[2023-03-15 05:43:38,790] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:43:38,798] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:43:38,798] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbb67e09-a56b-47ba-aabd-9edc300e1d1d/dqc_reference
[2023-03-15 05:43:39,884] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:43:39,884] [INFO] Task started: Prodigal
[2023-03-15 05:43:39,885] [INFO] Running command: cat /var/lib/cwl/stgc08ac318-b616-47ff-afa0-7c9b1d02df24/OceanDNA-b44036.fa | prodigal -d OceanDNA-b44036/cds.fna -a OceanDNA-b44036/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:43:45,818] [INFO] Task succeeded: Prodigal
[2023-03-15 05:43:45,818] [INFO] Task started: HMMsearch
[2023-03-15 05:43:45,818] [INFO] Running command: hmmsearch --tblout OceanDNA-b44036/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbb67e09-a56b-47ba-aabd-9edc300e1d1d/dqc_reference/reference_markers.hmm OceanDNA-b44036/protein.faa > /dev/null
[2023-03-15 05:43:45,974] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:43:45,975] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc08ac318-b616-47ff-afa0-7c9b1d02df24/OceanDNA-b44036.fa]
[2023-03-15 05:43:46,017] [INFO] Query marker FASTA was written to OceanDNA-b44036/markers.fasta
[2023-03-15 05:43:46,019] [INFO] Task started: Blastn
[2023-03-15 05:43:46,019] [INFO] Running command: blastn -query OceanDNA-b44036/markers.fasta -db /var/lib/cwl/stgfbb67e09-a56b-47ba-aabd-9edc300e1d1d/dqc_reference/reference_markers.fasta -out OceanDNA-b44036/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:43:46,550] [INFO] Task succeeded: Blastn
[2023-03-15 05:43:46,554] [INFO] Selected 7 target genomes.
[2023-03-15 05:43:46,554] [INFO] Target genome list was writen to OceanDNA-b44036/target_genomes.txt
[2023-03-15 05:43:46,558] [INFO] Task started: fastANI
[2023-03-15 05:43:46,558] [INFO] Running command: fastANI --query /var/lib/cwl/stgc08ac318-b616-47ff-afa0-7c9b1d02df24/OceanDNA-b44036.fa --refList OceanDNA-b44036/target_genomes.txt --output OceanDNA-b44036/fastani_result.tsv --threads 1
[2023-03-15 05:43:49,764] [INFO] Task succeeded: fastANI
[2023-03-15 05:43:49,765] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbb67e09-a56b-47ba-aabd-9edc300e1d1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:43:49,765] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbb67e09-a56b-47ba-aabd-9edc300e1d1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:43:49,765] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:43:49,765] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:43:49,765] [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 05:43:49,773] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44036/tc_result.tsv
[2023-03-15 05:43:49,787] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:43:49,787] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:43:49,787] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbb67e09-a56b-47ba-aabd-9edc300e1d1d/dqc_reference/checkm_data
[2023-03-15 05:43:49,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:43:49,804] [INFO] Task started: CheckM
[2023-03-15 05:43:49,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44036/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44036/checkm_input OceanDNA-b44036/checkm_result
[2023-03-15 05:44:11,441] [INFO] Task succeeded: CheckM
[2023-03-15 05:44:11,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.70%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 05:44:11,559] [INFO] ===== Completeness check finished =====
[2023-03-15 05:44:11,559] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:44:11,559] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44036/markers.fasta)
[2023-03-15 05:44:11,561] [INFO] Task started: Blastn
[2023-03-15 05:44:11,561] [INFO] Running command: blastn -query OceanDNA-b44036/markers.fasta -db /var/lib/cwl/stgfbb67e09-a56b-47ba-aabd-9edc300e1d1d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44036/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:44:12,343] [INFO] Task succeeded: Blastn
[2023-03-15 05:44:12,344] [INFO] Selected 13 target genomes.
[2023-03-15 05:44:12,344] [INFO] Target genome list was writen to OceanDNA-b44036/target_genomes_gtdb.txt
[2023-03-15 05:44:12,359] [INFO] Task started: fastANI
[2023-03-15 05:44:12,359] [INFO] Running command: fastANI --query /var/lib/cwl/stgc08ac318-b616-47ff-afa0-7c9b1d02df24/OceanDNA-b44036.fa --refList OceanDNA-b44036/target_genomes_gtdb.txt --output OceanDNA-b44036/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:44:15,694] [INFO] Task succeeded: fastANI
[2023-03-15 05:44:15,698] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:44:15,699] [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	98.6832	301	345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	97.81	97.81	0.81	0.81	2	conclusive
GCA_002717445.1	s__UBA11654 sp002717445	81.6263	239	345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902553145.1	s__UBA11654 sp902553145	81.0051	211	345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	95.92	95.45	0.83	0.82	5	-
GCA_002691465.1	s__UBA11654 sp002691465	79.8935	213	345	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	79.8076	206	345	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	79.0625	122	345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA11654;f__UBA11654;g__UBA11654	95.0	98.63	98.63	0.55	0.55	2	-
--------------------------------------------------------------------------------
[2023-03-15 05:44:15,699] [INFO] GTDB search result was written to OceanDNA-b44036/result_gtdb.tsv
[2023-03-15 05:44:15,699] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:44:15,700] [INFO] DFAST_QC result json was written to OceanDNA-b44036/dqc_result.json
[2023-03-15 05:44:15,700] [INFO] DFAST_QC completed!
[2023-03-15 05:44:15,700] [INFO] Total running time: 0h0m37s