[2023-03-19 00:33:19,065] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:33:19,065] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:33:19,065] [INFO] DQC Reference Directory: /var/lib/cwl/stgddefc3d9-c7bd-4c33-a8cc-596c69828f34/dqc_reference
[2023-03-19 00:33:20,246] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:33:20,246] [INFO] Task started: Prodigal
[2023-03-19 00:33:20,247] [INFO] Running command: cat /var/lib/cwl/stgc5dc9505-a366-4f1d-a07e-b7a681442440/OceanDNA-b41805.fa | prodigal -d OceanDNA-b41805/cds.fna -a OceanDNA-b41805/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:33:24,600] [INFO] Task succeeded: Prodigal
[2023-03-19 00:33:24,601] [INFO] Task started: HMMsearch
[2023-03-19 00:33:24,601] [INFO] Running command: hmmsearch --tblout OceanDNA-b41805/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddefc3d9-c7bd-4c33-a8cc-596c69828f34/dqc_reference/reference_markers.hmm OceanDNA-b41805/protein.faa > /dev/null
[2023-03-19 00:33:24,768] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:33:24,769] [INFO] Found 6/6 markers.
[2023-03-19 00:33:24,778] [INFO] Query marker FASTA was written to OceanDNA-b41805/markers.fasta
[2023-03-19 00:33:24,779] [INFO] Task started: Blastn
[2023-03-19 00:33:24,779] [INFO] Running command: blastn -query OceanDNA-b41805/markers.fasta -db /var/lib/cwl/stgddefc3d9-c7bd-4c33-a8cc-596c69828f34/dqc_reference/reference_markers.fasta -out OceanDNA-b41805/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:25,346] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:25,347] [INFO] Selected 18 target genomes.
[2023-03-19 00:33:25,347] [INFO] Target genome list was writen to OceanDNA-b41805/target_genomes.txt
[2023-03-19 00:33:25,362] [INFO] Task started: fastANI
[2023-03-19 00:33:25,362] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5dc9505-a366-4f1d-a07e-b7a681442440/OceanDNA-b41805.fa --refList OceanDNA-b41805/target_genomes.txt --output OceanDNA-b41805/fastani_result.tsv --threads 1
[2023-03-19 00:33:34,401] [INFO] Task succeeded: fastANI
[2023-03-19 00:33:34,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddefc3d9-c7bd-4c33-a8cc-596c69828f34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:33:34,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddefc3d9-c7bd-4c33-a8cc-596c69828f34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:33:34,402] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:33:34,402] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:33:34,402] [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 00:33:34,405] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41805/tc_result.tsv
[2023-03-19 00:33:34,405] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:33:34,405] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:33:34,406] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddefc3d9-c7bd-4c33-a8cc-596c69828f34/dqc_reference/checkm_data
[2023-03-19 00:33:34,409] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:33:34,417] [INFO] Task started: CheckM
[2023-03-19 00:33:34,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41805/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41805/checkm_input OceanDNA-b41805/checkm_result
[2023-03-19 00:33:52,389] [INFO] Task succeeded: CheckM
[2023-03-19 00:33:52,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.80%
Contamintation: 1.66%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 00:33:52,395] [INFO] ===== Completeness check finished =====
[2023-03-19 00:33:52,395] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:33:52,396] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41805/markers.fasta)
[2023-03-19 00:33:52,396] [INFO] Task started: Blastn
[2023-03-19 00:33:52,396] [INFO] Running command: blastn -query OceanDNA-b41805/markers.fasta -db /var/lib/cwl/stgddefc3d9-c7bd-4c33-a8cc-596c69828f34/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41805/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:53,335] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:53,340] [INFO] Selected 7 target genomes.
[2023-03-19 00:33:53,340] [INFO] Target genome list was writen to OceanDNA-b41805/target_genomes_gtdb.txt
[2023-03-19 00:33:53,365] [INFO] Task started: fastANI
[2023-03-19 00:33:53,365] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5dc9505-a366-4f1d-a07e-b7a681442440/OceanDNA-b41805.fa --refList OceanDNA-b41805/target_genomes_gtdb.txt --output OceanDNA-b41805/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:33:54,878] [INFO] Task succeeded: fastANI
[2023-03-19 00:33:54,883] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:33:54,883] [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_902614235.1	s__AG-339-G14 sp902614235	98.9652	244	275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.30	98.01	0.83	0.80	7	conclusive
GCA_902523885.1	s__AG-339-G14 sp902523885	94.7695	247	275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902525735.1	s__AG-339-G14 sp902525735	94.0123	257	275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.66	98.66	0.90	0.90	2	-
GCA_902635045.1	s__AG-339-G14 sp902635045	87.7918	241	275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	98.24	96.50	0.87	0.84	4	-
GCA_902524805.1	s__AG-339-G14 sp902524805	82.4956	162	275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902522825.1	s__AG-339-G14 sp902522825	80.1233	187	275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__AG-339-G14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:33:54,883] [INFO] GTDB search result was written to OceanDNA-b41805/result_gtdb.tsv
[2023-03-19 00:33:54,884] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:33:54,885] [INFO] DFAST_QC result json was written to OceanDNA-b41805/dqc_result.json
[2023-03-19 00:33:54,885] [INFO] DFAST_QC completed!
[2023-03-19 00:33:54,885] [INFO] Total running time: 0h0m36s