[2023-03-15 21:48:08,717] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:08,717] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:08,717] [INFO] DQC Reference Directory: /var/lib/cwl/stgca3d1f19-5157-4e08-a646-63dc97710582/dqc_reference
[2023-03-15 21:48:09,837] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:09,837] [INFO] Task started: Prodigal
[2023-03-15 21:48:09,838] [INFO] Running command: cat /var/lib/cwl/stg2f832763-92ad-4fca-a256-9ad018dbbf32/OceanDNA-b43141.fa | prodigal -d OceanDNA-b43141/cds.fna -a OceanDNA-b43141/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:15,916] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:15,916] [INFO] Task started: HMMsearch
[2023-03-15 21:48:15,916] [INFO] Running command: hmmsearch --tblout OceanDNA-b43141/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca3d1f19-5157-4e08-a646-63dc97710582/dqc_reference/reference_markers.hmm OceanDNA-b43141/protein.faa > /dev/null
[2023-03-15 21:48:16,091] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:16,092] [INFO] Found 6/6 markers.
[2023-03-15 21:48:16,102] [INFO] Query marker FASTA was written to OceanDNA-b43141/markers.fasta
[2023-03-15 21:48:16,103] [INFO] Task started: Blastn
[2023-03-15 21:48:16,103] [INFO] Running command: blastn -query OceanDNA-b43141/markers.fasta -db /var/lib/cwl/stgca3d1f19-5157-4e08-a646-63dc97710582/dqc_reference/reference_markers.fasta -out OceanDNA-b43141/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:16,662] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:16,663] [INFO] Selected 22 target genomes.
[2023-03-15 21:48:16,663] [INFO] Target genome list was writen to OceanDNA-b43141/target_genomes.txt
[2023-03-15 21:48:16,698] [INFO] Task started: fastANI
[2023-03-15 21:48:16,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f832763-92ad-4fca-a256-9ad018dbbf32/OceanDNA-b43141.fa --refList OceanDNA-b43141/target_genomes.txt --output OceanDNA-b43141/fastani_result.tsv --threads 1
[2023-03-15 21:48:27,273] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:27,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca3d1f19-5157-4e08-a646-63dc97710582/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:48:27,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca3d1f19-5157-4e08-a646-63dc97710582/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:48:27,277] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:48:27,277] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:48:27,277] [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	78.4986	189	387	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:48:27,277] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43141/tc_result.tsv
[2023-03-15 21:48:27,277] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:48:27,277] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:48:27,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca3d1f19-5157-4e08-a646-63dc97710582/dqc_reference/checkm_data
[2023-03-15 21:48:27,278] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:48:27,281] [INFO] Task started: CheckM
[2023-03-15 21:48:27,281] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43141/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43141/checkm_input OceanDNA-b43141/checkm_result
[2023-03-15 21:48:47,997] [INFO] Task succeeded: CheckM
[2023-03-15 21:48:47,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:48:48,010] [INFO] ===== Completeness check finished =====
[2023-03-15 21:48:48,010] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:48:48,010] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43141/markers.fasta)
[2023-03-15 21:48:48,012] [INFO] Task started: Blastn
[2023-03-15 21:48:48,012] [INFO] Running command: blastn -query OceanDNA-b43141/markers.fasta -db /var/lib/cwl/stgca3d1f19-5157-4e08-a646-63dc97710582/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43141/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:48,953] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:48,957] [INFO] Selected 10 target genomes.
[2023-03-15 21:48:48,957] [INFO] Target genome list was writen to OceanDNA-b43141/target_genomes_gtdb.txt
[2023-03-15 21:48:49,029] [INFO] Task started: fastANI
[2023-03-15 21:48:49,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f832763-92ad-4fca-a256-9ad018dbbf32/OceanDNA-b43141.fa --refList OceanDNA-b43141/target_genomes_gtdb.txt --output OceanDNA-b43141/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:48:51,480] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:51,486] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:48:51,487] [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
GCA_014384565.1	s__Pseudothioglobus aerophilus	99.1146	329	387	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	99.14	98.97	0.83	0.77	11	conclusive
GCA_905182815.1	s__Pseudothioglobus sp905182815	94.9421	290	387	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905618925.1	s__Pseudothioglobus sp905618925	89.0775	232	387	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.58	95.58	0.66	0.66	2	-
GCA_905614365.1	s__Pseudothioglobus sp905614365	88.392	236	387	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.68	96.27	0.61	0.56	4	-
GCA_905612405.1	s__Pseudothioglobus sp905612405	87.4056	224	387	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905620445.1	s__Pseudothioglobus sp905620445	86.7666	177	387	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003326015.1	s__Pseudothioglobus singularis_A	79.8714	221	387	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711905.1	s__Pseudothioglobus sp002711905	78.3676	104	387	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	97.25	97.13	0.60	0.55	8	-
GCA_902513495.1	s__Pseudothioglobus sp902513495	78.2888	117	387	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	97.65	97.05	0.53	0.51	3	-
GCA_002698045.1	s__Pseudothioglobus sp002698045	78.2533	111	387	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.47	95.47	0.68	0.68	2	-
--------------------------------------------------------------------------------
[2023-03-15 21:48:51,488] [INFO] GTDB search result was written to OceanDNA-b43141/result_gtdb.tsv
[2023-03-15 21:48:51,491] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:48:51,494] [INFO] DFAST_QC result json was written to OceanDNA-b43141/dqc_result.json
[2023-03-15 21:48:51,494] [INFO] DFAST_QC completed!
[2023-03-15 21:48:51,494] [INFO] Total running time: 0h0m43s