[2023-03-19 00:40:34,770] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:40:34,770] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:40:34,770] [INFO] DQC Reference Directory: /var/lib/cwl/stg4052d399-cf64-4b2e-996c-79acb8b136eb/dqc_reference
[2023-03-19 00:40:35,866] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:40:35,867] [INFO] Task started: Prodigal
[2023-03-19 00:40:35,867] [INFO] Running command: cat /var/lib/cwl/stgcd3ea71d-f4d0-4a75-a975-a5851b2deb93/OceanDNA-b42812.fa | prodigal -d OceanDNA-b42812/cds.fna -a OceanDNA-b42812/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:40:43,306] [INFO] Task succeeded: Prodigal
[2023-03-19 00:40:43,306] [INFO] Task started: HMMsearch
[2023-03-19 00:40:43,306] [INFO] Running command: hmmsearch --tblout OceanDNA-b42812/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4052d399-cf64-4b2e-996c-79acb8b136eb/dqc_reference/reference_markers.hmm OceanDNA-b42812/protein.faa > /dev/null
[2023-03-19 00:40:43,451] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:40:43,451] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcd3ea71d-f4d0-4a75-a975-a5851b2deb93/OceanDNA-b42812.fa]
[2023-03-19 00:40:43,463] [INFO] Query marker FASTA was written to OceanDNA-b42812/markers.fasta
[2023-03-19 00:40:43,463] [INFO] Task started: Blastn
[2023-03-19 00:40:43,463] [INFO] Running command: blastn -query OceanDNA-b42812/markers.fasta -db /var/lib/cwl/stg4052d399-cf64-4b2e-996c-79acb8b136eb/dqc_reference/reference_markers.fasta -out OceanDNA-b42812/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:40:43,995] [INFO] Task succeeded: Blastn
[2023-03-19 00:40:43,996] [INFO] Selected 17 target genomes.
[2023-03-19 00:40:43,996] [INFO] Target genome list was writen to OceanDNA-b42812/target_genomes.txt
[2023-03-19 00:40:44,003] [INFO] Task started: fastANI
[2023-03-19 00:40:44,003] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd3ea71d-f4d0-4a75-a975-a5851b2deb93/OceanDNA-b42812.fa --refList OceanDNA-b42812/target_genomes.txt --output OceanDNA-b42812/fastani_result.tsv --threads 1
[2023-03-19 00:40:53,502] [INFO] Task succeeded: fastANI
[2023-03-19 00:40:53,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4052d399-cf64-4b2e-996c-79acb8b136eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:40:53,502] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4052d399-cf64-4b2e-996c-79acb8b136eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:40:53,502] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:40:53,502] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:40:53,503] [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
--------------------------------------------------------------------------------
[2023-03-19 00:40:53,503] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42812/tc_result.tsv
[2023-03-19 00:40:53,503] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:40:53,504] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:40:53,504] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4052d399-cf64-4b2e-996c-79acb8b136eb/dqc_reference/checkm_data
[2023-03-19 00:40:53,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:40:53,531] [INFO] Task started: CheckM
[2023-03-19 00:40:53,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42812/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42812/checkm_input OceanDNA-b42812/checkm_result
[2023-03-19 00:41:16,916] [INFO] Task succeeded: CheckM
[2023-03-19 00:41:16,917] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:41:16,919] [INFO] ===== Completeness check finished =====
[2023-03-19 00:41:16,920] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:41:16,920] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42812/markers.fasta)
[2023-03-19 00:41:16,921] [INFO] Task started: Blastn
[2023-03-19 00:41:16,921] [INFO] Running command: blastn -query OceanDNA-b42812/markers.fasta -db /var/lib/cwl/stg4052d399-cf64-4b2e-996c-79acb8b136eb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42812/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:41:17,654] [INFO] Task succeeded: Blastn
[2023-03-19 00:41:17,656] [INFO] Selected 13 target genomes.
[2023-03-19 00:41:17,656] [INFO] Target genome list was writen to OceanDNA-b42812/target_genomes_gtdb.txt
[2023-03-19 00:41:17,673] [INFO] Task started: fastANI
[2023-03-19 00:41:17,673] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd3ea71d-f4d0-4a75-a975-a5851b2deb93/OceanDNA-b42812.fa --refList OceanDNA-b42812/target_genomes_gtdb.txt --output OceanDNA-b42812/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:41:23,815] [INFO] Task succeeded: fastANI
[2023-03-19 00:41:23,822] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:41:23,822] [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_018970145.1	s__UBA964 sp018970145	99.1931	373	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903910215.1	s__UBA964 sp903910215	84.9937	285	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	98.86	98.86	0.82	0.82	2	-
GCA_010031985.1	s__UBA964 sp010031985	78.8668	94	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	98.93	98.76	0.80	0.76	12	-
GCA_010029775.1	s__UBA964 sp010029775	78.8523	88	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885195.1	s__UBA964 sp903885195	78.3632	158	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	99.55	99.16	0.90	0.86	6	-
GCA_016874175.1	s__UBA964 sp016874175	78.2659	125	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874555.1	s__UBA964 sp016874555	78.0759	80	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883185.1	s__UBA964 sp018883185	78.0534	136	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009923475.1	s__UBA964 sp009923475	77.884	77	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010027845.1	s__UBA964 sp010027845	77.6236	103	399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:41:23,823] [INFO] GTDB search result was written to OceanDNA-b42812/result_gtdb.tsv
[2023-03-19 00:41:23,823] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:41:23,824] [INFO] DFAST_QC result json was written to OceanDNA-b42812/dqc_result.json
[2023-03-19 00:41:23,824] [INFO] DFAST_QC completed!
[2023-03-19 00:41:23,824] [INFO] Total running time: 0h0m49s