[2024-01-24 13:17:26,939] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:26,941] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:26,941] [INFO] DQC Reference Directory: /var/lib/cwl/stge2944b91-8c7d-4d08-b23a-732a780f7a5a/dqc_reference
[2024-01-24 13:17:28,121] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:28,121] [INFO] Task started: Prodigal
[2024-01-24 13:17:28,122] [INFO] Running command: gunzip -c /var/lib/cwl/stg16f1067f-ab99-4f45-830b-c01ce571989b/GCF_001281385.1_ASM128138v1_genomic.fna.gz | prodigal -d GCF_001281385.1_ASM128138v1_genomic.fna/cds.fna -a GCF_001281385.1_ASM128138v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:31,589] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:31,590] [INFO] Task started: HMMsearch
[2024-01-24 13:17:31,590] [INFO] Running command: hmmsearch --tblout GCF_001281385.1_ASM128138v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2944b91-8c7d-4d08-b23a-732a780f7a5a/dqc_reference/reference_markers.hmm GCF_001281385.1_ASM128138v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:31,817] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:31,819] [INFO] Found 6/6 markers.
[2024-01-24 13:17:31,845] [INFO] Query marker FASTA was written to GCF_001281385.1_ASM128138v1_genomic.fna/markers.fasta
[2024-01-24 13:17:31,846] [INFO] Task started: Blastn
[2024-01-24 13:17:31,846] [INFO] Running command: blastn -query GCF_001281385.1_ASM128138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2944b91-8c7d-4d08-b23a-732a780f7a5a/dqc_reference/reference_markers.fasta -out GCF_001281385.1_ASM128138v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:32,451] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:32,455] [INFO] Selected 19 target genomes.
[2024-01-24 13:17:32,455] [INFO] Target genome list was writen to GCF_001281385.1_ASM128138v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:32,486] [INFO] Task started: fastANI
[2024-01-24 13:17:32,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg16f1067f-ab99-4f45-830b-c01ce571989b/GCF_001281385.1_ASM128138v1_genomic.fna.gz --refList GCF_001281385.1_ASM128138v1_genomic.fna/target_genomes.txt --output GCF_001281385.1_ASM128138v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:39,856] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:39,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2944b91-8c7d-4d08-b23a-732a780f7a5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:39,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2944b91-8c7d-4d08-b23a-732a780f7a5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:39,863] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:39,864] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:39,864] [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
Candidatus Pseudothioglobus singularis	strain=PS1	GCA_001281385.1	1427364	1427364	type	True	100.0	571	571	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:17:39,866] [INFO] DFAST Taxonomy check result was written to GCF_001281385.1_ASM128138v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:39,867] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:39,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:39,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2944b91-8c7d-4d08-b23a-732a780f7a5a/dqc_reference/checkm_data
[2024-01-24 13:17:39,870] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:39,895] [INFO] Task started: CheckM
[2024-01-24 13:17:39,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001281385.1_ASM128138v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001281385.1_ASM128138v1_genomic.fna/checkm_input GCF_001281385.1_ASM128138v1_genomic.fna/checkm_result
[2024-01-24 13:17:58,077] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:58,078] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:58,106] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:58,107] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:58,107] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001281385.1_ASM128138v1_genomic.fna/markers.fasta)
[2024-01-24 13:17:58,108] [INFO] Task started: Blastn
[2024-01-24 13:17:58,108] [INFO] Running command: blastn -query GCF_001281385.1_ASM128138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2944b91-8c7d-4d08-b23a-732a780f7a5a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001281385.1_ASM128138v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:59,127] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:59,130] [INFO] Selected 9 target genomes.
[2024-01-24 13:17:59,130] [INFO] Target genome list was writen to GCF_001281385.1_ASM128138v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:59,179] [INFO] Task started: fastANI
[2024-01-24 13:17:59,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg16f1067f-ab99-4f45-830b-c01ce571989b/GCF_001281385.1_ASM128138v1_genomic.fna.gz --refList GCF_001281385.1_ASM128138v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001281385.1_ASM128138v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:02,290] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:02,307] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:02,308] [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_001281385.1	s__Pseudothioglobus singularis	100.0	571	571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.68	95.87	0.84	0.66	7	conclusive
GCA_902513495.1	s__Pseudothioglobus sp902513495	85.3993	279	571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	97.65	97.05	0.53	0.51	3	-
GCA_002711905.1	s__Pseudothioglobus sp002711905	85.0431	239	571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	97.25	97.13	0.60	0.55	8	-
GCA_902556205.1	s__Pseudothioglobus sp002169705	79.9646	280	571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.58	95.16	0.83	0.80	5	-
GCA_902511025.1	s__Pseudothioglobus sp902511025	79.9488	156	571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902509905.1	s__Pseudothioglobus sp902509905	79.9235	255	571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.83	95.81	0.73	0.73	3	-
GCA_902512305.1	s__Pseudothioglobus sp902512305	79.7801	289	571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.03	95.27	0.77	0.74	5	-
GCA_001628405.1	s__Pseudothioglobus sp001628405	79.2476	263	571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	97.86	96.69	0.86	0.83	3	-
GCA_905618925.1	s__Pseudothioglobus sp905618925	79.132	161	571	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.58	95.58	0.66	0.66	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:02,309] [INFO] GTDB search result was written to GCF_001281385.1_ASM128138v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:02,310] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:02,313] [INFO] DFAST_QC result json was written to GCF_001281385.1_ASM128138v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:02,314] [INFO] DFAST_QC completed!
[2024-01-24 13:18:02,314] [INFO] Total running time: 0h0m35s