[2023-03-18 01:16:48,820] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:16:48,820] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:16:48,820] [INFO] DQC Reference Directory: /var/lib/cwl/stg97aa0294-b65f-43bb-a514-85c0264085f7/dqc_reference
[2023-03-18 01:16:49,918] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:16:49,919] [INFO] Task started: Prodigal
[2023-03-18 01:16:49,920] [INFO] Running command: cat /var/lib/cwl/stgbab21279-2c10-4e27-bfe7-4175bf9a8f25/OceanDNA-a4086.fa | prodigal -d OceanDNA-a4086/cds.fna -a OceanDNA-a4086/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:16:56,562] [INFO] Task succeeded: Prodigal
[2023-03-18 01:16:56,562] [INFO] Task started: HMMsearch
[2023-03-18 01:16:56,562] [INFO] Running command: hmmsearch --tblout OceanDNA-a4086/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97aa0294-b65f-43bb-a514-85c0264085f7/dqc_reference/reference_markers.hmm OceanDNA-a4086/protein.faa > /dev/null
[2023-03-18 01:16:56,728] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:16:56,729] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgbab21279-2c10-4e27-bfe7-4175bf9a8f25/OceanDNA-a4086.fa]
[2023-03-18 01:16:56,738] [INFO] Query marker FASTA was written to OceanDNA-a4086/markers.fasta
[2023-03-18 01:16:56,739] [INFO] Task started: Blastn
[2023-03-18 01:16:56,739] [INFO] Running command: blastn -query OceanDNA-a4086/markers.fasta -db /var/lib/cwl/stg97aa0294-b65f-43bb-a514-85c0264085f7/dqc_reference/reference_markers.fasta -out OceanDNA-a4086/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:16:57,199] [INFO] Task succeeded: Blastn
[2023-03-18 01:16:57,200] [INFO] Selected 0 target genomes.
[2023-03-18 01:16:57,200] [INFO] Target genome list was writen to OceanDNA-a4086/target_genomes.txt
[2023-03-18 01:16:57,200] [ERROR] File is empty. [OceanDNA-a4086/target_genomes.txt]
[2023-03-18 01:16:57,200] [ERROR] Task failed. No target genome found.
[2023-03-18 01:16:57,200] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:16:57,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97aa0294-b65f-43bb-a514-85c0264085f7/dqc_reference/checkm_data
[2023-03-18 01:16:57,287] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:16:57,289] [INFO] Task started: CheckM
[2023-03-18 01:16:57,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4086/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4086/checkm_input OceanDNA-a4086/checkm_result
[2023-03-18 01:17:19,583] [INFO] Task succeeded: CheckM
[2023-03-18 01:17:19,583] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:17:19,613] [INFO] ===== Completeness check finished =====
[2023-03-18 01:17:19,613] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:17:19,613] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4086/markers.fasta)
[2023-03-18 01:17:19,614] [INFO] Task started: Blastn
[2023-03-18 01:17:19,614] [INFO] Running command: blastn -query OceanDNA-a4086/markers.fasta -db /var/lib/cwl/stg97aa0294-b65f-43bb-a514-85c0264085f7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4086/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:17:20,188] [INFO] Task succeeded: Blastn
[2023-03-18 01:17:20,190] [INFO] Selected 8 target genomes.
[2023-03-18 01:17:20,190] [INFO] Target genome list was writen to OceanDNA-a4086/target_genomes_gtdb.txt
[2023-03-18 01:17:20,194] [INFO] Task started: fastANI
[2023-03-18 01:17:20,194] [INFO] Running command: fastANI --query /var/lib/cwl/stgbab21279-2c10-4e27-bfe7-4175bf9a8f25/OceanDNA-a4086.fa --refList OceanDNA-a4086/target_genomes_gtdb.txt --output OceanDNA-a4086/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:17:22,579] [INFO] Task succeeded: fastANI
[2023-03-18 01:17:22,582] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:17:22,583] [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_003602515.1	s__MGIIb-O3 sp003602515	77.0314	67	382	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.42	99.42	0.80	0.80	2	-
GCA_002716085.1	s__MGIIb-O3 sp002716085	77.0239	78	382	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	97.47	97.47	0.87	0.87	2	-
GCA_014239955.1	s__MGIIb-O3 sp014239955	76.9817	54	382	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:17:22,583] [INFO] GTDB search result was written to OceanDNA-a4086/result_gtdb.tsv
[2023-03-18 01:17:22,584] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:17:22,584] [INFO] DFAST_QC result json was written to OceanDNA-a4086/dqc_result.json
[2023-03-18 01:17:22,584] [INFO] DFAST_QC completed!
[2023-03-18 01:17:22,584] [INFO] Total running time: 0h0m34s