[2023-03-15 08:55:06,629] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:55:06,629] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:55:06,630] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7e1cf7d-e81b-4c77-8e67-c5de03c04d99/dqc_reference
[2023-03-15 08:55:08,355] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:55:08,355] [INFO] Task started: Prodigal
[2023-03-15 08:55:08,355] [INFO] Running command: cat /var/lib/cwl/stgef3eab8d-893e-467d-88ea-38ab956b4c3f/OceanDNA-b43276.fa | prodigal -d OceanDNA-b43276/cds.fna -a OceanDNA-b43276/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:55:15,020] [INFO] Task succeeded: Prodigal
[2023-03-15 08:55:15,021] [INFO] Task started: HMMsearch
[2023-03-15 08:55:15,021] [INFO] Running command: hmmsearch --tblout OceanDNA-b43276/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7e1cf7d-e81b-4c77-8e67-c5de03c04d99/dqc_reference/reference_markers.hmm OceanDNA-b43276/protein.faa > /dev/null
[2023-03-15 08:55:15,224] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:55:15,225] [INFO] Found 6/6 markers.
[2023-03-15 08:55:15,236] [INFO] Query marker FASTA was written to OceanDNA-b43276/markers.fasta
[2023-03-15 08:55:15,236] [INFO] Task started: Blastn
[2023-03-15 08:55:15,236] [INFO] Running command: blastn -query OceanDNA-b43276/markers.fasta -db /var/lib/cwl/stgf7e1cf7d-e81b-4c77-8e67-c5de03c04d99/dqc_reference/reference_markers.fasta -out OceanDNA-b43276/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:15,862] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:15,863] [INFO] Selected 18 target genomes.
[2023-03-15 08:55:15,863] [INFO] Target genome list was writen to OceanDNA-b43276/target_genomes.txt
[2023-03-15 08:55:15,870] [INFO] Task started: fastANI
[2023-03-15 08:55:15,871] [INFO] Running command: fastANI --query /var/lib/cwl/stgef3eab8d-893e-467d-88ea-38ab956b4c3f/OceanDNA-b43276.fa --refList OceanDNA-b43276/target_genomes.txt --output OceanDNA-b43276/fastani_result.tsv --threads 1
[2023-03-15 08:55:26,645] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:26,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7e1cf7d-e81b-4c77-8e67-c5de03c04d99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:55:26,645] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7e1cf7d-e81b-4c77-8e67-c5de03c04d99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:55:26,648] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:55:26,648] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:55:26,648] [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	84.7077	329	413	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:55:26,648] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43276/tc_result.tsv
[2023-03-15 08:55:26,649] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:55:26,649] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:55:26,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7e1cf7d-e81b-4c77-8e67-c5de03c04d99/dqc_reference/checkm_data
[2023-03-15 08:55:26,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:55:26,652] [INFO] Task started: CheckM
[2023-03-15 08:55:26,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43276/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43276/checkm_input OceanDNA-b43276/checkm_result
[2023-03-15 08:55:48,944] [INFO] Task succeeded: CheckM
[2023-03-15 08:55:48,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:55:48,946] [INFO] ===== Completeness check finished =====
[2023-03-15 08:55:48,947] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:55:48,947] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43276/markers.fasta)
[2023-03-15 08:55:48,947] [INFO] Task started: Blastn
[2023-03-15 08:55:48,947] [INFO] Running command: blastn -query OceanDNA-b43276/markers.fasta -db /var/lib/cwl/stgf7e1cf7d-e81b-4c77-8e67-c5de03c04d99/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43276/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:49,730] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:49,731] [INFO] Selected 11 target genomes.
[2023-03-15 08:55:49,731] [INFO] Target genome list was writen to OceanDNA-b43276/target_genomes_gtdb.txt
[2023-03-15 08:55:49,741] [INFO] Task started: fastANI
[2023-03-15 08:55:49,741] [INFO] Running command: fastANI --query /var/lib/cwl/stgef3eab8d-893e-467d-88ea-38ab956b4c3f/OceanDNA-b43276.fa --refList OceanDNA-b43276/target_genomes_gtdb.txt --output OceanDNA-b43276/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:55:52,943] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:52,949] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:55:52,950] [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_002711905.1	s__Pseudothioglobus sp002711905	97.5456	212	413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	97.25	97.13	0.60	0.55	8	conclusive
GCA_902513495.1	s__Pseudothioglobus sp902513495	86.016	225	413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	97.65	97.05	0.53	0.51	3	-
GCF_001281385.1	s__Pseudothioglobus singularis	84.7077	329	413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.68	95.87	0.84	0.66	7	-
GCA_902512305.1	s__Pseudothioglobus sp902512305	80.3243	229	413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.03	95.27	0.77	0.74	5	-
GCA_902511025.1	s__Pseudothioglobus sp902511025	79.2916	116	413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902556205.1	s__Pseudothioglobus sp002169705	79.1192	211	413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.58	95.16	0.83	0.80	5	-
GCA_902509905.1	s__Pseudothioglobus sp902509905	78.9239	210	413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.83	95.81	0.73	0.73	3	-
GCA_001628405.1	s__Pseudothioglobus sp001628405	78.7417	224	413	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	78.3333	136	413	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.58	95.58	0.66	0.66	2	-
--------------------------------------------------------------------------------
[2023-03-15 08:55:52,950] [INFO] GTDB search result was written to OceanDNA-b43276/result_gtdb.tsv
[2023-03-15 08:55:52,950] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:55:52,951] [INFO] DFAST_QC result json was written to OceanDNA-b43276/dqc_result.json
[2023-03-15 08:55:52,951] [INFO] DFAST_QC completed!
[2023-03-15 08:55:52,951] [INFO] Total running time: 0h0m46s