[2024-01-24 14:46:57,549] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:57,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:57,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d0ad1d6-55c0-45cd-a44e-139daf52ba71/dqc_reference
[2024-01-24 14:46:58,965] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,966] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,966] [INFO] Running command: gunzip -c /var/lib/cwl/stg934f4777-affb-47e9-9c47-e3d61faef9a2/GCF_009720525.1_ASM972052v1_genomic.fna.gz | prodigal -d GCF_009720525.1_ASM972052v1_genomic.fna/cds.fna -a GCF_009720525.1_ASM972052v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:24,258] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:24,259] [INFO] Task started: HMMsearch
[2024-01-24 14:47:24,259] [INFO] Running command: hmmsearch --tblout GCF_009720525.1_ASM972052v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d0ad1d6-55c0-45cd-a44e-139daf52ba71/dqc_reference/reference_markers.hmm GCF_009720525.1_ASM972052v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:24,657] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:24,659] [INFO] Found 6/6 markers.
[2024-01-24 14:47:24,903] [INFO] Query marker FASTA was written to GCF_009720525.1_ASM972052v1_genomic.fna/markers.fasta
[2024-01-24 14:47:24,904] [INFO] Task started: Blastn
[2024-01-24 14:47:24,904] [INFO] Running command: blastn -query GCF_009720525.1_ASM972052v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d0ad1d6-55c0-45cd-a44e-139daf52ba71/dqc_reference/reference_markers.fasta -out GCF_009720525.1_ASM972052v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:25,634] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:25,641] [INFO] Selected 12 target genomes.
[2024-01-24 14:47:25,642] [INFO] Target genome list was writen to GCF_009720525.1_ASM972052v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:25,648] [INFO] Task started: fastANI
[2024-01-24 14:47:25,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg934f4777-affb-47e9-9c47-e3d61faef9a2/GCF_009720525.1_ASM972052v1_genomic.fna.gz --refList GCF_009720525.1_ASM972052v1_genomic.fna/target_genomes.txt --output GCF_009720525.1_ASM972052v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:40,288] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:40,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d0ad1d6-55c0-45cd-a44e-139daf52ba71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:40,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d0ad1d6-55c0-45cd-a44e-139daf52ba71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:40,297] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:47:40,297] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:47:40,297] [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
Gimesia benthica	strain=E7	GCA_009720525.1	2608982	2608982	type	True	100.0	2675	2675	95	inconclusive
Gimesia chilikensis	strain=JC646	GCA_008329715.1	2605989	2605989	type	True	95.0199	2235	2675	95	inconclusive
Gimesia panareensis	strain=Enr10	GCA_007748155.1	2527978	2527978	type	True	83.4542	1905	2675	95	below_threshold
Gimesia algae	strain=Pan161	GCA_007746795.1	2527971	2527971	type	True	78.7044	943	2675	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_008298035.1	122	122	type	True	78.6944	985	2675	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_000181475.1	122	122	type	True	78.6862	959	2675	95	below_threshold
Gimesia alba	strain=Pan241w	GCA_007744675.1	2527973	2527973	type	True	78.5338	908	2675	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:40,301] [INFO] DFAST Taxonomy check result was written to GCF_009720525.1_ASM972052v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:40,301] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:40,302] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:40,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d0ad1d6-55c0-45cd-a44e-139daf52ba71/dqc_reference/checkm_data
[2024-01-24 14:47:40,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:40,385] [INFO] Task started: CheckM
[2024-01-24 14:47:40,385] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009720525.1_ASM972052v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009720525.1_ASM972052v1_genomic.fna/checkm_input GCF_009720525.1_ASM972052v1_genomic.fna/checkm_result
[2024-01-24 14:48:51,265] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:51,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:51,293] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:51,294] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:51,294] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009720525.1_ASM972052v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:51,295] [INFO] Task started: Blastn
[2024-01-24 14:48:51,295] [INFO] Running command: blastn -query GCF_009720525.1_ASM972052v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d0ad1d6-55c0-45cd-a44e-139daf52ba71/dqc_reference/reference_markers_gtdb.fasta -out GCF_009720525.1_ASM972052v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:52,135] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:52,138] [INFO] Selected 8 target genomes.
[2024-01-24 14:48:52,138] [INFO] Target genome list was writen to GCF_009720525.1_ASM972052v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:52,145] [INFO] Task started: fastANI
[2024-01-24 14:48:52,146] [INFO] Running command: fastANI --query /var/lib/cwl/stg934f4777-affb-47e9-9c47-e3d61faef9a2/GCF_009720525.1_ASM972052v1_genomic.fna.gz --refList GCF_009720525.1_ASM972052v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009720525.1_ASM972052v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:07,348] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:07,361] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:07,361] [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_009720525.1	s__Gimesia benthica	100.0	2674	2675	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0249	95.18	95.18	0.86	0.86	2	conclusive
GCF_008329715.1	s__Gimesia chilikensis	95.0107	2236	2675	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0249	95.30	95.11	0.90	0.87	4	-
GCF_007748155.1	s__Gimesia panareensis	83.447	1907	2675	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	96.61	95.86	0.91	0.90	3	-
GCA_002706765.1	s__Gimesia sp002706765	79.4253	1048	2675	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	99.96	99.96	0.97	0.97	2	-
GCF_007746795.1	s__Gimesia algae	78.7089	942	2675	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008298035.1	s__Gimesia maris	78.7038	986	2675	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	98.48	97.03	0.94	0.89	7	-
GCF_007744675.1	s__Gimesia alba	78.5462	908	2675	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007754425.1	s__Gimesia fumaroli	78.3257	883	2675	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:07,363] [INFO] GTDB search result was written to GCF_009720525.1_ASM972052v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:07,363] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:07,366] [INFO] DFAST_QC result json was written to GCF_009720525.1_ASM972052v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:07,366] [INFO] DFAST_QC completed!
[2024-01-24 14:49:07,366] [INFO] Total running time: 0h2m10s