[2024-01-24 13:45:59,825] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:59,827] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:59,827] [INFO] DQC Reference Directory: /var/lib/cwl/stg0abf43df-fc0b-4ac1-9a90-52a4fc6c1684/dqc_reference
[2024-01-24 13:46:01,108] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:01,109] [INFO] Task started: Prodigal
[2024-01-24 13:46:01,110] [INFO] Running command: gunzip -c /var/lib/cwl/stg04cd0de3-2b96-439d-a711-c16bbc1b09fa/GCF_008298035.1_ASM829803v1_genomic.fna.gz | prodigal -d GCF_008298035.1_ASM829803v1_genomic.fna/cds.fna -a GCF_008298035.1_ASM829803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:25,983] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:25,984] [INFO] Task started: HMMsearch
[2024-01-24 13:46:25,984] [INFO] Running command: hmmsearch --tblout GCF_008298035.1_ASM829803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0abf43df-fc0b-4ac1-9a90-52a4fc6c1684/dqc_reference/reference_markers.hmm GCF_008298035.1_ASM829803v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:26,347] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:26,349] [INFO] Found 6/6 markers.
[2024-01-24 13:46:26,407] [INFO] Query marker FASTA was written to GCF_008298035.1_ASM829803v1_genomic.fna/markers.fasta
[2024-01-24 13:46:26,408] [INFO] Task started: Blastn
[2024-01-24 13:46:26,408] [INFO] Running command: blastn -query GCF_008298035.1_ASM829803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0abf43df-fc0b-4ac1-9a90-52a4fc6c1684/dqc_reference/reference_markers.fasta -out GCF_008298035.1_ASM829803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:26,996] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:27,000] [INFO] Selected 14 target genomes.
[2024-01-24 13:46:27,000] [INFO] Target genome list was writen to GCF_008298035.1_ASM829803v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:27,036] [INFO] Task started: fastANI
[2024-01-24 13:46:27,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg04cd0de3-2b96-439d-a711-c16bbc1b09fa/GCF_008298035.1_ASM829803v1_genomic.fna.gz --refList GCF_008298035.1_ASM829803v1_genomic.fna/target_genomes.txt --output GCF_008298035.1_ASM829803v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:46,171] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:46,172] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0abf43df-fc0b-4ac1-9a90-52a4fc6c1684/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:46,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0abf43df-fc0b-4ac1-9a90-52a4fc6c1684/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:46,180] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:46:46,181] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:46,181] [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_008298035.1	122	122	type	True	100.0	2605	2605	95	conclusive
Gimesia maris	strain=DSM 8797	GCA_009720545.1	122	122	type	True	99.9962	2604	2605	95	conclusive
Gimesia maris	strain=DSM 8797	GCA_000181475.1	122	122	type	True	99.9584	2525	2605	95	conclusive
Gimesia algae	strain=Pan161	GCA_007746795.1	2527971	2527971	type	True	87.9128	2125	2605	95	below_threshold
Gimesia fumaroli	strain=Enr17	GCA_007754425.1	2527976	2527976	type	True	78.9351	1036	2605	95	below_threshold
Gimesia alba	strain=Pan241w	GCA_007744675.1	2527973	2527973	type	True	78.9122	1025	2605	95	below_threshold
Gimesia panareensis	strain=Enr10	GCA_007748155.1	2527978	2527978	type	True	78.8544	1021	2605	95	below_threshold
Gimesia benthica	strain=E7	GCA_009720525.1	2608982	2608982	type	True	78.7761	968	2605	95	below_threshold
Gimesia chilikensis	strain=JC646	GCA_008329715.1	2605989	2605989	type	True	78.5402	988	2605	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:46,182] [INFO] DFAST Taxonomy check result was written to GCF_008298035.1_ASM829803v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:46,183] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:46,183] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:46,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0abf43df-fc0b-4ac1-9a90-52a4fc6c1684/dqc_reference/checkm_data
[2024-01-24 13:46:46,184] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:46,258] [INFO] Task started: CheckM
[2024-01-24 13:46:46,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008298035.1_ASM829803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008298035.1_ASM829803v1_genomic.fna/checkm_input GCF_008298035.1_ASM829803v1_genomic.fna/checkm_result
[2024-01-24 13:48:02,266] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:02,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:02,289] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:02,289] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:02,289] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008298035.1_ASM829803v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:02,290] [INFO] Task started: Blastn
[2024-01-24 13:48:02,290] [INFO] Running command: blastn -query GCF_008298035.1_ASM829803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0abf43df-fc0b-4ac1-9a90-52a4fc6c1684/dqc_reference/reference_markers_gtdb.fasta -out GCF_008298035.1_ASM829803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:03,020] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:03,024] [INFO] Selected 9 target genomes.
[2024-01-24 13:48:03,025] [INFO] Target genome list was writen to GCF_008298035.1_ASM829803v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:03,072] [INFO] Task started: fastANI
[2024-01-24 13:48:03,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg04cd0de3-2b96-439d-a711-c16bbc1b09fa/GCF_008298035.1_ASM829803v1_genomic.fna.gz --refList GCF_008298035.1_ASM829803v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008298035.1_ASM829803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:17,099] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:17,112] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:17,112] [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	100.0	2605	2605	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	87.9197	2122	2605	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	85.0038	1979	2605	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	78.9184	1035	2605	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Gimesia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007744675.1	s__Gimesia alba	78.9063	1026	2605	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	78.8534	1022	2605	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	78.765	974	2605	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	78.5413	989	2605	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 13:48:17,114] [INFO] GTDB search result was written to GCF_008298035.1_ASM829803v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:17,115] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:17,118] [INFO] DFAST_QC result json was written to GCF_008298035.1_ASM829803v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:17,118] [INFO] DFAST_QC completed!
[2024-01-24 13:48:17,118] [INFO] Total running time: 0h2m17s