[2023-03-14 12:36:36,469] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:36:36,469] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:36:36,469] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b2a7580-ff01-4fed-807c-392302727d02/dqc_reference
[2023-03-14 12:36:37,563] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:36:37,563] [INFO] Task started: Prodigal
[2023-03-14 12:36:37,563] [INFO] Running command: cat /var/lib/cwl/stg5542e0bc-0d9e-404d-8fbf-d0d82ac1e138/OceanDNA-b43088.fa | prodigal -d OceanDNA-b43088/cds.fna -a OceanDNA-b43088/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:36:44,658] [INFO] Task succeeded: Prodigal
[2023-03-14 12:36:44,658] [INFO] Task started: HMMsearch
[2023-03-14 12:36:44,658] [INFO] Running command: hmmsearch --tblout OceanDNA-b43088/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b2a7580-ff01-4fed-807c-392302727d02/dqc_reference/reference_markers.hmm OceanDNA-b43088/protein.faa > /dev/null
[2023-03-14 12:36:45,003] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:36:45,003] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5542e0bc-0d9e-404d-8fbf-d0d82ac1e138/OceanDNA-b43088.fa]
[2023-03-14 12:36:45,014] [INFO] Query marker FASTA was written to OceanDNA-b43088/markers.fasta
[2023-03-14 12:36:45,021] [INFO] Task started: Blastn
[2023-03-14 12:36:45,021] [INFO] Running command: blastn -query OceanDNA-b43088/markers.fasta -db /var/lib/cwl/stg7b2a7580-ff01-4fed-807c-392302727d02/dqc_reference/reference_markers.fasta -out OceanDNA-b43088/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:36:45,606] [INFO] Task succeeded: Blastn
[2023-03-14 12:36:45,607] [INFO] Selected 16 target genomes.
[2023-03-14 12:36:45,607] [INFO] Target genome list was writen to OceanDNA-b43088/target_genomes.txt
[2023-03-14 12:36:45,618] [INFO] Task started: fastANI
[2023-03-14 12:36:45,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg5542e0bc-0d9e-404d-8fbf-d0d82ac1e138/OceanDNA-b43088.fa --refList OceanDNA-b43088/target_genomes.txt --output OceanDNA-b43088/fastani_result.tsv --threads 1
[2023-03-14 12:36:52,505] [INFO] Task succeeded: fastANI
[2023-03-14 12:36:52,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b2a7580-ff01-4fed-807c-392302727d02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:36:52,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b2a7580-ff01-4fed-807c-392302727d02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:36:52,517] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:36:52,517] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:36:52,517] [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	77.9982	149	381	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:36:52,517] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43088/tc_result.tsv
[2023-03-14 12:36:52,518] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:36:52,518] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:36:52,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b2a7580-ff01-4fed-807c-392302727d02/dqc_reference/checkm_data
[2023-03-14 12:36:52,519] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:36:52,789] [INFO] Task started: CheckM
[2023-03-14 12:36:52,789] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43088/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43088/checkm_input OceanDNA-b43088/checkm_result
[2023-03-14 12:37:14,886] [INFO] Task succeeded: CheckM
[2023-03-14 12:37:14,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 12:37:14,888] [INFO] ===== Completeness check finished =====
[2023-03-14 12:37:14,889] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:37:14,889] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43088/markers.fasta)
[2023-03-14 12:37:14,890] [INFO] Task started: Blastn
[2023-03-14 12:37:14,890] [INFO] Running command: blastn -query OceanDNA-b43088/markers.fasta -db /var/lib/cwl/stg7b2a7580-ff01-4fed-807c-392302727d02/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43088/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:37:15,857] [INFO] Task succeeded: Blastn
[2023-03-14 12:37:15,858] [INFO] Selected 15 target genomes.
[2023-03-14 12:37:15,858] [INFO] Target genome list was writen to OceanDNA-b43088/target_genomes_gtdb.txt
[2023-03-14 12:37:15,898] [INFO] Task started: fastANI
[2023-03-14 12:37:15,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg5542e0bc-0d9e-404d-8fbf-d0d82ac1e138/OceanDNA-b43088.fa --refList OceanDNA-b43088/target_genomes_gtdb.txt --output OceanDNA-b43088/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:37:20,204] [INFO] Task succeeded: fastANI
[2023-03-14 12:37:20,211] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:37:20,212] [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_002698045.1	s__Pseudothioglobus sp002698045	94.0121	174	381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.47	95.47	0.68	0.68	2	-
GCA_902606745.1	s__Pseudothioglobus sp902606745	80.0478	122	381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182815.1	s__Pseudothioglobus sp905182815	79.6525	202	381	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	79.6059	161	381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.58	95.58	0.66	0.66	2	-
GCA_000372785.1	s__Pseudothioglobus sp000372785	79.5635	129	381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.69	95.69	0.64	0.64	2	-
GCA_905620445.1	s__Pseudothioglobus sp905620445	79.4248	129	381	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	79.2487	219	381	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	79.0909	145	381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384565.1	s__Pseudothioglobus aerophilus	78.9862	207	381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	99.14	98.97	0.83	0.77	11	-
GCA_905614365.1	s__Pseudothioglobus sp905614365	78.9287	150	381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.68	96.27	0.61	0.56	4	-
GCA_002711905.1	s__Pseudothioglobus sp002711905	77.6028	95	381	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	77.601	102	381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	97.65	97.05	0.53	0.51	3	-
--------------------------------------------------------------------------------
[2023-03-14 12:37:20,212] [INFO] GTDB search result was written to OceanDNA-b43088/result_gtdb.tsv
[2023-03-14 12:37:20,212] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:37:20,213] [INFO] DFAST_QC result json was written to OceanDNA-b43088/dqc_result.json
[2023-03-14 12:37:20,213] [INFO] DFAST_QC completed!
[2023-03-14 12:37:20,213] [INFO] Total running time: 0h0m44s