[2024-01-24 14:22:44,760] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:44,764] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:44,764] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2a578a3-b398-4960-a51c-1d558d309173/dqc_reference
[2024-01-24 14:22:46,054] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:46,055] [INFO] Task started: Prodigal
[2024-01-24 14:22:46,055] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb81b4bb-1440-4ca6-bc6f-1cfc2fa1ca8a/GCF_030160615.1_ASM3016061v1_genomic.fna.gz | prodigal -d GCF_030160615.1_ASM3016061v1_genomic.fna/cds.fna -a GCF_030160615.1_ASM3016061v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:51,571] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:51,572] [INFO] Task started: HMMsearch
[2024-01-24 14:22:51,572] [INFO] Running command: hmmsearch --tblout GCF_030160615.1_ASM3016061v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2a578a3-b398-4960-a51c-1d558d309173/dqc_reference/reference_markers.hmm GCF_030160615.1_ASM3016061v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:51,894] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:51,896] [INFO] Found 6/6 markers.
[2024-01-24 14:22:51,923] [INFO] Query marker FASTA was written to GCF_030160615.1_ASM3016061v1_genomic.fna/markers.fasta
[2024-01-24 14:22:51,924] [INFO] Task started: Blastn
[2024-01-24 14:22:51,924] [INFO] Running command: blastn -query GCF_030160615.1_ASM3016061v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2a578a3-b398-4960-a51c-1d558d309173/dqc_reference/reference_markers.fasta -out GCF_030160615.1_ASM3016061v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:52,589] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:52,593] [INFO] Selected 25 target genomes.
[2024-01-24 14:22:52,594] [INFO] Target genome list was writen to GCF_030160615.1_ASM3016061v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:52,741] [INFO] Task started: fastANI
[2024-01-24 14:22:52,742] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb81b4bb-1440-4ca6-bc6f-1cfc2fa1ca8a/GCF_030160615.1_ASM3016061v1_genomic.fna.gz --refList GCF_030160615.1_ASM3016061v1_genomic.fna/target_genomes.txt --output GCF_030160615.1_ASM3016061v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:07,828] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:07,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2a578a3-b398-4960-a51c-1d558d309173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:07,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2a578a3-b398-4960-a51c-1d558d309173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:07,840] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:07,840] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:07,840] [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
Marinospirillum insulare	strain=DSM 21763	GCA_000686905.1	217169	217169	type	True	99.9641	921	943	95	conclusive
Marinospirillum minutulum	strain=DSM 6287	GCA_000422325.1	64974	64974	type	True	84.2181	711	943	95	below_threshold
Marinospirillum perlucidum	strain=F3212	GCA_003336805.1	1982602	1982602	type	True	77.5143	72	943	95	below_threshold
Marinospirillum celere	strain=DSM 18438	GCA_900112235.1	1122252	1122252	type	True	76.8494	92	943	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:07,842] [INFO] DFAST Taxonomy check result was written to GCF_030160615.1_ASM3016061v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:07,842] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:07,843] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:07,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2a578a3-b398-4960-a51c-1d558d309173/dqc_reference/checkm_data
[2024-01-24 14:23:07,844] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:07,878] [INFO] Task started: CheckM
[2024-01-24 14:23:07,878] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160615.1_ASM3016061v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160615.1_ASM3016061v1_genomic.fna/checkm_input GCF_030160615.1_ASM3016061v1_genomic.fna/checkm_result
[2024-01-24 14:23:32,311] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:32,312] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:32,353] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:32,354] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:32,354] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160615.1_ASM3016061v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:32,355] [INFO] Task started: Blastn
[2024-01-24 14:23:32,355] [INFO] Running command: blastn -query GCF_030160615.1_ASM3016061v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2a578a3-b398-4960-a51c-1d558d309173/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160615.1_ASM3016061v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:33,445] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:33,448] [INFO] Selected 17 target genomes.
[2024-01-24 14:23:33,448] [INFO] Target genome list was writen to GCF_030160615.1_ASM3016061v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:33,461] [INFO] Task started: fastANI
[2024-01-24 14:23:33,461] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb81b4bb-1440-4ca6-bc6f-1cfc2fa1ca8a/GCF_030160615.1_ASM3016061v1_genomic.fna.gz --refList GCF_030160615.1_ASM3016061v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160615.1_ASM3016061v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:46,982] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:46,993] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:46,993] [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_000686905.1	s__Marinospirillum insulare	99.9641	921	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Marinospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000422325.1	s__Marinospirillum minutulum	84.2383	709	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Marinospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012727935.1	s__Marinospirillum sp012727935	80.9902	405	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Marinospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859565.1	s__Marinospirillum sp014859565	77.5177	120	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Marinospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112235.1	s__Marinospirillum celere	76.8494	92	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Marinospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119985.1	s__Marinospirillum sp007119985	76.5337	64	943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Marinospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:46,995] [INFO] GTDB search result was written to GCF_030160615.1_ASM3016061v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:46,996] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:46,999] [INFO] DFAST_QC result json was written to GCF_030160615.1_ASM3016061v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:46,999] [INFO] DFAST_QC completed!
[2024-01-24 14:23:47,000] [INFO] Total running time: 0h1m2s