[2024-01-24 13:54:11,183] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:54:11,185] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:54:11,185] [INFO] DQC Reference Directory: /var/lib/cwl/stge7dddb93-1015-4710-b252-b87d63316743/dqc_reference
[2024-01-24 13:54:12,529] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:54:12,530] [INFO] Task started: Prodigal
[2024-01-24 13:54:12,530] [INFO] Running command: gunzip -c /var/lib/cwl/stg88e06a34-d3d9-4147-8303-98885f7da30d/GCF_000213975.1_ASM21397v1_genomic.fna.gz | prodigal -d GCF_000213975.1_ASM21397v1_genomic.fna/cds.fna -a GCF_000213975.1_ASM21397v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:54:21,465] [INFO] Task succeeded: Prodigal
[2024-01-24 13:54:21,466] [INFO] Task started: HMMsearch
[2024-01-24 13:54:21,466] [INFO] Running command: hmmsearch --tblout GCF_000213975.1_ASM21397v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7dddb93-1015-4710-b252-b87d63316743/dqc_reference/reference_markers.hmm GCF_000213975.1_ASM21397v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:54:21,821] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:54:21,822] [INFO] Found 6/6 markers.
[2024-01-24 13:54:21,854] [INFO] Query marker FASTA was written to GCF_000213975.1_ASM21397v1_genomic.fna/markers.fasta
[2024-01-24 13:54:21,854] [INFO] Task started: Blastn
[2024-01-24 13:54:21,854] [INFO] Running command: blastn -query GCF_000213975.1_ASM21397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7dddb93-1015-4710-b252-b87d63316743/dqc_reference/reference_markers.fasta -out GCF_000213975.1_ASM21397v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:54:22,520] [INFO] Task succeeded: Blastn
[2024-01-24 13:54:22,524] [INFO] Selected 12 target genomes.
[2024-01-24 13:54:22,524] [INFO] Target genome list was writen to GCF_000213975.1_ASM21397v1_genomic.fna/target_genomes.txt
[2024-01-24 13:54:22,528] [INFO] Task started: fastANI
[2024-01-24 13:54:22,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg88e06a34-d3d9-4147-8303-98885f7da30d/GCF_000213975.1_ASM21397v1_genomic.fna.gz --refList GCF_000213975.1_ASM21397v1_genomic.fna/target_genomes.txt --output GCF_000213975.1_ASM21397v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:54:30,652] [INFO] Task succeeded: fastANI
[2024-01-24 13:54:30,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7dddb93-1015-4710-b252-b87d63316743/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:54:30,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7dddb93-1015-4710-b252-b87d63316743/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:54:30,663] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:54:30,663] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:54:30,663] [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 timonae	strain=Marseille-Q3039	GCA_014250475.1	2754044	2754044	type	True	84.9147	611	917	95	below_threshold
Selenomonas infelix	strain=ATCC 43532	GCA_000234095.1	135082	135082	type	True	84.8435	587	917	95	below_threshold
Selenomonas felix	strain=Marseille-P3560	GCA_900186465.1	1944634	1944634	type	True	82.4109	500	917	95	below_threshold
Selenomonas noxia	strain=ATCC 43541	GCA_000160555.1	135083	135083	type	True	81.7739	470	917	95	below_threshold
Selenomonas flueggei	strain=ATCC 43531	GCA_000160695.1	135080	135080	type	True	81.5568	439	917	95	below_threshold
Selenomonas artemidis	strain=DSM 19719	GCA_000426665.1	671224	671224	type	True	81.0948	403	917	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:54:30,665] [INFO] DFAST Taxonomy check result was written to GCF_000213975.1_ASM21397v1_genomic.fna/tc_result.tsv
[2024-01-24 13:54:30,666] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:54:30,666] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:54:30,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7dddb93-1015-4710-b252-b87d63316743/dqc_reference/checkm_data
[2024-01-24 13:54:30,668] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:54:30,698] [INFO] Task started: CheckM
[2024-01-24 13:54:30,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000213975.1_ASM21397v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000213975.1_ASM21397v1_genomic.fna/checkm_input GCF_000213975.1_ASM21397v1_genomic.fna/checkm_result
[2024-01-24 13:55:03,060] [INFO] Task succeeded: CheckM
[2024-01-24 13:55:03,061] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:55:03,083] [INFO] ===== Completeness check finished =====
[2024-01-24 13:55:03,083] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:55:03,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000213975.1_ASM21397v1_genomic.fna/markers.fasta)
[2024-01-24 13:55:03,084] [INFO] Task started: Blastn
[2024-01-24 13:55:03,085] [INFO] Running command: blastn -query GCF_000213975.1_ASM21397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge7dddb93-1015-4710-b252-b87d63316743/dqc_reference/reference_markers_gtdb.fasta -out GCF_000213975.1_ASM21397v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:04,097] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:04,102] [INFO] Selected 9 target genomes.
[2024-01-24 13:55:04,103] [INFO] Target genome list was writen to GCF_000213975.1_ASM21397v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:55:04,105] [INFO] Task started: fastANI
[2024-01-24 13:55:04,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg88e06a34-d3d9-4147-8303-98885f7da30d/GCF_000213975.1_ASM21397v1_genomic.fna.gz --refList GCF_000213975.1_ASM21397v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000213975.1_ASM21397v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:55:11,344] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:11,357] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:55:11,358] [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_000213975.1	s__Centipeda periodontii	99.9901	909	917	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Centipeda	95.0	98.08	98.08	0.86	0.86	2	conclusive
GCF_900290285.1	s__Centipeda massiliensis	86.0329	631	917	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Centipeda	95.0	97.87	97.87	0.91	0.91	2	-
GCF_001717585.1	s__Centipeda sp001717585	85.4145	598	917	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Centipeda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905372865.1	s__Centipeda sp905372865	85.1639	560	917	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Centipeda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000286455.1	s__Centipeda sp000286455	85.0591	581	917	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Centipeda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014250475.1	s__Centipeda sp000318175	84.9142	610	917	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Centipeda	95.0	96.58	96.58	0.89	0.89	2	-
GCF_001683335.1	s__Centipeda sp001683335	84.9075	649	917	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Centipeda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000234095.1	s__Centipeda infelix	84.8142	590	917	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Centipeda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000468035.1	s__Centipeda sp000468035	84.2	550	917	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Centipeda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:55:11,360] [INFO] GTDB search result was written to GCF_000213975.1_ASM21397v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:55:11,360] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:55:11,364] [INFO] DFAST_QC result json was written to GCF_000213975.1_ASM21397v1_genomic.fna/dqc_result.json
[2024-01-24 13:55:11,364] [INFO] DFAST_QC completed!
[2024-01-24 13:55:11,365] [INFO] Total running time: 0h1m0s