[2023-03-15 09:48:16,561] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:48:16,561] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:48:16,561] [INFO] DQC Reference Directory: /var/lib/cwl/stg086a2728-9978-4557-b4f8-66d5886bc64c/dqc_reference
[2023-03-15 09:48:18,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:48:18,228] [INFO] Task started: Prodigal
[2023-03-15 09:48:18,229] [INFO] Running command: cat /var/lib/cwl/stg4958cdd7-79c9-47f1-9583-dcd82c806388/OceanDNA-a2822.fa | prodigal -d OceanDNA-a2822/cds.fna -a OceanDNA-a2822/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:48:24,065] [INFO] Task succeeded: Prodigal
[2023-03-15 09:48:24,066] [INFO] Task started: HMMsearch
[2023-03-15 09:48:24,066] [INFO] Running command: hmmsearch --tblout OceanDNA-a2822/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg086a2728-9978-4557-b4f8-66d5886bc64c/dqc_reference/reference_markers.hmm OceanDNA-a2822/protein.faa > /dev/null
[2023-03-15 09:48:24,213] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:48:24,214] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4958cdd7-79c9-47f1-9583-dcd82c806388/OceanDNA-a2822.fa]
[2023-03-15 09:48:24,226] [INFO] Query marker FASTA was written to OceanDNA-a2822/markers.fasta
[2023-03-15 09:48:24,226] [INFO] Task started: Blastn
[2023-03-15 09:48:24,227] [INFO] Running command: blastn -query OceanDNA-a2822/markers.fasta -db /var/lib/cwl/stg086a2728-9978-4557-b4f8-66d5886bc64c/dqc_reference/reference_markers.fasta -out OceanDNA-a2822/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:24,713] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:24,713] [INFO] Selected 3 target genomes.
[2023-03-15 09:48:24,714] [INFO] Target genome list was writen to OceanDNA-a2822/target_genomes.txt
[2023-03-15 09:48:24,716] [INFO] Task started: fastANI
[2023-03-15 09:48:24,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg4958cdd7-79c9-47f1-9583-dcd82c806388/OceanDNA-a2822.fa --refList OceanDNA-a2822/target_genomes.txt --output OceanDNA-a2822/fastani_result.tsv --threads 1
[2023-03-15 09:48:25,907] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:25,907] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg086a2728-9978-4557-b4f8-66d5886bc64c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:48:25,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg086a2728-9978-4557-b4f8-66d5886bc64c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:48:25,908] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:48:25,908] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 09:48:25,908] [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
--------------------------------------------------------------------------------
[2023-03-15 09:48:25,908] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2822/tc_result.tsv
[2023-03-15 09:48:25,908] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:48:25,908] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:48:25,908] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg086a2728-9978-4557-b4f8-66d5886bc64c/dqc_reference/checkm_data
[2023-03-15 09:48:26,107] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:48:26,110] [INFO] Task started: CheckM
[2023-03-15 09:48:26,110] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2822/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2822/checkm_input OceanDNA-a2822/checkm_result
[2023-03-15 09:48:50,622] [INFO] Task succeeded: CheckM
[2023-03-15 09:48:50,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.34%
Contamintation: 5.15%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-15 09:48:50,624] [INFO] ===== Completeness check finished =====
[2023-03-15 09:48:50,625] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:48:50,625] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2822/markers.fasta)
[2023-03-15 09:48:50,625] [INFO] Task started: Blastn
[2023-03-15 09:48:50,625] [INFO] Running command: blastn -query OceanDNA-a2822/markers.fasta -db /var/lib/cwl/stg086a2728-9978-4557-b4f8-66d5886bc64c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2822/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:48:51,423] [INFO] Task succeeded: Blastn
[2023-03-15 09:48:51,424] [INFO] Selected 6 target genomes.
[2023-03-15 09:48:51,424] [INFO] Target genome list was writen to OceanDNA-a2822/target_genomes_gtdb.txt
[2023-03-15 09:48:51,850] [INFO] Task started: fastANI
[2023-03-15 09:48:51,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg4958cdd7-79c9-47f1-9583-dcd82c806388/OceanDNA-a2822.fa --refList OceanDNA-a2822/target_genomes_gtdb.txt --output OceanDNA-a2822/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:48:53,770] [INFO] Task succeeded: fastANI
[2023-03-15 09:48:53,775] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:48:53,775] [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_018645535.1	s__MGIIa-L2 sp018645535	87.9554	197	272	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777125.1	s__MGIIa-L2 sp016777125	87.481	252	272	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.94	99.94	0.96	0.96	2	-
GCA_009887135.1	s__MGIIa-L2 sp009887135	87.3375	233	272	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	98.87	98.45	0.83	0.81	3	-
GCA_003602665.1	s__MGIIa-L2 sp003602665	85.8214	226	272	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666575.1	s__MGIIa-L2 sp018666575	82.8921	220	272	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.20	99.20	0.82	0.82	2	-
GCA_002171315.2	s__MGIIa-L2 sp002171315	82.2059	186	272	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:48:53,775] [INFO] GTDB search result was written to OceanDNA-a2822/result_gtdb.tsv
[2023-03-15 09:48:53,775] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:48:53,776] [INFO] DFAST_QC result json was written to OceanDNA-a2822/dqc_result.json
[2023-03-15 09:48:53,776] [INFO] DFAST_QC completed!
[2023-03-15 09:48:53,776] [INFO] Total running time: 0h0m37s