[2024-01-24 13:13:26,456] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:26,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:26,459] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ed7ecdc-d412-4d7d-aa29-064caf2d399e/dqc_reference
[2024-01-24 13:13:27,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:27,765] [INFO] Task started: Prodigal
[2024-01-24 13:13:27,765] [INFO] Running command: gunzip -c /var/lib/cwl/stgcaf5c5a5-f509-443d-bfd5-797f1184bd98/GCF_007754425.1_ASM775442v1_genomic.fna.gz | prodigal -d GCF_007754425.1_ASM775442v1_genomic.fna/cds.fna -a GCF_007754425.1_ASM775442v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:52,629] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:52,629] [INFO] Task started: HMMsearch
[2024-01-24 13:13:52,630] [INFO] Running command: hmmsearch --tblout GCF_007754425.1_ASM775442v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ed7ecdc-d412-4d7d-aa29-064caf2d399e/dqc_reference/reference_markers.hmm GCF_007754425.1_ASM775442v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:53,049] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:53,051] [INFO] Found 6/6 markers.
[2024-01-24 13:13:53,112] [INFO] Query marker FASTA was written to GCF_007754425.1_ASM775442v1_genomic.fna/markers.fasta
[2024-01-24 13:13:53,113] [INFO] Task started: Blastn
[2024-01-24 13:13:53,113] [INFO] Running command: blastn -query GCF_007754425.1_ASM775442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ed7ecdc-d412-4d7d-aa29-064caf2d399e/dqc_reference/reference_markers.fasta -out GCF_007754425.1_ASM775442v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:53,697] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:53,701] [INFO] Selected 15 target genomes.
[2024-01-24 13:13:53,701] [INFO] Target genome list was writen to GCF_007754425.1_ASM775442v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:53,731] [INFO] Task started: fastANI
[2024-01-24 13:13:53,731] [INFO] Running command: fastANI --query /var/lib/cwl/stgcaf5c5a5-f509-443d-bfd5-797f1184bd98/GCF_007754425.1_ASM775442v1_genomic.fna.gz --refList GCF_007754425.1_ASM775442v1_genomic.fna/target_genomes.txt --output GCF_007754425.1_ASM775442v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:13,848] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:13,848] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ed7ecdc-d412-4d7d-aa29-064caf2d399e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:13,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ed7ecdc-d412-4d7d-aa29-064caf2d399e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:13,858] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:13,858] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:13,858] [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 fumaroli	strain=Enr17	GCA_007754425.1	2527976	2527976	type	True	100.0	2568	2568	95	conclusive
Gimesia alba	strain=Pan241w	GCA_007744675.1	2527973	2527973	type	True	89.0845	2143	2568	95	below_threshold
Gimesia algae	strain=Pan161	GCA_007746795.1	2527971	2527971	type	True	79.3676	1065	2568	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_009720545.1	122	122	type	True	78.7488	1057	2568	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_000181475.1	122	122	type	True	78.739	1051	2568	95	below_threshold
Gimesia maris	strain=DSM 8797	GCA_008298035.1	122	122	type	True	78.7296	1064	2568	95	below_threshold
Gimesia panareensis	strain=Enr10	GCA_007748155.1	2527978	2527978	type	True	78.4672	981	2568	95	below_threshold
Gimesia benthica	strain=E7	GCA_009720525.1	2608982	2608982	type	True	78.2802	898	2568	95	below_threshold
Gimesia aquarii	strain=V144	GCA_007748195.1	2527964	2527964	type	True	78.2194	839	2568	95	below_threshold
Gimesia chilikensis	strain=JC646	GCA_008329715.1	2605989	2605989	type	True	78.1529	887	2568	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:13,860] [INFO] DFAST Taxonomy check result was written to GCF_007754425.1_ASM775442v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:13,861] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:13,861] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:13,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ed7ecdc-d412-4d7d-aa29-064caf2d399e/dqc_reference/checkm_data
[2024-01-24 13:14:13,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:13,937] [INFO] Task started: CheckM
[2024-01-24 13:14:13,937] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007754425.1_ASM775442v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007754425.1_ASM775442v1_genomic.fna/checkm_input GCF_007754425.1_ASM775442v1_genomic.fna/checkm_result
[2024-01-24 13:15:28,894] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:28,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:28,928] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:28,929] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:28,929] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007754425.1_ASM775442v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:28,930] [INFO] Task started: Blastn
[2024-01-24 13:15:28,930] [INFO] Running command: blastn -query GCF_007754425.1_ASM775442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ed7ecdc-d412-4d7d-aa29-064caf2d399e/dqc_reference/reference_markers_gtdb.fasta -out GCF_007754425.1_ASM775442v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:29,657] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:29,661] [INFO] Selected 9 target genomes.
[2024-01-24 13:15:29,662] [INFO] Target genome list was writen to GCF_007754425.1_ASM775442v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:29,690] [INFO] Task started: fastANI
[2024-01-24 13:15:29,690] [INFO] Running command: fastANI --query /var/lib/cwl/stgcaf5c5a5-f509-443d-bfd5-797f1184bd98/GCF_007754425.1_ASM775442v1_genomic.fna.gz --refList GCF_007754425.1_ASM775442v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007754425.1_ASM775442v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:44,707] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:44,715] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:44,716] [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_007754425.1	s__Gimesia fumaroli	100.0	2568	2568	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007744675.1	s__Gimesia alba	89.0789	2144	2568	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007746795.1	s__Gimesia algae	79.36	1067	2568	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	78.7312	1066	2568	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	98.48	97.03	0.94	0.89	7	-
GCA_002706765.1	s__Gimesia sp002706765	78.7212	977	2568	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	99.96	99.96	0.97	0.97	2	-
GCF_007748155.1	s__Gimesia panareensis	78.4817	982	2568	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	96.61	95.86	0.91	0.90	3	-
GCF_009720525.1	s__Gimesia benthica	78.287	900	2568	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0249	95.18	95.18	0.86	0.86	2	-
GCF_007748195.1	s__Gimesia aquarii	78.1947	840	2568	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	95.04	95.04	0.88	0.88	2	-
GCF_008329715.1	s__Gimesia chilikensis	78.147	889	2568	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 13:15:44,717] [INFO] GTDB search result was written to GCF_007754425.1_ASM775442v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:44,718] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:44,722] [INFO] DFAST_QC result json was written to GCF_007754425.1_ASM775442v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:44,722] [INFO] DFAST_QC completed!
[2024-01-24 13:15:44,722] [INFO] Total running time: 0h2m18s