[2023-03-15 23:38:54,759] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:38:54,770] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:38:54,770] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbe99505-9d82-4398-bc1e-52476245a89d/dqc_reference
[2023-03-15 23:38:55,876] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:38:55,876] [INFO] Task started: Prodigal
[2023-03-15 23:38:55,876] [INFO] Running command: cat /var/lib/cwl/stg2fdb0b8c-1b0c-4a93-b789-95d11696f703/OceanDNA-b16587.fa | prodigal -d OceanDNA-b16587/cds.fna -a OceanDNA-b16587/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:39:13,549] [INFO] Task succeeded: Prodigal
[2023-03-15 23:39:13,550] [INFO] Task started: HMMsearch
[2023-03-15 23:39:13,550] [INFO] Running command: hmmsearch --tblout OceanDNA-b16587/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbe99505-9d82-4398-bc1e-52476245a89d/dqc_reference/reference_markers.hmm OceanDNA-b16587/protein.faa > /dev/null
[2023-03-15 23:39:13,733] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:39:13,734] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2fdb0b8c-1b0c-4a93-b789-95d11696f703/OceanDNA-b16587.fa]
[2023-03-15 23:39:13,808] [INFO] Query marker FASTA was written to OceanDNA-b16587/markers.fasta
[2023-03-15 23:39:13,810] [INFO] Task started: Blastn
[2023-03-15 23:39:13,810] [INFO] Running command: blastn -query OceanDNA-b16587/markers.fasta -db /var/lib/cwl/stgdbe99505-9d82-4398-bc1e-52476245a89d/dqc_reference/reference_markers.fasta -out OceanDNA-b16587/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:39:14,341] [INFO] Task succeeded: Blastn
[2023-03-15 23:39:14,360] [INFO] Selected 23 target genomes.
[2023-03-15 23:39:14,361] [INFO] Target genome list was writen to OceanDNA-b16587/target_genomes.txt
[2023-03-15 23:39:14,376] [INFO] Task started: fastANI
[2023-03-15 23:39:14,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fdb0b8c-1b0c-4a93-b789-95d11696f703/OceanDNA-b16587.fa --refList OceanDNA-b16587/target_genomes.txt --output OceanDNA-b16587/fastani_result.tsv --threads 1
[2023-03-15 23:39:30,163] [INFO] Task succeeded: fastANI
[2023-03-15 23:39:30,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbe99505-9d82-4398-bc1e-52476245a89d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:39:30,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbe99505-9d82-4398-bc1e-52476245a89d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:39:30,167] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:39:30,167] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:39:30,167] [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
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	77.9309	188	637	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:39:30,177] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16587/tc_result.tsv
[2023-03-15 23:39:30,194] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:39:30,194] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:39:30,194] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbe99505-9d82-4398-bc1e-52476245a89d/dqc_reference/checkm_data
[2023-03-15 23:39:30,195] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:39:30,207] [INFO] Task started: CheckM
[2023-03-15 23:39:30,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16587/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16587/checkm_input OceanDNA-b16587/checkm_result
[2023-03-15 23:40:19,311] [INFO] Task succeeded: CheckM
[2023-03-15 23:40:19,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.16%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 23:40:19,387] [INFO] ===== Completeness check finished =====
[2023-03-15 23:40:19,387] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:40:19,387] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16587/markers.fasta)
[2023-03-15 23:40:19,389] [INFO] Task started: Blastn
[2023-03-15 23:40:19,389] [INFO] Running command: blastn -query OceanDNA-b16587/markers.fasta -db /var/lib/cwl/stgdbe99505-9d82-4398-bc1e-52476245a89d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16587/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:40:20,175] [INFO] Task succeeded: Blastn
[2023-03-15 23:40:20,217] [INFO] Selected 6 target genomes.
[2023-03-15 23:40:20,217] [INFO] Target genome list was writen to OceanDNA-b16587/target_genomes_gtdb.txt
[2023-03-15 23:40:20,224] [INFO] Task started: fastANI
[2023-03-15 23:40:20,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg2fdb0b8c-1b0c-4a93-b789-95d11696f703/OceanDNA-b16587.fa --refList OceanDNA-b16587/target_genomes_gtdb.txt --output OceanDNA-b16587/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:40:23,311] [INFO] Task succeeded: fastANI
[2023-03-15 23:40:23,315] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 23:40:23,315] [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
GCF_000153285.1	s__Synechococcus_C sp000153285	99.0725	630	637	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014279875.1	s__Synechococcus_C sp002172935	87.86	550	637	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	98.09	98.09	0.93	0.93	2	-
GCF_014279795.1	s__Synechococcus_C sp014279795	87.6383	550	637	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	96.67	96.56	0.92	0.91	3	-
GCA_000063505.1	s__Synechococcus_C sp000063505	85.262	546	637	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	97.52	97.52	0.89	0.89	2	-
GCA_011523835.1	s__Synechococcus_C sp011523835	84.3197	435	637	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779825.1	s__Synechococcus_E sp016779825	81.3708	146	637	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:40:23,319] [INFO] GTDB search result was written to OceanDNA-b16587/result_gtdb.tsv
[2023-03-15 23:40:23,326] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:40:23,333] [INFO] DFAST_QC result json was written to OceanDNA-b16587/dqc_result.json
[2023-03-15 23:40:23,333] [INFO] DFAST_QC completed!
[2023-03-15 23:40:23,333] [INFO] Total running time: 0h1m29s