[2023-03-17 03:11:36,281] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:11:36,281] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:11:36,281] [INFO] DQC Reference Directory: /var/lib/cwl/stg16cd32e6-79a7-4eec-9969-46561ba8827e/dqc_reference
[2023-03-17 03:11:37,572] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:11:37,572] [INFO] Task started: Prodigal
[2023-03-17 03:11:37,572] [INFO] Running command: cat /var/lib/cwl/stg0878f3df-3c99-4f27-99f9-b6c9c97c4f6e/OceanDNA-b44000.fa | prodigal -d OceanDNA-b44000/cds.fna -a OceanDNA-b44000/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:11:42,763] [INFO] Task succeeded: Prodigal
[2023-03-17 03:11:42,763] [INFO] Task started: HMMsearch
[2023-03-17 03:11:42,763] [INFO] Running command: hmmsearch --tblout OceanDNA-b44000/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16cd32e6-79a7-4eec-9969-46561ba8827e/dqc_reference/reference_markers.hmm OceanDNA-b44000/protein.faa > /dev/null
[2023-03-17 03:11:42,947] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:11:42,948] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0878f3df-3c99-4f27-99f9-b6c9c97c4f6e/OceanDNA-b44000.fa]
[2023-03-17 03:11:42,962] [INFO] Query marker FASTA was written to OceanDNA-b44000/markers.fasta
[2023-03-17 03:11:42,962] [INFO] Task started: Blastn
[2023-03-17 03:11:42,962] [INFO] Running command: blastn -query OceanDNA-b44000/markers.fasta -db /var/lib/cwl/stg16cd32e6-79a7-4eec-9969-46561ba8827e/dqc_reference/reference_markers.fasta -out OceanDNA-b44000/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:11:43,517] [INFO] Task succeeded: Blastn
[2023-03-17 03:11:43,912] [INFO] Selected 8 target genomes.
[2023-03-17 03:11:43,912] [INFO] Target genome list was writen to OceanDNA-b44000/target_genomes.txt
[2023-03-17 03:11:43,994] [INFO] Task started: fastANI
[2023-03-17 03:11:43,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg0878f3df-3c99-4f27-99f9-b6c9c97c4f6e/OceanDNA-b44000.fa --refList OceanDNA-b44000/target_genomes.txt --output OceanDNA-b44000/fastani_result.tsv --threads 1
[2023-03-17 03:11:47,340] [INFO] Task succeeded: fastANI
[2023-03-17 03:11:47,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16cd32e6-79a7-4eec-9969-46561ba8827e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:11:47,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16cd32e6-79a7-4eec-9969-46561ba8827e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:11:47,341] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:11:47,341] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 03:11:47,341] [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
--------------------------------------------------------------------------------
[2023-03-17 03:11:47,341] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44000/tc_result.tsv
[2023-03-17 03:11:47,342] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:11:47,342] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:11:47,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16cd32e6-79a7-4eec-9969-46561ba8827e/dqc_reference/checkm_data
[2023-03-17 03:11:47,349] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:11:47,357] [INFO] Task started: CheckM
[2023-03-17 03:11:47,358] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44000/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44000/checkm_input OceanDNA-b44000/checkm_result
[2023-03-17 03:12:06,876] [INFO] Task succeeded: CheckM
[2023-03-17 03:12:06,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.69%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:12:06,878] [INFO] ===== Completeness check finished =====
[2023-03-17 03:12:06,878] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:12:06,878] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44000/markers.fasta)
[2023-03-17 03:12:06,879] [INFO] Task started: Blastn
[2023-03-17 03:12:06,879] [INFO] Running command: blastn -query OceanDNA-b44000/markers.fasta -db /var/lib/cwl/stg16cd32e6-79a7-4eec-9969-46561ba8827e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44000/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:12:07,595] [INFO] Task succeeded: Blastn
[2023-03-17 03:12:07,596] [INFO] Selected 12 target genomes.
[2023-03-17 03:12:07,596] [INFO] Target genome list was writen to OceanDNA-b44000/target_genomes_gtdb.txt
[2023-03-17 03:12:07,665] [INFO] Task started: fastANI
[2023-03-17 03:12:07,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg0878f3df-3c99-4f27-99f9-b6c9c97c4f6e/OceanDNA-b44000.fa --refList OceanDNA-b44000/target_genomes_gtdb.txt --output OceanDNA-b44000/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:12:11,236] [INFO] Task succeeded: fastANI
[2023-03-17 03:12:11,241] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:12:11,241] [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_902553145.1	s__UBA11654 sp902553145	96.521	277	302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	95.92	95.45	0.83	0.82	5	conclusive
GCA_002691465.1	s__UBA11654 sp002691465	92.4098	277	302	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	80.5991	227	302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	96.90	95.86	0.87	0.81	6	-
GCA_002718375.1	s__UBA11654 sp002718375	80.3067	137	302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	98.63	98.63	0.55	0.55	2	-
GCA_002691305.1	s__UBA11654 sp002691305	79.3444	177	302	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	79.2384	191	302	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:12:11,241] [INFO] GTDB search result was written to OceanDNA-b44000/result_gtdb.tsv
[2023-03-17 03:12:11,242] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:12:11,242] [INFO] DFAST_QC result json was written to OceanDNA-b44000/dqc_result.json
[2023-03-17 03:12:11,242] [INFO] DFAST_QC completed!
[2023-03-17 03:12:11,243] [INFO] Total running time: 0h0m35s