[2023-03-17 15:42:57,788] [INFO] DFAST_QC pipeline started.
[2023-03-17 15:42:57,788] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 15:42:57,789] [INFO] DQC Reference Directory: /var/lib/cwl/stg55fa91dc-83ca-43bb-b9bd-f4ecdd963cde/dqc_reference
[2023-03-17 15:42:58,890] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 15:42:58,891] [INFO] Task started: Prodigal
[2023-03-17 15:42:58,891] [INFO] Running command: cat /var/lib/cwl/stg034b0bbf-3bd3-4be8-ae39-9e7cc6d4daf1/OceanDNA-a3348.fa | prodigal -d OceanDNA-a3348/cds.fna -a OceanDNA-a3348/protein.faa -g 11 -q > /dev/null
[2023-03-17 15:43:05,266] [INFO] Task succeeded: Prodigal
[2023-03-17 15:43:05,266] [INFO] Task started: HMMsearch
[2023-03-17 15:43:05,266] [INFO] Running command: hmmsearch --tblout OceanDNA-a3348/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55fa91dc-83ca-43bb-b9bd-f4ecdd963cde/dqc_reference/reference_markers.hmm OceanDNA-a3348/protein.faa > /dev/null
[2023-03-17 15:43:05,615] [INFO] Task succeeded: HMMsearch
[2023-03-17 15:43:05,616] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg034b0bbf-3bd3-4be8-ae39-9e7cc6d4daf1/OceanDNA-a3348.fa]
[2023-03-17 15:43:05,624] [INFO] Query marker FASTA was written to OceanDNA-a3348/markers.fasta
[2023-03-17 15:43:05,627] [INFO] Task started: Blastn
[2023-03-17 15:43:05,627] [INFO] Running command: blastn -query OceanDNA-a3348/markers.fasta -db /var/lib/cwl/stg55fa91dc-83ca-43bb-b9bd-f4ecdd963cde/dqc_reference/reference_markers.fasta -out OceanDNA-a3348/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 15:43:06,893] [INFO] Task succeeded: Blastn
[2023-03-17 15:43:06,893] [INFO] Selected 3 target genomes.
[2023-03-17 15:43:06,893] [INFO] Target genome list was writen to OceanDNA-a3348/target_genomes.txt
[2023-03-17 15:43:06,896] [INFO] Task started: fastANI
[2023-03-17 15:43:06,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg034b0bbf-3bd3-4be8-ae39-9e7cc6d4daf1/OceanDNA-a3348.fa --refList OceanDNA-a3348/target_genomes.txt --output OceanDNA-a3348/fastani_result.tsv --threads 1
[2023-03-17 15:43:09,528] [INFO] Task succeeded: fastANI
[2023-03-17 15:43:09,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55fa91dc-83ca-43bb-b9bd-f4ecdd963cde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 15:43:09,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55fa91dc-83ca-43bb-b9bd-f4ecdd963cde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 15:43:09,528] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 15:43:09,528] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 15:43:09,528] [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
--------------------------------------------------------------------------------
[2023-03-17 15:43:09,529] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3348/tc_result.tsv
[2023-03-17 15:43:09,529] [INFO] ===== Taxonomy check completed =====
[2023-03-17 15:43:09,529] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 15:43:09,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55fa91dc-83ca-43bb-b9bd-f4ecdd963cde/dqc_reference/checkm_data
[2023-03-17 15:43:09,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 15:43:09,582] [INFO] Task started: CheckM
[2023-03-17 15:43:09,582] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3348/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3348/checkm_input OceanDNA-a3348/checkm_result
[2023-03-17 15:43:43,392] [INFO] Task succeeded: CheckM
[2023-03-17 15:43:43,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 15:43:43,393] [INFO] ===== Completeness check finished =====
[2023-03-17 15:43:43,394] [INFO] ===== Start GTDB Search =====
[2023-03-17 15:43:43,394] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3348/markers.fasta)
[2023-03-17 15:43:43,395] [INFO] Task started: Blastn
[2023-03-17 15:43:43,396] [INFO] Running command: blastn -query OceanDNA-a3348/markers.fasta -db /var/lib/cwl/stg55fa91dc-83ca-43bb-b9bd-f4ecdd963cde/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3348/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 15:43:44,149] [INFO] Task succeeded: Blastn
[2023-03-17 15:43:44,150] [INFO] Selected 8 target genomes.
[2023-03-17 15:43:44,150] [INFO] Target genome list was writen to OceanDNA-a3348/target_genomes_gtdb.txt
[2023-03-17 15:43:44,161] [INFO] Task started: fastANI
[2023-03-17 15:43:44,161] [INFO] Running command: fastANI --query /var/lib/cwl/stg034b0bbf-3bd3-4be8-ae39-9e7cc6d4daf1/OceanDNA-a3348.fa --refList OceanDNA-a3348/target_genomes_gtdb.txt --output OceanDNA-a3348/fastani_result_gtdb.tsv --threads 1
[2023-03-17 15:43:47,272] [INFO] Task succeeded: fastANI
[2023-03-17 15:43:47,276] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 15:43:47,277] [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_002717835.1	s__MGIIb-N1 sp002717835	99.638	299	352	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002504845.1	s__MGIIb-N1 sp002504845	85.4873	260	352	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	98.34	97.20	0.81	0.69	5	-
GCA_002712645.1	s__MGIIb-N1 sp002712645	83.1059	284	352	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002497295.1	s__MGIIb-N1 sp002497295	83.1051	285	352	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002170775.2	s__MGIIb-N1 sp002170775	82.5076	284	352	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002505455.1	s__MGIIb-N1 sp002505455	81.3382	271	352	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	98.69	95.53	0.89	0.80	5	-
--------------------------------------------------------------------------------
[2023-03-17 15:43:47,277] [INFO] GTDB search result was written to OceanDNA-a3348/result_gtdb.tsv
[2023-03-17 15:43:47,277] [INFO] ===== GTDB Search completed =====
[2023-03-17 15:43:47,278] [INFO] DFAST_QC result json was written to OceanDNA-a3348/dqc_result.json
[2023-03-17 15:43:47,278] [INFO] DFAST_QC completed!
[2023-03-17 15:43:47,278] [INFO] Total running time: 0h0m49s