDB search result was written to GCF_008271345.1_ASM827134v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:49,592] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:49,598] [INFO] DFAST_QC result json was written to GCF_008271345.1_ASM827134v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:49,599] [INFO] DFAST_QC completed!
[2024-01-24 12:31:49,599] [INFO] Total running time: 0h0m57s