[2023-03-16 08:12:41,231] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:12:41,231] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:12:41,231] [INFO] DQC Reference Directory: /var/lib/cwl/stg91645113-1a45-410d-a266-56aeb2d7fe56/dqc_reference
[2023-03-16 08:12:42,310] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:12:42,313] [INFO] Task started: Prodigal
[2023-03-16 08:12:42,313] [INFO] Running command: cat /var/lib/cwl/stga29a4d43-e1ff-47d3-a628-99f6af0614aa/OceanDNA-b38478.fa | prodigal -d OceanDNA-b38478/cds.fna -a OceanDNA-b38478/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:12:51,029] [INFO] Task succeeded: Prodigal
[2023-03-16 08:12:51,029] [INFO] Task started: HMMsearch
[2023-03-16 08:12:51,030] [INFO] Running command: hmmsearch --tblout OceanDNA-b38478/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91645113-1a45-410d-a266-56aeb2d7fe56/dqc_reference/reference_markers.hmm OceanDNA-b38478/protein.faa > /dev/null
[2023-03-16 08:12:51,211] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:12:51,212] [INFO] Found 6/6 markers.
[2023-03-16 08:12:51,225] [INFO] Query marker FASTA was written to OceanDNA-b38478/markers.fasta
[2023-03-16 08:12:51,226] [INFO] Task started: Blastn
[2023-03-16 08:12:51,226] [INFO] Running command: blastn -query OceanDNA-b38478/markers.fasta -db /var/lib/cwl/stg91645113-1a45-410d-a266-56aeb2d7fe56/dqc_reference/reference_markers.fasta -out OceanDNA-b38478/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:12:51,811] [INFO] Task succeeded: Blastn
[2023-03-16 08:12:51,812] [INFO] Selected 27 target genomes.
[2023-03-16 08:12:51,812] [INFO] Target genome list was writen to OceanDNA-b38478/target_genomes.txt
[2023-03-16 08:12:51,847] [INFO] Task started: fastANI
[2023-03-16 08:12:51,847] [INFO] Running command: fastANI --query /var/lib/cwl/stga29a4d43-e1ff-47d3-a628-99f6af0614aa/OceanDNA-b38478.fa --refList OceanDNA-b38478/target_genomes.txt --output OceanDNA-b38478/fastani_result.tsv --threads 1
[2023-03-16 08:13:06,312] [INFO] Task succeeded: fastANI
[2023-03-16 08:13:06,312] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91645113-1a45-410d-a266-56aeb2d7fe56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:13:06,312] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91645113-1a45-410d-a266-56aeb2d7fe56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:13:06,312] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:13:06,312] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:13:06,313] [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
--------------------------------------------------------------------------------
[2023-03-16 08:13:06,313] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38478/tc_result.tsv
[2023-03-16 08:13:06,313] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:13:06,313] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:13:06,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91645113-1a45-410d-a266-56aeb2d7fe56/dqc_reference/checkm_data
[2023-03-16 08:13:06,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:13:06,319] [INFO] Task started: CheckM
[2023-03-16 08:13:06,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38478/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38478/checkm_input OceanDNA-b38478/checkm_result
[2023-03-16 08:13:33,276] [INFO] Task succeeded: CheckM
[2023-03-16 08:13:33,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.52%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 08:13:33,310] [INFO] ===== Completeness check finished =====
[2023-03-16 08:13:33,310] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:13:33,311] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38478/markers.fasta)
[2023-03-16 08:13:33,312] [INFO] Task started: Blastn
[2023-03-16 08:13:33,312] [INFO] Running command: blastn -query OceanDNA-b38478/markers.fasta -db /var/lib/cwl/stg91645113-1a45-410d-a266-56aeb2d7fe56/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38478/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:13:34,244] [INFO] Task succeeded: Blastn
[2023-03-16 08:13:34,254] [INFO] Selected 19 target genomes.
[2023-03-16 08:13:34,254] [INFO] Target genome list was writen to OceanDNA-b38478/target_genomes_gtdb.txt
[2023-03-16 08:13:34,275] [INFO] Task started: fastANI
[2023-03-16 08:13:34,275] [INFO] Running command: fastANI --query /var/lib/cwl/stga29a4d43-e1ff-47d3-a628-99f6af0614aa/OceanDNA-b38478.fa --refList OceanDNA-b38478/target_genomes_gtdb.txt --output OceanDNA-b38478/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:13:41,999] [INFO] Task succeeded: fastANI
[2023-03-16 08:13:42,005] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:13:42,005] [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_002705795.1	s__HIMB30 sp002705795	99.6044	429	502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	97.89	95.78	0.86	0.73	3	conclusive
GCA_902541775.1	s__HIMB30 sp902541775	80.0164	120	502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902594275.1	s__HIMB30 sp902594275	80.0105	123	502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902536515.1	s__HIMB30 sp902536515	80.0063	94	502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002705325.1	s__HIMB30 sp002705325	79.6711	188	502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	97.62	96.19	0.76	0.70	4	-
GCA_902558075.1	s__HIMB30 sp902558075	79.3831	127	502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008087055.1	s__HIMB30 sp008087055	79.0568	222	502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010024125.1	s__HIMB30 sp010024125	79.0127	206	502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	98.50	98.43	0.79	0.78	4	-
GCA_000227525.2	s__HIMB30 sp000227525	78.7514	182	502	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	98.38	98.38	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-16 08:13:42,011] [INFO] GTDB search result was written to OceanDNA-b38478/result_gtdb.tsv
[2023-03-16 08:13:42,026] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:13:42,026] [INFO] DFAST_QC result json was written to OceanDNA-b38478/dqc_result.json
[2023-03-16 08:13:42,027] [INFO] DFAST_QC completed!
[2023-03-16 08:13:42,027] [INFO] Total running time: 0h1m1s