[2023-03-18 08:17:18,477] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:18,477] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:18,477] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a4699f0-8b99-4825-81d6-6c9fe134490e/dqc_reference
[2023-03-18 08:17:20,268] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:20,268] [INFO] Task started: Prodigal
[2023-03-18 08:17:20,269] [INFO] Running command: cat /var/lib/cwl/stg8f40321e-6da9-4b9e-aee4-9fca0afddd62/OceanDNA-b42995.fa | prodigal -d OceanDNA-b42995/cds.fna -a OceanDNA-b42995/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:24,552] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:24,552] [INFO] Task started: HMMsearch
[2023-03-18 08:17:24,552] [INFO] Running command: hmmsearch --tblout OceanDNA-b42995/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a4699f0-8b99-4825-81d6-6c9fe134490e/dqc_reference/reference_markers.hmm OceanDNA-b42995/protein.faa > /dev/null
[2023-03-18 08:17:24,707] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:24,708] [INFO] Found 6/6 markers.
[2023-03-18 08:17:24,717] [INFO] Query marker FASTA was written to OceanDNA-b42995/markers.fasta
[2023-03-18 08:17:24,717] [INFO] Task started: Blastn
[2023-03-18 08:17:24,717] [INFO] Running command: blastn -query OceanDNA-b42995/markers.fasta -db /var/lib/cwl/stg4a4699f0-8b99-4825-81d6-6c9fe134490e/dqc_reference/reference_markers.fasta -out OceanDNA-b42995/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:26,586] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:26,586] [INFO] Selected 21 target genomes.
[2023-03-18 08:17:26,587] [INFO] Target genome list was writen to OceanDNA-b42995/target_genomes.txt
[2023-03-18 08:17:26,595] [INFO] Task started: fastANI
[2023-03-18 08:17:26,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f40321e-6da9-4b9e-aee4-9fca0afddd62/OceanDNA-b42995.fa --refList OceanDNA-b42995/target_genomes.txt --output OceanDNA-b42995/fastani_result.tsv --threads 1
[2023-03-18 08:17:38,559] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:38,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a4699f0-8b99-4825-81d6-6c9fe134490e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:38,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a4699f0-8b99-4825-81d6-6c9fe134490e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:38,562] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:38,562] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:17:38,562] [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	78.4082	111	257	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:17:38,563] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42995/tc_result.tsv
[2023-03-18 08:17:38,563] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:38,563] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:38,563] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a4699f0-8b99-4825-81d6-6c9fe134490e/dqc_reference/checkm_data
[2023-03-18 08:17:38,564] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:38,566] [INFO] Task started: CheckM
[2023-03-18 08:17:38,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42995/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42995/checkm_input OceanDNA-b42995/checkm_result
[2023-03-18 08:17:55,502] [INFO] Task succeeded: CheckM
[2023-03-18 08:17:55,503] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.86%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 08:17:55,504] [INFO] ===== Completeness check finished =====
[2023-03-18 08:17:55,504] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:17:55,505] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42995/markers.fasta)
[2023-03-18 08:17:55,505] [INFO] Task started: Blastn
[2023-03-18 08:17:55,505] [INFO] Running command: blastn -query OceanDNA-b42995/markers.fasta -db /var/lib/cwl/stg4a4699f0-8b99-4825-81d6-6c9fe134490e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42995/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:56,427] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:56,428] [INFO] Selected 15 target genomes.
[2023-03-18 08:17:56,428] [INFO] Target genome list was writen to OceanDNA-b42995/target_genomes_gtdb.txt
[2023-03-18 08:17:56,473] [INFO] Task started: fastANI
[2023-03-18 08:17:56,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f40321e-6da9-4b9e-aee4-9fca0afddd62/OceanDNA-b42995.fa --refList OceanDNA-b42995/target_genomes_gtdb.txt --output OceanDNA-b42995/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:17:59,828] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:59,837] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:17:59,837] [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_003326015.1	s__Pseudothioglobus singularis_A	98.495	253	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905614365.1	s__Pseudothioglobus sp905614365	79.4022	110	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.68	96.27	0.61	0.56	4	-
GCA_905182815.1	s__Pseudothioglobus sp905182815	79.1742	132	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612405.1	s__Pseudothioglobus sp905612405	79.1727	110	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698045.1	s__Pseudothioglobus sp002698045	78.8391	75	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.47	95.47	0.68	0.68	2	-
GCA_905618925.1	s__Pseudothioglobus sp905618925	78.7104	104	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.58	95.58	0.66	0.66	2	-
GCA_014384565.1	s__Pseudothioglobus aerophilus	78.4084	138	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	99.14	98.97	0.83	0.77	11	-
GCF_001281385.1	s__Pseudothioglobus singularis	78.4082	111	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.68	95.87	0.84	0.66	7	-
GCA_905620445.1	s__Pseudothioglobus sp905620445	78.1379	75	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902511025.1	s__Pseudothioglobus sp902511025	78.0133	51	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512305.1	s__Pseudothioglobus sp902512305	77.9516	97	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.03	95.27	0.77	0.74	5	-
GCA_002711905.1	s__Pseudothioglobus sp002711905	77.869	70	257	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	77.8551	99	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.58	95.16	0.83	0.80	5	-
GCA_902513495.1	s__Pseudothioglobus sp902513495	77.2508	68	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	97.65	97.05	0.53	0.51	3	-
GCA_902606745.1	s__Pseudothioglobus sp902606745	77.1533	65	257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:17:59,838] [INFO] GTDB search result was written to OceanDNA-b42995/result_gtdb.tsv
[2023-03-18 08:17:59,838] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:17:59,839] [INFO] DFAST_QC result json was written to OceanDNA-b42995/dqc_result.json
[2023-03-18 08:17:59,839] [INFO] DFAST_QC completed!
[2023-03-18 08:17:59,839] [INFO] Total running time: 0h0m41s