[2023-03-15 08:55:06,632] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:55:06,632] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:55:06,632] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8f3fdf3-3219-4078-8278-61e7793406b7/dqc_reference
[2023-03-15 08:55:08,344] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:55:08,344] [INFO] Task started: Prodigal
[2023-03-15 08:55:08,344] [INFO] Running command: cat /var/lib/cwl/stg43333092-c8b3-487d-9f53-01547a48ac62/OceanDNA-b24423.fa | prodigal -d OceanDNA-b24423/cds.fna -a OceanDNA-b24423/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:55:14,510] [INFO] Task succeeded: Prodigal
[2023-03-15 08:55:14,510] [INFO] Task started: HMMsearch
[2023-03-15 08:55:14,510] [INFO] Running command: hmmsearch --tblout OceanDNA-b24423/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8f3fdf3-3219-4078-8278-61e7793406b7/dqc_reference/reference_markers.hmm OceanDNA-b24423/protein.faa > /dev/null
[2023-03-15 08:55:14,704] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:55:14,704] [INFO] Found 6/6 markers.
[2023-03-15 08:55:14,712] [INFO] Query marker FASTA was written to OceanDNA-b24423/markers.fasta
[2023-03-15 08:55:14,712] [INFO] Task started: Blastn
[2023-03-15 08:55:14,712] [INFO] Running command: blastn -query OceanDNA-b24423/markers.fasta -db /var/lib/cwl/stgf8f3fdf3-3219-4078-8278-61e7793406b7/dqc_reference/reference_markers.fasta -out OceanDNA-b24423/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:15,275] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:15,276] [INFO] Selected 21 target genomes.
[2023-03-15 08:55:15,276] [INFO] Target genome list was writen to OceanDNA-b24423/target_genomes.txt
[2023-03-15 08:55:15,291] [INFO] Task started: fastANI
[2023-03-15 08:55:15,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg43333092-c8b3-487d-9f53-01547a48ac62/OceanDNA-b24423.fa --refList OceanDNA-b24423/target_genomes.txt --output OceanDNA-b24423/fastani_result.tsv --threads 1
[2023-03-15 08:55:23,540] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:23,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8f3fdf3-3219-4078-8278-61e7793406b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:55:23,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8f3fdf3-3219-4078-8278-61e7793406b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:55:23,540] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:55:23,540] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:55:23,540] [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
--------------------------------------------------------------------------------
[2023-03-15 08:55:23,541] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24423/tc_result.tsv
[2023-03-15 08:55:23,541] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:55:23,541] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:55:23,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8f3fdf3-3219-4078-8278-61e7793406b7/dqc_reference/checkm_data
[2023-03-15 08:55:23,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:55:23,546] [INFO] Task started: CheckM
[2023-03-15 08:55:23,546] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24423/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24423/checkm_input OceanDNA-b24423/checkm_result
[2023-03-15 08:55:43,257] [INFO] Task succeeded: CheckM
[2023-03-15 08:55:43,257] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:55:43,259] [INFO] ===== Completeness check finished =====
[2023-03-15 08:55:43,259] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:55:43,259] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24423/markers.fasta)
[2023-03-15 08:55:43,259] [INFO] Task started: Blastn
[2023-03-15 08:55:43,259] [INFO] Running command: blastn -query OceanDNA-b24423/markers.fasta -db /var/lib/cwl/stgf8f3fdf3-3219-4078-8278-61e7793406b7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24423/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:44,210] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:44,210] [INFO] Selected 19 target genomes.
[2023-03-15 08:55:44,211] [INFO] Target genome list was writen to OceanDNA-b24423/target_genomes_gtdb.txt
[2023-03-15 08:55:44,246] [INFO] Task started: fastANI
[2023-03-15 08:55:44,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg43333092-c8b3-487d-9f53-01547a48ac62/OceanDNA-b24423.fa --refList OceanDNA-b24423/target_genomes_gtdb.txt --output OceanDNA-b24423/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:55:48,342] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:48,348] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:55:48,348] [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_017639935.1	s__JAGFWP01 sp017639935	99.7927	273	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__JAGFWP01	95.0	99.64	99.12	0.86	0.76	8	conclusive
GCA_902607435.1	s__CACLJX01 sp902607435	78.4372	105	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__CACLJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002938195.1	s__MarineAlpha5-Bin7 sp002938195	76.9611	96	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin7	95.0	99.81	99.67	0.81	0.76	3	-
GCA_002937895.1	s__PTKV01 sp002937895	76.6711	56	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__PTKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902577425.1	s__MarineAlpha5-Bin3 sp902577425	76.6107	85	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin3	95.0	95.54	95.54	0.86	0.86	2	-
GCA_002938205.1	s__AG-337-I02 sp002938205	76.3044	70	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	99.93	99.93	0.95	0.95	2	-
GCA_902577905.1	s__AG-337-I02 sp902577905	76.2686	52	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902602515.1	s__AG-337-I02 sp902602515	75.9739	51	317	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	99.95	99.95	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-15 08:55:48,348] [INFO] GTDB search result was written to OceanDNA-b24423/result_gtdb.tsv
[2023-03-15 08:55:48,348] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:55:48,349] [INFO] DFAST_QC result json was written to OceanDNA-b24423/dqc_result.json
[2023-03-15 08:55:48,349] [INFO] DFAST_QC completed!
[2023-03-15 08:55:48,349] [INFO] Total running time: 0h0m42s