[2023-03-18 23:22:48,485] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:22:48,486] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:22:48,486] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bc169b9-60a3-46d9-976a-869ca2df1105/dqc_reference
[2023-03-18 23:22:49,618] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:22:49,618] [INFO] Task started: Prodigal
[2023-03-18 23:22:49,619] [INFO] Running command: cat /var/lib/cwl/stgcec45df7-a976-417d-bcaa-7f07611585db/OceanDNA-b32784.fa | prodigal -d OceanDNA-b32784/cds.fna -a OceanDNA-b32784/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:23:00,515] [INFO] Task succeeded: Prodigal
[2023-03-18 23:23:00,515] [INFO] Task started: HMMsearch
[2023-03-18 23:23:00,515] [INFO] Running command: hmmsearch --tblout OceanDNA-b32784/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bc169b9-60a3-46d9-976a-869ca2df1105/dqc_reference/reference_markers.hmm OceanDNA-b32784/protein.faa > /dev/null
[2023-03-18 23:23:00,675] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:23:00,676] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcec45df7-a976-417d-bcaa-7f07611585db/OceanDNA-b32784.fa]
[2023-03-18 23:23:00,696] [INFO] Query marker FASTA was written to OceanDNA-b32784/markers.fasta
[2023-03-18 23:23:00,697] [INFO] Task started: Blastn
[2023-03-18 23:23:00,697] [INFO] Running command: blastn -query OceanDNA-b32784/markers.fasta -db /var/lib/cwl/stg5bc169b9-60a3-46d9-976a-869ca2df1105/dqc_reference/reference_markers.fasta -out OceanDNA-b32784/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:23:01,195] [INFO] Task succeeded: Blastn
[2023-03-18 23:23:01,196] [INFO] Selected 24 target genomes.
[2023-03-18 23:23:01,197] [INFO] Target genome list was writen to OceanDNA-b32784/target_genomes.txt
[2023-03-18 23:23:01,212] [INFO] Task started: fastANI
[2023-03-18 23:23:01,212] [INFO] Running command: fastANI --query /var/lib/cwl/stgcec45df7-a976-417d-bcaa-7f07611585db/OceanDNA-b32784.fa --refList OceanDNA-b32784/target_genomes.txt --output OceanDNA-b32784/fastani_result.tsv --threads 1
[2023-03-18 23:23:19,448] [INFO] Task succeeded: fastANI
[2023-03-18 23:23:19,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bc169b9-60a3-46d9-976a-869ca2df1105/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:23:19,449] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bc169b9-60a3-46d9-976a-869ca2df1105/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:23:19,452] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:23:19,452] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:23:19,452] [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
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.6127	57	465	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	75.5401	53	465	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:23:19,453] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32784/tc_result.tsv
[2023-03-18 23:23:19,453] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:23:19,453] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:23:19,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bc169b9-60a3-46d9-976a-869ca2df1105/dqc_reference/checkm_data
[2023-03-18 23:23:19,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:23:19,459] [INFO] Task started: CheckM
[2023-03-18 23:23:19,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32784/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32784/checkm_input OceanDNA-b32784/checkm_result
[2023-03-18 23:23:50,253] [INFO] Task succeeded: CheckM
[2023-03-18 23:23:50,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.15%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:23:50,257] [INFO] ===== Completeness check finished =====
[2023-03-18 23:23:50,257] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:23:50,257] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32784/markers.fasta)
[2023-03-18 23:23:50,258] [INFO] Task started: Blastn
[2023-03-18 23:23:50,258] [INFO] Running command: blastn -query OceanDNA-b32784/markers.fasta -db /var/lib/cwl/stg5bc169b9-60a3-46d9-976a-869ca2df1105/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32784/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:23:50,864] [INFO] Task succeeded: Blastn
[2023-03-18 23:23:50,865] [INFO] Selected 9 target genomes.
[2023-03-18 23:23:50,865] [INFO] Target genome list was writen to OceanDNA-b32784/target_genomes_gtdb.txt
[2023-03-18 23:23:50,871] [INFO] Task started: fastANI
[2023-03-18 23:23:50,871] [INFO] Running command: fastANI --query /var/lib/cwl/stgcec45df7-a976-417d-bcaa-7f07611585db/OceanDNA-b32784.fa --refList OceanDNA-b32784/target_genomes_gtdb.txt --output OceanDNA-b32784/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:23:56,746] [INFO] Task succeeded: fastANI
[2023-03-18 23:23:56,752] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:23:56,752] [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_018702955.1	s__UBA8079 sp018702955	99.4935	448	465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.54	99.39	0.93	0.91	5	conclusive
GCA_018667335.1	s__UBA8079 sp018667335	84.4934	421	465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.89	99.79	0.96	0.96	6	-
GCA_002727315.1	s__UBA8079 sp002727315	78.8461	213	465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724635.1	s__UBA8079 sp002724635	78.6316	230	465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643325.1	s__JABJAG01 sp017643325	77.9598	183	465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666195.1	s__JABJAG01 sp018666195	76.9564	127	465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011087645.1	s__JABDJY01 sp011087645	76.1892	107	465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABDJY01	95.0	99.97	99.97	0.97	0.97	2	-
GCA_017305915.1	s__Reyranella sp017305915	75.6027	57	465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307375.1	s__JAFKFH01 sp017307375	75.5824	64	465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:23:56,753] [INFO] GTDB search result was written to OceanDNA-b32784/result_gtdb.tsv
[2023-03-18 23:23:56,754] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:23:56,755] [INFO] DFAST_QC result json was written to OceanDNA-b32784/dqc_result.json
[2023-03-18 23:23:56,755] [INFO] DFAST_QC completed!
[2023-03-18 23:23:56,755] [INFO] Total running time: 0h1m8s