[2023-03-17 04:35:35,449] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:35:35,450] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:35:35,450] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe1909b1-49a4-4776-8909-b3593482b07b/dqc_reference
[2023-03-17 04:35:36,687] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:35:36,688] [INFO] Task started: Prodigal
[2023-03-17 04:35:36,688] [INFO] Running command: cat /var/lib/cwl/stgbb644f7d-9366-49c7-b0ae-37b532af1176/OceanDNA-b28311.fa | prodigal -d OceanDNA-b28311/cds.fna -a OceanDNA-b28311/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:35:42,905] [INFO] Task succeeded: Prodigal
[2023-03-17 04:35:42,905] [INFO] Task started: HMMsearch
[2023-03-17 04:35:42,905] [INFO] Running command: hmmsearch --tblout OceanDNA-b28311/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe1909b1-49a4-4776-8909-b3593482b07b/dqc_reference/reference_markers.hmm OceanDNA-b28311/protein.faa > /dev/null
[2023-03-17 04:35:43,061] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:35:43,062] [INFO] Found 6/6 markers.
[2023-03-17 04:35:43,075] [INFO] Query marker FASTA was written to OceanDNA-b28311/markers.fasta
[2023-03-17 04:35:43,076] [INFO] Task started: Blastn
[2023-03-17 04:35:43,076] [INFO] Running command: blastn -query OceanDNA-b28311/markers.fasta -db /var/lib/cwl/stgbe1909b1-49a4-4776-8909-b3593482b07b/dqc_reference/reference_markers.fasta -out OceanDNA-b28311/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:35:43,587] [INFO] Task succeeded: Blastn
[2023-03-17 04:35:43,588] [INFO] Selected 15 target genomes.
[2023-03-17 04:35:43,588] [INFO] Target genome list was writen to OceanDNA-b28311/target_genomes.txt
[2023-03-17 04:35:43,594] [INFO] Task started: fastANI
[2023-03-17 04:35:43,594] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb644f7d-9366-49c7-b0ae-37b532af1176/OceanDNA-b28311.fa --refList OceanDNA-b28311/target_genomes.txt --output OceanDNA-b28311/fastani_result.tsv --threads 1
[2023-03-17 04:35:50,332] [INFO] Task succeeded: fastANI
[2023-03-17 04:35:50,333] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe1909b1-49a4-4776-8909-b3593482b07b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:35:50,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe1909b1-49a4-4776-8909-b3593482b07b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:35:50,333] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:35:50,333] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 04:35:50,333] [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
--------------------------------------------------------------------------------
[2023-03-17 04:35:50,333] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28311/tc_result.tsv
[2023-03-17 04:35:50,333] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:35:50,333] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:35:50,334] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe1909b1-49a4-4776-8909-b3593482b07b/dqc_reference/checkm_data
[2023-03-17 04:35:50,336] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:35:50,340] [INFO] Task started: CheckM
[2023-03-17 04:35:50,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28311/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28311/checkm_input OceanDNA-b28311/checkm_result
[2023-03-17 04:36:11,672] [INFO] Task succeeded: CheckM
[2023-03-17 04:36:11,672] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.36%
Contamintation: 4.78%
Strain heterogeneity: 83.33%
--------------------------------------------------------------------------------
[2023-03-17 04:36:11,674] [INFO] ===== Completeness check finished =====
[2023-03-17 04:36:11,674] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:36:11,674] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28311/markers.fasta)
[2023-03-17 04:36:11,675] [INFO] Task started: Blastn
[2023-03-17 04:36:11,675] [INFO] Running command: blastn -query OceanDNA-b28311/markers.fasta -db /var/lib/cwl/stgbe1909b1-49a4-4776-8909-b3593482b07b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28311/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:36:12,414] [INFO] Task succeeded: Blastn
[2023-03-17 04:36:12,415] [INFO] Selected 17 target genomes.
[2023-03-17 04:36:12,415] [INFO] Target genome list was writen to OceanDNA-b28311/target_genomes_gtdb.txt
[2023-03-17 04:36:12,928] [INFO] Task started: fastANI
[2023-03-17 04:36:12,928] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb644f7d-9366-49c7-b0ae-37b532af1176/OceanDNA-b28311.fa --refList OceanDNA-b28311/target_genomes_gtdb.txt --output OceanDNA-b28311/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:36:17,644] [INFO] Task succeeded: fastANI
[2023-03-17 04:36:17,648] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-17 04:36:17,649] [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_902578545.1	s__CACIIZ01 sp902578545	97.79	236	332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	96.87	95.99	0.65	0.64	7	inconclusive
GCA_902573735.1	s__CACIIZ01 sp902573735	95.4858	188	332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902625475.1	s__CACIIZ01 sp902625475	94.841	187	332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902562285.1	s__CACIIZ01 sp902562285	81.3514	170	332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902611605.1	s__CACIIZ01 sp902611605	81.1515	155	332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	96.35	96.35	0.51	0.51	2	-
GCA_902570265.1	s__CACIIZ01 sp902570265	80.7397	212	332	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:36:17,649] [INFO] GTDB search result was written to OceanDNA-b28311/result_gtdb.tsv
[2023-03-17 04:36:17,649] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:36:17,650] [INFO] DFAST_QC result json was written to OceanDNA-b28311/dqc_result.json
[2023-03-17 04:36:17,650] [INFO] DFAST_QC completed!
[2023-03-17 04:36:17,650] [INFO] Total running time: 0h0m42s