[2024-01-24 13:40:34,851] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,853] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,853] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1a73be8-af21-49dd-b033-43b5666220ce/dqc_reference
[2024-01-24 13:40:36,362] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,362] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,363] [INFO] Running command: gunzip -c /var/lib/cwl/stg71a271f1-4ad7-4ee4-8006-b8674853273b/GCF_007752345.1_ASM775234v1_genomic.fna.gz | prodigal -d GCF_007752345.1_ASM775234v1_genomic.fna/cds.fna -a GCF_007752345.1_ASM775234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:52,565] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:52,566] [INFO] Task started: HMMsearch
[2024-01-24 13:40:52,566] [INFO] Running command: hmmsearch --tblout GCF_007752345.1_ASM775234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1a73be8-af21-49dd-b033-43b5666220ce/dqc_reference/reference_markers.hmm GCF_007752345.1_ASM775234v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:52,965] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:52,966] [INFO] Found 6/6 markers.
[2024-01-24 13:40:53,015] [INFO] Query marker FASTA was written to GCF_007752345.1_ASM775234v1_genomic.fna/markers.fasta
[2024-01-24 13:40:53,016] [INFO] Task started: Blastn
[2024-01-24 13:40:53,016] [INFO] Running command: blastn -query GCF_007752345.1_ASM775234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1a73be8-af21-49dd-b033-43b5666220ce/dqc_reference/reference_markers.fasta -out GCF_007752345.1_ASM775234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:53,707] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:53,710] [INFO] Selected 13 target genomes.
[2024-01-24 13:40:53,711] [INFO] Target genome list was writen to GCF_007752345.1_ASM775234v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:53,719] [INFO] Task started: fastANI
[2024-01-24 13:40:53,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg71a271f1-4ad7-4ee4-8006-b8674853273b/GCF_007752345.1_ASM775234v1_genomic.fna.gz --refList GCF_007752345.1_ASM775234v1_genomic.fna/target_genomes.txt --output GCF_007752345.1_ASM775234v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:05,941] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:05,941] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1a73be8-af21-49dd-b033-43b5666220ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:05,942] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1a73be8-af21-49dd-b033-43b5666220ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:05,947] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:05,948] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:05,948] [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
Planctopirus ephydatiae	strain=spb1	GCA_007752345.1	2528019	2528019	type	True	100.0	1737	1738	95	conclusive
Planctopirus limnophila	strain=DSM 3776	GCA_000092105.1	120	120	type	True	93.6128	1565	1738	95	below_threshold
Planctopirus hydrillae	strain=JC280	GCA_001707835.1	1841610	1841610	type	True	92.2942	1526	1738	95	below_threshold
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.8132	51	1738	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:05,949] [INFO] DFAST Taxonomy check result was written to GCF_007752345.1_ASM775234v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:05,950] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:05,950] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:05,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1a73be8-af21-49dd-b033-43b5666220ce/dqc_reference/checkm_data
[2024-01-24 13:41:05,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:06,002] [INFO] Task started: CheckM
[2024-01-24 13:41:06,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007752345.1_ASM775234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007752345.1_ASM775234v1_genomic.fna/checkm_input GCF_007752345.1_ASM775234v1_genomic.fna/checkm_result
[2024-01-24 13:41:58,711] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:58,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:58,736] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:58,737] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:58,737] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007752345.1_ASM775234v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:58,738] [INFO] Task started: Blastn
[2024-01-24 13:41:58,738] [INFO] Running command: blastn -query GCF_007752345.1_ASM775234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1a73be8-af21-49dd-b033-43b5666220ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_007752345.1_ASM775234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:59,581] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:59,584] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:59,585] [INFO] Target genome list was writen to GCF_007752345.1_ASM775234v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:59,782] [INFO] Task started: fastANI
[2024-01-24 13:41:59,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg71a271f1-4ad7-4ee4-8006-b8674853273b/GCF_007752345.1_ASM775234v1_genomic.fna.gz --refList GCF_007752345.1_ASM775234v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007752345.1_ASM775234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:13,377] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:13,388] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:13,389] [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_007752345.1	s__Planctopirus ephydatiae	100.0	1737	1738	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctopirus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000092105.1	s__Planctopirus limnophila	93.6128	1565	1738	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctopirus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001707835.1	s__Planctopirus hydrillae	92.2842	1527	1738	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctopirus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822855.1	s__Planctopirus sp013822855	77.9279	380	1738	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctopirus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903840265.1	s__Schlesneria sp903840265	75.1111	55	1738	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	99.98	99.98	0.97	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:13,391] [INFO] GTDB search result was written to GCF_007752345.1_ASM775234v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:13,391] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:13,394] [INFO] DFAST_QC result json was written to GCF_007752345.1_ASM775234v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:13,394] [INFO] DFAST_QC completed!
[2024-01-24 13:42:13,394] [INFO] Total running time: 0h1m39s