[2023-03-18 00:53:42,859] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:53:42,860] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:53:42,860] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e3573f9-6229-44ca-a769-2fec48caa680/dqc_reference
[2023-03-18 00:53:44,410] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:53:44,411] [INFO] Task started: Prodigal
[2023-03-18 00:53:44,411] [INFO] Running command: cat /var/lib/cwl/stgf0e3f787-a3f6-4839-8b73-c7f10e68b87c/OceanDNA-b1945.fa | prodigal -d OceanDNA-b1945/cds.fna -a OceanDNA-b1945/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:53:52,837] [INFO] Task succeeded: Prodigal
[2023-03-18 00:53:52,837] [INFO] Task started: HMMsearch
[2023-03-18 00:53:52,837] [INFO] Running command: hmmsearch --tblout OceanDNA-b1945/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e3573f9-6229-44ca-a769-2fec48caa680/dqc_reference/reference_markers.hmm OceanDNA-b1945/protein.faa > /dev/null
[2023-03-18 00:53:52,977] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:53:52,977] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf0e3f787-a3f6-4839-8b73-c7f10e68b87c/OceanDNA-b1945.fa]
[2023-03-18 00:53:52,988] [INFO] Query marker FASTA was written to OceanDNA-b1945/markers.fasta
[2023-03-18 00:53:52,988] [INFO] Task started: Blastn
[2023-03-18 00:53:52,988] [INFO] Running command: blastn -query OceanDNA-b1945/markers.fasta -db /var/lib/cwl/stg7e3573f9-6229-44ca-a769-2fec48caa680/dqc_reference/reference_markers.fasta -out OceanDNA-b1945/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:53:53,414] [INFO] Task succeeded: Blastn
[2023-03-18 00:53:53,415] [INFO] Selected 9 target genomes.
[2023-03-18 00:53:53,415] [INFO] Target genome list was writen to OceanDNA-b1945/target_genomes.txt
[2023-03-18 00:53:53,421] [INFO] Task started: fastANI
[2023-03-18 00:53:53,421] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0e3f787-a3f6-4839-8b73-c7f10e68b87c/OceanDNA-b1945.fa --refList OceanDNA-b1945/target_genomes.txt --output OceanDNA-b1945/fastani_result.tsv --threads 1
[2023-03-18 00:53:57,146] [INFO] Task succeeded: fastANI
[2023-03-18 00:53:57,146] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e3573f9-6229-44ca-a769-2fec48caa680/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:53:57,146] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e3573f9-6229-44ca-a769-2fec48caa680/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:53:57,146] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:53:57,146] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:53:57,146] [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
--------------------------------------------------------------------------------
[2023-03-18 00:53:57,147] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1945/tc_result.tsv
[2023-03-18 00:53:57,147] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:53:57,147] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:53:57,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e3573f9-6229-44ca-a769-2fec48caa680/dqc_reference/checkm_data
[2023-03-18 00:53:57,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:53:57,152] [INFO] Task started: CheckM
[2023-03-18 00:53:57,152] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1945/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1945/checkm_input OceanDNA-b1945/checkm_result
[2023-03-18 00:54:22,908] [INFO] Task succeeded: CheckM
[2023-03-18 00:54:22,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:54:22,910] [INFO] ===== Completeness check finished =====
[2023-03-18 00:54:22,910] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:54:22,910] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1945/markers.fasta)
[2023-03-18 00:54:22,911] [INFO] Task started: Blastn
[2023-03-18 00:54:22,911] [INFO] Running command: blastn -query OceanDNA-b1945/markers.fasta -db /var/lib/cwl/stg7e3573f9-6229-44ca-a769-2fec48caa680/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1945/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:54:23,328] [INFO] Task succeeded: Blastn
[2023-03-18 00:54:23,329] [INFO] Selected 8 target genomes.
[2023-03-18 00:54:23,329] [INFO] Target genome list was writen to OceanDNA-b1945/target_genomes_gtdb.txt
[2023-03-18 00:54:23,336] [INFO] Task started: fastANI
[2023-03-18 00:54:23,336] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0e3f787-a3f6-4839-8b73-c7f10e68b87c/OceanDNA-b1945.fa --refList OceanDNA-b1945/target_genomes_gtdb.txt --output OceanDNA-b1945/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:54:26,152] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:26,157] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:54:26,157] [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_002713485.1	s__UBA8592 sp002713485	96.9676	334	501	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	97.04	97.04	0.72	0.72	2	conclusive
GCA_002295705.1	s__UBA8592 sp002295705	80.4824	153	501	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	99.20	99.08	0.80	0.73	4	-
GCA_011523005.1	s__UBA8592 sp002380145	79.6353	167	501	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	97.37	95.83	0.82	0.81	6	-
GCA_002712415.1	s__UBA8592 sp002712415	79.3939	107	501	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	97.66	97.33	0.73	0.67	3	-
GCA_002712325.1	s__UBA8592 sp002712325	78.9346	103	501	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	99.19	99.19	0.77	0.77	2	-
GCA_002341185.1	s__UBA8592 sp002341185	78.6469	183	501	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	99.95	99.95	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-18 00:54:26,157] [INFO] GTDB search result was written to OceanDNA-b1945/result_gtdb.tsv
[2023-03-18 00:54:26,157] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:54:26,158] [INFO] DFAST_QC result json was written to OceanDNA-b1945/dqc_result.json
[2023-03-18 00:54:26,158] [INFO] DFAST_QC completed!
[2023-03-18 00:54:26,158] [INFO] Total running time: 0h0m43s