[2024-01-24 13:30:12,324] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:30:12,327] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:30:12,327] [INFO] DQC Reference Directory: /var/lib/cwl/stg537327b3-99cb-41ee-bf4d-b38cd0f440ff/dqc_reference
[2024-01-24 13:30:13,623] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:30:13,624] [INFO] Task started: Prodigal
[2024-01-24 13:30:13,624] [INFO] Running command: gunzip -c /var/lib/cwl/stg4abd25bb-87d2-4516-8e47-64500c50047c/GCF_009720545.1_ASM972054v1_genomic.fna.gz | prodigal -d GCF_009720545.1_ASM972054v1_genomic.fna/cds.fna -a GCF_009720545.1_ASM972054v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:30:39,432] [INFO] Task succeeded: Prodigal
[2024-01-24 13:30:39,432] [INFO] Task started: HMMsearch
[2024-01-24 13:30:39,433] [INFO] Running command: hmmsearch --tblout GCF_009720545.1_ASM972054v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg537327b3-99cb-41ee-bf4d-b38cd0f440ff/dqc_reference/reference_markers.hmm GCF_009720545.1_ASM972054v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:30:39,791] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:30:39,792] [INFO] Found 6/6 markers.
[2024-01-24 13:30:39,855] [INFO] Query marker FASTA was written to GCF_009720545.1_ASM972054v1_genomic.fna/markers.fasta
[2024-01-24 13:30:39,856] [INFO] Task started: Blastn
[2024-01-24 13:30:39,856] [INFO] Running command: blastn -query GCF_009720545.1_ASM972054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg537327b3-99cb-41ee-bf4d-b38cd0f440ff/dqc_reference/reference_markers.fasta -out GCF_009720545.1_ASM972054v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:40,431] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:40,436] [INFO] Selected 14 target genomes.
[2024-01-24 13:30:40,437] [INFO] Target genome list was writen to GCF_009720545.1_ASM972054v1_genomic.fna/target_genomes.txt
[2024-01-24 13:30:40,500] [INFO] Task started: fastANI
[2024-01-24 13:30:40,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg4abd25bb-87d2-4516-8e47-64500c50047c/GCF_009720545.1_ASM972054v1_genomic.fna.gz --refList GCF_009720545.1_ASM972054v1_genomic.fna/target_genomes.txt --output GCF_009720545.1_ASM972054v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:30:59,481] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:59,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg537327b3-99cb-41ee-bf4d-b38cd0f440ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:30:59,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg537327b3-99cb-41ee-bf4d-b38cd0f440ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:30:59,494] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:30:59,495] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:30:59,495] [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 maris	strain=DSM 8797	GCA_009720545.1	122	122	type	True	100.0	2606	2606	95	conclusive
Gimesia maris	strain=DSM 8797	GCA_008298035.1	122	122	type	True	99.9943	2606	2606	95	conclusive
Gimesia maris	strain=DSM 8797	GCA_000181475.1	122	122	type	True	99.9564	2526	2606	95	conclusive
Gimesia algae	strain=Pan161	GCA_007746795.1	2527971	2527971	type	True	87.8695	2138	2606	95	below_threshold
Gimesia fumaroli	strain=Enr17	GCA_007754425.1	2527976	2527976	type	True	78.91	1029	2606	95	below_threshold
Gimesia panareensis	strain=Enr10	GCA_007748155.1	2527978	2527978	type	True	78.7687	1032	2606	95	below_threshold
Gimesia alba	strain=Pan241w	GCA_007744675.1	2527973	2527973	type	True	78.7137	1058	2606	95	below_threshold
Gimesia benthica	strain=E7	GCA_009720525.1	2608982	2608982	type	True	78.6933	972	2606	95	below_threshold
Gimesia chilikensis	strain=JC646	GCA_008329715.1	2605989	2605989	type	True	78.5178	978	2606	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:30:59,496] [INFO] DFAST Taxonomy check result was written to GCF_009720545.1_ASM972054v1_genomic.fna/tc_result.tsv
[2024-01-24 13:30:59,497] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:30:59,497] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:30:59,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg537327b3-99cb-41ee-bf4d-b38cd0f440ff/dqc_reference/checkm_data
[2024-01-24 13:30:59,498] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:30:59,569] [INFO] Task started: CheckM
[2024-01-24 13:30:59,569] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009720545.1_ASM972054v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009720545.1_ASM972054v1_genomic.fna/checkm_input GCF_009720545.1_ASM972054v1_genomic.fna/checkm_result
[2024-01-24 13:32:15,652] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:15,653] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:15,681] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:15,681] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:15,682] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009720545.1_ASM972054v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:15,682] [INFO] Task started: Blastn
[2024-01-24 13:32:15,682] [INFO] Running command: blastn -query GCF_009720545.1_ASM972054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg537327b3-99cb-41ee-bf4d-b38cd0f440ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_009720545.1_ASM972054v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:16,485] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:16,490] [INFO] Selected 9 target genomes.
[2024-01-24 13:32:16,490] [INFO] Target genome list was writen to GCF_009720545.1_ASM972054v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:16,630] [INFO] Task started: fastANI
[2024-01-24 13:32:16,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg4abd25bb-87d2-4516-8e47-64500c50047c/GCF_009720545.1_ASM972054v1_genomic.fna.gz --refList GCF_009720545.1_ASM972054v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009720545.1_ASM972054v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:30,720] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:30,733] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:30,733] [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_008298035.1	s__Gimesia maris	99.9943	2606	2606	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	98.48	97.03	0.94	0.89	7	conclusive
GCF_007746795.1	s__Gimesia algae	87.8771	2136	2606	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706765.1	s__Gimesia sp002706765	84.9871	1980	2606	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	99.96	99.96	0.97	0.97	2	-
GCF_007754425.1	s__Gimesia fumaroli	78.9225	1032	2606	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007748155.1	s__Gimesia panareensis	78.7741	1032	2606	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	96.61	95.86	0.91	0.90	3	-
GCF_007744675.1	s__Gimesia alba	78.7131	1058	2606	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720525.1	s__Gimesia benthica	78.6882	971	2606	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0249	95.18	95.18	0.86	0.86	2	-
GCF_008329715.1	s__Gimesia chilikensis	78.5113	979	2606	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0249	95.30	95.11	0.90	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:30,735] [INFO] GTDB search result was written to GCF_009720545.1_ASM972054v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:30,736] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:30,740] [INFO] DFAST_QC result json was written to GCF_009720545.1_ASM972054v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:30,740] [INFO] DFAST_QC completed!
[2024-01-24 13:32:30,740] [INFO] Total running time: 0h2m18s