[2024-01-24 13:09:29,565] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:29,567] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:29,567] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc45f207-bd08-47dc-8417-3af64e7001f1/dqc_reference
[2024-01-24 13:09:30,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:30,774] [INFO] Task started: Prodigal
[2024-01-24 13:09:30,774] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd5baa6a-f13d-42a9-a20b-b9d72e423271/GCF_008041945.1_ASM804194v1_genomic.fna.gz | prodigal -d GCF_008041945.1_ASM804194v1_genomic.fna/cds.fna -a GCF_008041945.1_ASM804194v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:37,590] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:37,590] [INFO] Task started: HMMsearch
[2024-01-24 13:09:37,590] [INFO] Running command: hmmsearch --tblout GCF_008041945.1_ASM804194v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc45f207-bd08-47dc-8417-3af64e7001f1/dqc_reference/reference_markers.hmm GCF_008041945.1_ASM804194v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:37,896] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:37,898] [INFO] Found 6/6 markers.
[2024-01-24 13:09:37,929] [INFO] Query marker FASTA was written to GCF_008041945.1_ASM804194v1_genomic.fna/markers.fasta
[2024-01-24 13:09:37,930] [INFO] Task started: Blastn
[2024-01-24 13:09:37,930] [INFO] Running command: blastn -query GCF_008041945.1_ASM804194v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc45f207-bd08-47dc-8417-3af64e7001f1/dqc_reference/reference_markers.fasta -out GCF_008041945.1_ASM804194v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:38,641] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:38,646] [INFO] Selected 27 target genomes.
[2024-01-24 13:09:38,647] [INFO] Target genome list was writen to GCF_008041945.1_ASM804194v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:38,664] [INFO] Task started: fastANI
[2024-01-24 13:09:38,665] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd5baa6a-f13d-42a9-a20b-b9d72e423271/GCF_008041945.1_ASM804194v1_genomic.fna.gz --refList GCF_008041945.1_ASM804194v1_genomic.fna/target_genomes.txt --output GCF_008041945.1_ASM804194v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:53,697] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:53,698] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc45f207-bd08-47dc-8417-3af64e7001f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:53,698] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc45f207-bd08-47dc-8417-3af64e7001f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:53,711] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:53,712] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:53,712] [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
Reinekea thalattae	strain=SSH23	GCA_008041945.1	2593301	2593301	type	True	100.0	978	978	95	conclusive
Reinekea marinisedimentorum	strain=DSM 15388	GCA_004341165.1	230495	230495	type	True	78.2435	195	978	95	below_threshold
Reinekea forsetii	strain=Hel1_31_D35	GCA_002795845.1	1336806	1336806	type	True	77.772	62	978	95	below_threshold
Reinekea blandensis	strain=MED297	GCA_000153185.1	374838	374838	type	True	77.6865	83	978	95	below_threshold
Saccharospirillum mangrovi	strain=HK-33	GCA_003367315.1	2161747	2161747	type	True	76.4804	55	978	95	below_threshold
Saccharospirillum mangrovi	strain=HK-33	GCA_003054775.1	2161747	2161747	type	True	76.3772	55	978	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:53,713] [INFO] DFAST Taxonomy check result was written to GCF_008041945.1_ASM804194v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:53,714] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:53,714] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:53,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc45f207-bd08-47dc-8417-3af64e7001f1/dqc_reference/checkm_data
[2024-01-24 13:09:53,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:53,748] [INFO] Task started: CheckM
[2024-01-24 13:09:53,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008041945.1_ASM804194v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008041945.1_ASM804194v1_genomic.fna/checkm_input GCF_008041945.1_ASM804194v1_genomic.fna/checkm_result
[2024-01-24 13:10:20,773] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:20,775] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:20,797] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:20,797] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:20,798] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008041945.1_ASM804194v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:20,798] [INFO] Task started: Blastn
[2024-01-24 13:10:20,799] [INFO] Running command: blastn -query GCF_008041945.1_ASM804194v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc45f207-bd08-47dc-8417-3af64e7001f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_008041945.1_ASM804194v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:21,969] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:21,973] [INFO] Selected 21 target genomes.
[2024-01-24 13:10:21,974] [INFO] Target genome list was writen to GCF_008041945.1_ASM804194v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:21,992] [INFO] Task started: fastANI
[2024-01-24 13:10:21,992] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd5baa6a-f13d-42a9-a20b-b9d72e423271/GCF_008041945.1_ASM804194v1_genomic.fna.gz --refList GCF_008041945.1_ASM804194v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008041945.1_ASM804194v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:34,933] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:34,940] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:34,940] [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_008041945.1	s__Reinekea thalattae	100.0	978	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004341165.1	s__Reinekea marinisedimentorum	78.2435	195	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015687175.1	s__Reinekea sp015687175	78.0484	95	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860385.1	s__Reinekea forsetii_A	78.0388	81	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153185.1	s__Reinekea blandensis	77.7239	82	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795845.1	s__Reinekea forsetii	77.7221	63	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Reinekea	95.0	99.43	98.93	0.96	0.91	7	-
GCF_003054965.1	s__Saccharospirillum sp003054965	76.2889	57	978	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:34,942] [INFO] GTDB search result was written to GCF_008041945.1_ASM804194v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:34,942] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:34,945] [INFO] DFAST_QC result json was written to GCF_008041945.1_ASM804194v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:34,945] [INFO] DFAST_QC completed!
[2024-01-24 13:10:34,945] [INFO] Total running time: 0h1m5s