[2023-03-14 11:40:05,654] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:40:05,655] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:40:05,655] [INFO] DQC Reference Directory: /var/lib/cwl/stg86b3588c-229d-4b14-acfa-cde8e7530b32/dqc_reference
[2023-03-14 11:40:06,752] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:40:06,753] [INFO] Task started: Prodigal
[2023-03-14 11:40:06,753] [INFO] Running command: cat /var/lib/cwl/stg73197665-76d8-443d-8e9c-93500b437663/OceanDNA-b12725.fa | prodigal -d OceanDNA-b12725/cds.fna -a OceanDNA-b12725/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:40:19,514] [INFO] Task succeeded: Prodigal
[2023-03-14 11:40:19,514] [INFO] Task started: HMMsearch
[2023-03-14 11:40:19,515] [INFO] Running command: hmmsearch --tblout OceanDNA-b12725/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86b3588c-229d-4b14-acfa-cde8e7530b32/dqc_reference/reference_markers.hmm OceanDNA-b12725/protein.faa > /dev/null
[2023-03-14 11:40:19,684] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:40:19,685] [INFO] Found 6/6 markers.
[2023-03-14 11:40:19,713] [INFO] Query marker FASTA was written to OceanDNA-b12725/markers.fasta
[2023-03-14 11:40:19,713] [INFO] Task started: Blastn
[2023-03-14 11:40:19,713] [INFO] Running command: blastn -query OceanDNA-b12725/markers.fasta -db /var/lib/cwl/stg86b3588c-229d-4b14-acfa-cde8e7530b32/dqc_reference/reference_markers.fasta -out OceanDNA-b12725/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:40:20,235] [INFO] Task succeeded: Blastn
[2023-03-14 11:40:20,239] [INFO] Selected 27 target genomes.
[2023-03-14 11:40:20,239] [INFO] Target genome list was writen to OceanDNA-b12725/target_genomes.txt
[2023-03-14 11:40:20,256] [INFO] Task started: fastANI
[2023-03-14 11:40:20,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg73197665-76d8-443d-8e9c-93500b437663/OceanDNA-b12725.fa --refList OceanDNA-b12725/target_genomes.txt --output OceanDNA-b12725/fastani_result.tsv --threads 1
[2023-03-14 11:40:36,899] [INFO] Task succeeded: fastANI
[2023-03-14 11:40:36,899] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86b3588c-229d-4b14-acfa-cde8e7530b32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:40:36,899] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86b3588c-229d-4b14-acfa-cde8e7530b32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:40:36,899] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:40:36,899] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:40:36,899] [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
--------------------------------------------------------------------------------
[2023-03-14 11:40:36,902] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12725/tc_result.tsv
[2023-03-14 11:40:36,903] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:40:36,903] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:40:36,903] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86b3588c-229d-4b14-acfa-cde8e7530b32/dqc_reference/checkm_data
[2023-03-14 11:40:36,906] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:40:36,911] [INFO] Task started: CheckM
[2023-03-14 11:40:36,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12725/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12725/checkm_input OceanDNA-b12725/checkm_result
[2023-03-14 11:41:12,833] [INFO] Task succeeded: CheckM
[2023-03-14 11:41:12,834] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:41:12,857] [INFO] ===== Completeness check finished =====
[2023-03-14 11:41:12,857] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:41:12,857] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12725/markers.fasta)
[2023-03-14 11:41:12,858] [INFO] Task started: Blastn
[2023-03-14 11:41:12,858] [INFO] Running command: blastn -query OceanDNA-b12725/markers.fasta -db /var/lib/cwl/stg86b3588c-229d-4b14-acfa-cde8e7530b32/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12725/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:41:13,576] [INFO] Task succeeded: Blastn
[2023-03-14 11:41:13,582] [INFO] Selected 28 target genomes.
[2023-03-14 11:41:13,582] [INFO] Target genome list was writen to OceanDNA-b12725/target_genomes_gtdb.txt
[2023-03-14 11:41:13,613] [INFO] Task started: fastANI
[2023-03-14 11:41:13,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg73197665-76d8-443d-8e9c-93500b437663/OceanDNA-b12725.fa --refList OceanDNA-b12725/target_genomes_gtdb.txt --output OceanDNA-b12725/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:41:27,032] [INFO] Task succeeded: fastANI
[2023-03-14 11:41:27,036] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:41:27,036] [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_016779945.1	s__UBA9320 sp016779945	81.2414	364	631	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017857855.1	s__UBA9320 sp003516975	76.7049	61	631	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	99.31	99.21	0.89	0.84	3	-
GCA_002746305.1	s__UBA9320 sp002746305	76.5975	81	631	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402155.1	s__UBA9320 sp018402155	76.4281	56	631	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042025.1	s__UBA9320 sp013042025	76.1447	59	631	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:41:27,041] [INFO] GTDB search result was written to OceanDNA-b12725/result_gtdb.tsv
[2023-03-14 11:41:27,045] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:41:27,049] [INFO] DFAST_QC result json was written to OceanDNA-b12725/dqc_result.json
[2023-03-14 11:41:27,049] [INFO] DFAST_QC completed!
[2023-03-14 11:41:27,049] [INFO] Total running time: 0h1m21s