[2023-03-14 13:48:56,012] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:48:56,013] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:48:56,013] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d6e6a2c-d528-4451-874b-e6982ef23fac/dqc_reference
[2023-03-14 13:48:57,421] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:48:57,422] [INFO] Task started: Prodigal
[2023-03-14 13:48:57,423] [INFO] Running command: cat /var/lib/cwl/stg2d325902-45fd-4162-91ee-2fd2ded62b60/OceanDNA-b25991.fa | prodigal -d OceanDNA-b25991/cds.fna -a OceanDNA-b25991/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:49:09,552] [INFO] Task succeeded: Prodigal
[2023-03-14 13:49:09,553] [INFO] Task started: HMMsearch
[2023-03-14 13:49:09,553] [INFO] Running command: hmmsearch --tblout OceanDNA-b25991/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d6e6a2c-d528-4451-874b-e6982ef23fac/dqc_reference/reference_markers.hmm OceanDNA-b25991/protein.faa > /dev/null
[2023-03-14 13:49:09,734] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:49:09,735] [INFO] Found 6/6 markers.
[2023-03-14 13:49:09,750] [INFO] Query marker FASTA was written to OceanDNA-b25991/markers.fasta
[2023-03-14 13:49:09,751] [INFO] Task started: Blastn
[2023-03-14 13:49:09,751] [INFO] Running command: blastn -query OceanDNA-b25991/markers.fasta -db /var/lib/cwl/stg8d6e6a2c-d528-4451-874b-e6982ef23fac/dqc_reference/reference_markers.fasta -out OceanDNA-b25991/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:49:10,316] [INFO] Task succeeded: Blastn
[2023-03-14 13:49:10,317] [INFO] Selected 20 target genomes.
[2023-03-14 13:49:10,317] [INFO] Target genome list was writen to OceanDNA-b25991/target_genomes.txt
[2023-03-14 13:49:10,330] [INFO] Task started: fastANI
[2023-03-14 13:49:10,330] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d325902-45fd-4162-91ee-2fd2ded62b60/OceanDNA-b25991.fa --refList OceanDNA-b25991/target_genomes.txt --output OceanDNA-b25991/fastani_result.tsv --threads 1
[2023-03-14 13:49:18,786] [INFO] Task succeeded: fastANI
[2023-03-14 13:49:18,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d6e6a2c-d528-4451-874b-e6982ef23fac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:49:18,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d6e6a2c-d528-4451-874b-e6982ef23fac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:49:18,787] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:49:18,787] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:49:18,787] [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 13:49:18,787] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25991/tc_result.tsv
[2023-03-14 13:49:18,787] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:49:18,787] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:49:18,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d6e6a2c-d528-4451-874b-e6982ef23fac/dqc_reference/checkm_data
[2023-03-14 13:49:18,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:49:18,837] [INFO] Task started: CheckM
[2023-03-14 13:49:18,837] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25991/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25991/checkm_input OceanDNA-b25991/checkm_result
[2023-03-14 13:49:47,220] [INFO] Task succeeded: CheckM
[2023-03-14 13:49:47,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:49:47,224] [INFO] ===== Completeness check finished =====
[2023-03-14 13:49:47,224] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:49:47,224] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25991/markers.fasta)
[2023-03-14 13:49:47,226] [INFO] Task started: Blastn
[2023-03-14 13:49:47,226] [INFO] Running command: blastn -query OceanDNA-b25991/markers.fasta -db /var/lib/cwl/stg8d6e6a2c-d528-4451-874b-e6982ef23fac/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25991/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:49:48,883] [INFO] Task succeeded: Blastn
[2023-03-14 13:49:48,884] [INFO] Selected 13 target genomes.
[2023-03-14 13:49:48,884] [INFO] Target genome list was writen to OceanDNA-b25991/target_genomes_gtdb.txt
[2023-03-14 13:49:48,894] [INFO] Task started: fastANI
[2023-03-14 13:49:48,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d325902-45fd-4162-91ee-2fd2ded62b60/OceanDNA-b25991.fa --refList OceanDNA-b25991/target_genomes_gtdb.txt --output OceanDNA-b25991/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:49:53,513] [INFO] Task succeeded: fastANI
[2023-03-14 13:49:53,521] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:49:53,521] [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_902619805.1	s__AAA536-G10 sp902619805	98.4594	434	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902543145.1	s__AAA536-G10 sp902543145	92.4029	391	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	99.74	99.74	0.81	0.81	2	-
GCA_902529515.1	s__AAA536-G10 sp902529515	92.3573	264	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	97.18	97.18	0.52	0.52	2	-
GCA_902619485.1	s__AAA536-G10 sp902619485	92.2375	357	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902542765.1	s__AAA536-G10 sp902542765	92.1746	227	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902539895.1	s__AAA536-G10 sp902539895	92.1059	298	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902589185.1	s__AAA536-G10 sp902589185	91.2828	299	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517815.1	s__AAA536-G10 sp902517815	91.0691	417	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595145.1	s__AAA536-G10 sp902595145	90.6608	317	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558885.1	s__AAA536-G10 sp902558885	89.8689	362	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902616615.1	s__AAA536-G10 sp902616615	89.108	334	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902592615.1	s__AAA536-G10 sp902592615	88.9258	342	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902618025.1	s__AAA536-G10 sp902618025	87.3006	302	535	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:49:53,522] [INFO] GTDB search result was written to OceanDNA-b25991/result_gtdb.tsv
[2023-03-14 13:49:53,522] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:49:53,523] [INFO] DFAST_QC result json was written to OceanDNA-b25991/dqc_result.json
[2023-03-14 13:49:53,523] [INFO] DFAST_QC completed!
[2023-03-14 13:49:53,523] [INFO] Total running time: 0h0m58s