[2023-03-19 00:15:41,728] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:15:41,728] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:15:41,728] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdcb5193-4547-4023-b20c-c18d5cb14e73/dqc_reference
[2023-03-19 00:15:43,439] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:15:43,439] [INFO] Task started: Prodigal
[2023-03-19 00:15:43,439] [INFO] Running command: cat /var/lib/cwl/stgf4243df7-71ae-4812-b27d-57e6c504994d/OceanDNA-b20559.fa | prodigal -d OceanDNA-b20559/cds.fna -a OceanDNA-b20559/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:15:48,417] [INFO] Task succeeded: Prodigal
[2023-03-19 00:15:48,417] [INFO] Task started: HMMsearch
[2023-03-19 00:15:48,418] [INFO] Running command: hmmsearch --tblout OceanDNA-b20559/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdcb5193-4547-4023-b20c-c18d5cb14e73/dqc_reference/reference_markers.hmm OceanDNA-b20559/protein.faa > /dev/null
[2023-03-19 00:15:48,613] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:15:48,613] [INFO] Found 6/6 markers.
[2023-03-19 00:15:48,624] [INFO] Query marker FASTA was written to OceanDNA-b20559/markers.fasta
[2023-03-19 00:15:48,624] [INFO] Task started: Blastn
[2023-03-19 00:15:48,625] [INFO] Running command: blastn -query OceanDNA-b20559/markers.fasta -db /var/lib/cwl/stgcdcb5193-4547-4023-b20c-c18d5cb14e73/dqc_reference/reference_markers.fasta -out OceanDNA-b20559/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:15:49,193] [INFO] Task succeeded: Blastn
[2023-03-19 00:15:49,194] [INFO] Selected 21 target genomes.
[2023-03-19 00:15:49,195] [INFO] Target genome list was writen to OceanDNA-b20559/target_genomes.txt
[2023-03-19 00:15:49,207] [INFO] Task started: fastANI
[2023-03-19 00:15:49,207] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4243df7-71ae-4812-b27d-57e6c504994d/OceanDNA-b20559.fa --refList OceanDNA-b20559/target_genomes.txt --output OceanDNA-b20559/fastani_result.tsv --threads 1
[2023-03-19 00:16:00,252] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:00,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdcb5193-4547-4023-b20c-c18d5cb14e73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:16:00,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdcb5193-4547-4023-b20c-c18d5cb14e73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:16:00,253] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:16:00,253] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:16:00,253] [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 00:16:00,253] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20559/tc_result.tsv
[2023-03-19 00:16:00,253] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:16:00,253] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:16:00,253] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdcb5193-4547-4023-b20c-c18d5cb14e73/dqc_reference/checkm_data
[2023-03-19 00:16:00,256] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:16:00,259] [INFO] Task started: CheckM
[2023-03-19 00:16:00,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20559/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20559/checkm_input OceanDNA-b20559/checkm_result
[2023-03-19 00:16:19,098] [INFO] Task succeeded: CheckM
[2023-03-19 00:16:19,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.64%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:16:19,101] [INFO] ===== Completeness check finished =====
[2023-03-19 00:16:19,101] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:16:19,101] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20559/markers.fasta)
[2023-03-19 00:16:19,101] [INFO] Task started: Blastn
[2023-03-19 00:16:19,101] [INFO] Running command: blastn -query OceanDNA-b20559/markers.fasta -db /var/lib/cwl/stgcdcb5193-4547-4023-b20c-c18d5cb14e73/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20559/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:16:19,918] [INFO] Task succeeded: Blastn
[2023-03-19 00:16:19,920] [INFO] Selected 24 target genomes.
[2023-03-19 00:16:19,920] [INFO] Target genome list was writen to OceanDNA-b20559/target_genomes_gtdb.txt
[2023-03-19 00:16:19,959] [INFO] Task started: fastANI
[2023-03-19 00:16:19,959] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4243df7-71ae-4812-b27d-57e6c504994d/OceanDNA-b20559.fa --refList OceanDNA-b20559/target_genomes_gtdb.txt --output OceanDNA-b20559/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:16:27,038] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:27,042] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:16:27,042] [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_002717625.1	s__GCA-2717625 sp002717625	77.7559	123	325	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-2717625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707765.1	s__GCA-002718585 sp002707765	77.7079	85	325	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002718585	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718585.1	s__GCA-002718585 sp002718585	77.4338	115	325	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002718585	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002705605.1	s__GCA-002707645 sp002705605	76.4932	56	325	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:16:27,043] [INFO] GTDB search result was written to OceanDNA-b20559/result_gtdb.tsv
[2023-03-19 00:16:27,043] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:16:27,044] [INFO] DFAST_QC result json was written to OceanDNA-b20559/dqc_result.json
[2023-03-19 00:16:27,044] [INFO] DFAST_QC completed!
[2023-03-19 00:16:27,044] [INFO] Total running time: 0h0m45s