[2023-03-17 10:48:47,644] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:48:47,644] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:48:47,644] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fad8085-0ece-4231-9859-3159e87d69d4/dqc_reference
[2023-03-17 10:48:48,765] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:48:48,766] [INFO] Task started: Prodigal
[2023-03-17 10:48:48,767] [INFO] Running command: cat /var/lib/cwl/stg5a9f354d-2458-4a67-b9e0-dc886aaaf275/OceanDNA-b42847.fa | prodigal -d OceanDNA-b42847/cds.fna -a OceanDNA-b42847/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:48:58,849] [INFO] Task succeeded: Prodigal
[2023-03-17 10:48:58,849] [INFO] Task started: HMMsearch
[2023-03-17 10:48:58,849] [INFO] Running command: hmmsearch --tblout OceanDNA-b42847/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fad8085-0ece-4231-9859-3159e87d69d4/dqc_reference/reference_markers.hmm OceanDNA-b42847/protein.faa > /dev/null
[2023-03-17 10:48:59,089] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:48:59,090] [INFO] Found 6/6 markers.
[2023-03-17 10:48:59,104] [INFO] Query marker FASTA was written to OceanDNA-b42847/markers.fasta
[2023-03-17 10:48:59,104] [INFO] Task started: Blastn
[2023-03-17 10:48:59,104] [INFO] Running command: blastn -query OceanDNA-b42847/markers.fasta -db /var/lib/cwl/stg6fad8085-0ece-4231-9859-3159e87d69d4/dqc_reference/reference_markers.fasta -out OceanDNA-b42847/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:48:59,696] [INFO] Task succeeded: Blastn
[2023-03-17 10:48:59,697] [INFO] Selected 22 target genomes.
[2023-03-17 10:48:59,698] [INFO] Target genome list was writen to OceanDNA-b42847/target_genomes.txt
[2023-03-17 10:48:59,731] [INFO] Task started: fastANI
[2023-03-17 10:48:59,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a9f354d-2458-4a67-b9e0-dc886aaaf275/OceanDNA-b42847.fa --refList OceanDNA-b42847/target_genomes.txt --output OceanDNA-b42847/fastani_result.tsv --threads 1
[2023-03-17 10:49:13,062] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:13,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fad8085-0ece-4231-9859-3159e87d69d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:49:13,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fad8085-0ece-4231-9859-3159e87d69d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:49:13,066] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:49:13,066] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:49:13,066] [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	77.2406	62	573	95	below_threshold
Candidatus Thioglobus autotrophicus	strain=EF1	GCA_001293165.1	1705394	1705394	type	True	76.7501	52	573	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:49:13,067] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42847/tc_result.tsv
[2023-03-17 10:49:13,067] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:49:13,067] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:49:13,067] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fad8085-0ece-4231-9859-3159e87d69d4/dqc_reference/checkm_data
[2023-03-17 10:49:13,068] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:49:13,084] [INFO] Task started: CheckM
[2023-03-17 10:49:13,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42847/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42847/checkm_input OceanDNA-b42847/checkm_result
[2023-03-17 10:49:42,450] [INFO] Task succeeded: CheckM
[2023-03-17 10:49:42,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:49:42,452] [INFO] ===== Completeness check finished =====
[2023-03-17 10:49:42,452] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:49:42,453] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42847/markers.fasta)
[2023-03-17 10:49:42,453] [INFO] Task started: Blastn
[2023-03-17 10:49:42,453] [INFO] Running command: blastn -query OceanDNA-b42847/markers.fasta -db /var/lib/cwl/stg6fad8085-0ece-4231-9859-3159e87d69d4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42847/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:43,398] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:43,399] [INFO] Selected 20 target genomes.
[2023-03-17 10:49:43,399] [INFO] Target genome list was writen to OceanDNA-b42847/target_genomes_gtdb.txt
[2023-03-17 10:49:43,536] [INFO] Task started: fastANI
[2023-03-17 10:49:43,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a9f354d-2458-4a67-b9e0-dc886aaaf275/OceanDNA-b42847.fa --refList OceanDNA-b42847/target_genomes_gtdb.txt --output OceanDNA-b42847/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:49:48,452] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:48,457] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:49:48,457] [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_012959965.1	s__DUCF01 sp012959965	83.6779	379	573	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__DUCF01	95.0	99.73	99.73	0.89	0.89	2	-
GCA_000372785.1	s__Pseudothioglobus sp000372785	78.8062	70	573	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.69	95.69	0.64	0.64	2	-
GCA_905614365.1	s__Pseudothioglobus sp905614365	77.673	52	573	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.68	96.27	0.61	0.56	4	-
GCA_014384345.1	s__Thioglobus pontius	76.6912	51	573	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	99.87	99.85	0.90	0.85	3	-
GCA_002335045.1	s__UBA2013 sp002335045	76.4358	53	573	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__UBA2013	95.0	98.42	96.96	0.95	0.94	3	-
GCA_018644675.1	s__Thioglobus sp018644675	76.3739	52	573	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Thioglobus	95.0	99.74	99.56	0.96	0.91	16	-
--------------------------------------------------------------------------------
[2023-03-17 10:49:48,457] [INFO] GTDB search result was written to OceanDNA-b42847/result_gtdb.tsv
[2023-03-17 10:49:48,457] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:49:48,458] [INFO] DFAST_QC result json was written to OceanDNA-b42847/dqc_result.json
[2023-03-17 10:49:48,458] [INFO] DFAST_QC completed!
[2023-03-17 10:49:48,458] [INFO] Total running time: 0h1m1s