[2023-03-15 15:18:22,009] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:18:22,010] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:18:22,010] [INFO] DQC Reference Directory: /var/lib/cwl/stge5bb747a-2eed-4d15-b0e9-00eeacaf4a72/dqc_reference
[2023-03-15 15:18:23,197] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:18:23,198] [INFO] Task started: Prodigal
[2023-03-15 15:18:23,198] [INFO] Running command: cat /var/lib/cwl/stg438fd4b4-14af-4575-b01e-c85424fa2f99/OceanDNA-b11107.fa | prodigal -d OceanDNA-b11107/cds.fna -a OceanDNA-b11107/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:18:33,701] [INFO] Task succeeded: Prodigal
[2023-03-15 15:18:33,701] [INFO] Task started: HMMsearch
[2023-03-15 15:18:33,701] [INFO] Running command: hmmsearch --tblout OceanDNA-b11107/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5bb747a-2eed-4d15-b0e9-00eeacaf4a72/dqc_reference/reference_markers.hmm OceanDNA-b11107/protein.faa > /dev/null
[2023-03-15 15:18:33,906] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:18:33,906] [INFO] Found 6/6 markers.
[2023-03-15 15:18:33,934] [INFO] Query marker FASTA was written to OceanDNA-b11107/markers.fasta
[2023-03-15 15:18:33,936] [INFO] Task started: Blastn
[2023-03-15 15:18:33,936] [INFO] Running command: blastn -query OceanDNA-b11107/markers.fasta -db /var/lib/cwl/stge5bb747a-2eed-4d15-b0e9-00eeacaf4a72/dqc_reference/reference_markers.fasta -out OceanDNA-b11107/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:18:34,472] [INFO] Task succeeded: Blastn
[2023-03-15 15:18:34,476] [INFO] Selected 34 target genomes.
[2023-03-15 15:18:34,476] [INFO] Target genome list was writen to OceanDNA-b11107/target_genomes.txt
[2023-03-15 15:18:34,499] [INFO] Task started: fastANI
[2023-03-15 15:18:34,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg438fd4b4-14af-4575-b01e-c85424fa2f99/OceanDNA-b11107.fa --refList OceanDNA-b11107/target_genomes.txt --output OceanDNA-b11107/fastani_result.tsv --threads 1
[2023-03-15 15:18:56,739] [INFO] Task succeeded: fastANI
[2023-03-15 15:18:56,740] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5bb747a-2eed-4d15-b0e9-00eeacaf4a72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:18:56,740] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5bb747a-2eed-4d15-b0e9-00eeacaf4a72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:18:56,740] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:18:56,740] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:18:56,740] [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 15:18:56,742] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11107/tc_result.tsv
[2023-03-15 15:18:56,742] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:18:56,743] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:18:56,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5bb747a-2eed-4d15-b0e9-00eeacaf4a72/dqc_reference/checkm_data
[2023-03-15 15:18:56,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:18:56,786] [INFO] Task started: CheckM
[2023-03-15 15:18:56,787] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11107/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11107/checkm_input OceanDNA-b11107/checkm_result
[2023-03-15 15:19:27,666] [INFO] Task succeeded: CheckM
[2023-03-15 15:19:27,666] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:19:27,676] [INFO] ===== Completeness check finished =====
[2023-03-15 15:19:27,676] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:19:27,677] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11107/markers.fasta)
[2023-03-15 15:19:27,678] [INFO] Task started: Blastn
[2023-03-15 15:19:27,678] [INFO] Running command: blastn -query OceanDNA-b11107/markers.fasta -db /var/lib/cwl/stge5bb747a-2eed-4d15-b0e9-00eeacaf4a72/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11107/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:19:28,405] [INFO] Task succeeded: Blastn
[2023-03-15 15:19:28,408] [INFO] Selected 9 target genomes.
[2023-03-15 15:19:28,408] [INFO] Target genome list was writen to OceanDNA-b11107/target_genomes_gtdb.txt
[2023-03-15 15:19:28,416] [INFO] Task started: fastANI
[2023-03-15 15:19:28,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg438fd4b4-14af-4575-b01e-c85424fa2f99/OceanDNA-b11107.fa --refList OceanDNA-b11107/target_genomes_gtdb.txt --output OceanDNA-b11107/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:19:31,708] [INFO] Task succeeded: fastANI
[2023-03-15 15:19:31,713] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:19:31,713] [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_003331305.1	s__UBA7446 sp002470745	99.7414	435	464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.36	99.14	0.86	0.83	3	conclusive
GCA_009937085.1	s__UBA7446 sp009937085	85.4903	318	464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017856205.1	s__UBA7446 sp017856205	80.3323	285	464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478685.1	s__UBA7446 sp002478685	79.8538	274	464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.74	99.74	0.91	0.91	3	-
GCA_009886265.1	s__UBA7446 sp009886265	79.0183	149	464	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 15:19:31,714] [INFO] GTDB search result was written to OceanDNA-b11107/result_gtdb.tsv
[2023-03-15 15:19:31,714] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:19:31,716] [INFO] DFAST_QC result json was written to OceanDNA-b11107/dqc_result.json
[2023-03-15 15:19:31,716] [INFO] DFAST_QC completed!
[2023-03-15 15:19:31,716] [INFO] Total running time: 0h1m10s