[2023-03-14 12:33:24,277] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:33:24,277] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:33:24,277] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a297036-0ed6-474e-b5b1-5b573a734943/dqc_reference
[2023-03-14 12:33:25,383] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:33:25,383] [INFO] Task started: Prodigal
[2023-03-14 12:33:25,383] [INFO] Running command: cat /var/lib/cwl/stg20b07118-efc1-4aa2-bf52-5070421e15cd/OceanDNA-b43999.fa | prodigal -d OceanDNA-b43999/cds.fna -a OceanDNA-b43999/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:33:31,023] [INFO] Task succeeded: Prodigal
[2023-03-14 12:33:31,023] [INFO] Task started: HMMsearch
[2023-03-14 12:33:31,023] [INFO] Running command: hmmsearch --tblout OceanDNA-b43999/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a297036-0ed6-474e-b5b1-5b573a734943/dqc_reference/reference_markers.hmm OceanDNA-b43999/protein.faa > /dev/null
[2023-03-14 12:33:31,170] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:33:31,170] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg20b07118-efc1-4aa2-bf52-5070421e15cd/OceanDNA-b43999.fa]
[2023-03-14 12:33:31,179] [INFO] Query marker FASTA was written to OceanDNA-b43999/markers.fasta
[2023-03-14 12:33:31,181] [INFO] Task started: Blastn
[2023-03-14 12:33:31,181] [INFO] Running command: blastn -query OceanDNA-b43999/markers.fasta -db /var/lib/cwl/stg1a297036-0ed6-474e-b5b1-5b573a734943/dqc_reference/reference_markers.fasta -out OceanDNA-b43999/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:33:31,730] [INFO] Task succeeded: Blastn
[2023-03-14 12:33:31,731] [INFO] Selected 9 target genomes.
[2023-03-14 12:33:31,731] [INFO] Target genome list was writen to OceanDNA-b43999/target_genomes.txt
[2023-03-14 12:33:31,737] [INFO] Task started: fastANI
[2023-03-14 12:33:31,737] [INFO] Running command: fastANI --query /var/lib/cwl/stg20b07118-efc1-4aa2-bf52-5070421e15cd/OceanDNA-b43999.fa --refList OceanDNA-b43999/target_genomes.txt --output OceanDNA-b43999/fastani_result.tsv --threads 1
[2023-03-14 12:33:35,794] [INFO] Task succeeded: fastANI
[2023-03-14 12:33:35,795] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a297036-0ed6-474e-b5b1-5b573a734943/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:33:35,795] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a297036-0ed6-474e-b5b1-5b573a734943/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:33:35,795] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:33:35,795] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:33:35,795] [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 12:33:35,795] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43999/tc_result.tsv
[2023-03-14 12:33:35,795] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:33:35,795] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:33:35,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a297036-0ed6-474e-b5b1-5b573a734943/dqc_reference/checkm_data
[2023-03-14 12:33:35,798] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:33:35,801] [INFO] Task started: CheckM
[2023-03-14 12:33:35,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43999/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43999/checkm_input OceanDNA-b43999/checkm_result
[2023-03-14 12:33:55,936] [INFO] Task succeeded: CheckM
[2023-03-14 12:33:55,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:33:55,938] [INFO] ===== Completeness check finished =====
[2023-03-14 12:33:55,939] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:33:55,939] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43999/markers.fasta)
[2023-03-14 12:33:55,939] [INFO] Task started: Blastn
[2023-03-14 12:33:55,939] [INFO] Running command: blastn -query OceanDNA-b43999/markers.fasta -db /var/lib/cwl/stg1a297036-0ed6-474e-b5b1-5b573a734943/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43999/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:33:56,830] [INFO] Task succeeded: Blastn
[2023-03-14 12:33:56,831] [INFO] Selected 14 target genomes.
[2023-03-14 12:33:56,831] [INFO] Target genome list was writen to OceanDNA-b43999/target_genomes_gtdb.txt
[2023-03-14 12:33:56,840] [INFO] Task started: fastANI
[2023-03-14 12:33:56,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg20b07118-efc1-4aa2-bf52-5070421e15cd/OceanDNA-b43999.fa --refList OceanDNA-b43999/target_genomes_gtdb.txt --output OceanDNA-b43999/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:34:01,024] [INFO] Task succeeded: fastANI
[2023-03-14 12:34:01,029] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:34:01,029] [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_002691305.1	s__UBA11654 sp002691305	91.8373	258	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	97.81	97.81	0.81	0.81	2	-
GCA_002717445.1	s__UBA11654 sp002717445	81.9286	228	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718375.1	s__UBA11654 sp002718375	79.6081	109	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	98.63	98.63	0.55	0.55	2	-
GCA_002691465.1	s__UBA11654 sp002691465	79.3033	195	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	100.00	100.00	0.95	0.95	2	-
GCA_902595845.1	s__UBA11654 sp001629325	79.2984	187	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	96.90	95.86	0.87	0.81	6	-
GCA_902553145.1	s__UBA11654 sp902553145	79.109	199	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	95.92	95.45	0.83	0.82	5	-
--------------------------------------------------------------------------------
[2023-03-14 12:34:01,030] [INFO] GTDB search result was written to OceanDNA-b43999/result_gtdb.tsv
[2023-03-14 12:34:01,030] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:34:01,032] [INFO] DFAST_QC result json was written to OceanDNA-b43999/dqc_result.json
[2023-03-14 12:34:01,032] [INFO] DFAST_QC completed!
[2023-03-14 12:34:01,032] [INFO] Total running time: 0h0m37s