[2023-03-18 06:30:24,811] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:30:24,812] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:30:24,813] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9eda72e-4303-435c-aeb4-967ec80f23bd/dqc_reference
[2023-03-18 06:30:25,923] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:30:25,923] [INFO] Task started: Prodigal
[2023-03-18 06:30:25,924] [INFO] Running command: cat /var/lib/cwl/stga3b01a1c-a9d0-4fe7-bf01-d08938582e0e/OceanDNA-a4089.fa | prodigal -d OceanDNA-a4089/cds.fna -a OceanDNA-a4089/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:30:31,531] [INFO] Task succeeded: Prodigal
[2023-03-18 06:30:31,532] [INFO] Task started: HMMsearch
[2023-03-18 06:30:31,532] [INFO] Running command: hmmsearch --tblout OceanDNA-a4089/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9eda72e-4303-435c-aeb4-967ec80f23bd/dqc_reference/reference_markers.hmm OceanDNA-a4089/protein.faa > /dev/null
[2023-03-18 06:30:31,686] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:30:31,686] [WARNING] Found 1/6 markers. [/var/lib/cwl/stga3b01a1c-a9d0-4fe7-bf01-d08938582e0e/OceanDNA-a4089.fa]
[2023-03-18 06:30:31,697] [INFO] Query marker FASTA was written to OceanDNA-a4089/markers.fasta
[2023-03-18 06:30:31,698] [INFO] Task started: Blastn
[2023-03-18 06:30:31,698] [INFO] Running command: blastn -query OceanDNA-a4089/markers.fasta -db /var/lib/cwl/stgb9eda72e-4303-435c-aeb4-967ec80f23bd/dqc_reference/reference_markers.fasta -out OceanDNA-a4089/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:30:32,121] [INFO] Task succeeded: Blastn
[2023-03-18 06:30:32,123] [INFO] Selected 0 target genomes.
[2023-03-18 06:30:32,123] [INFO] Target genome list was writen to OceanDNA-a4089/target_genomes.txt
[2023-03-18 06:30:32,123] [ERROR] File is empty. [OceanDNA-a4089/target_genomes.txt]
[2023-03-18 06:30:32,123] [ERROR] Task failed. No target genome found.
[2023-03-18 06:30:32,123] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:30:32,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9eda72e-4303-435c-aeb4-967ec80f23bd/dqc_reference/checkm_data
[2023-03-18 06:30:32,186] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:30:32,190] [INFO] Task started: CheckM
[2023-03-18 06:30:32,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4089/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4089/checkm_input OceanDNA-a4089/checkm_result
[2023-03-18 06:30:54,460] [INFO] Task succeeded: CheckM
[2023-03-18 06:30:54,461] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.45%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 06:30:54,537] [INFO] ===== Completeness check finished =====
[2023-03-18 06:30:54,537] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:30:54,537] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4089/markers.fasta)
[2023-03-18 06:30:54,537] [INFO] Task started: Blastn
[2023-03-18 06:30:54,537] [INFO] Running command: blastn -query OceanDNA-a4089/markers.fasta -db /var/lib/cwl/stgb9eda72e-4303-435c-aeb4-967ec80f23bd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4089/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:30:55,590] [INFO] Task succeeded: Blastn
[2023-03-18 06:30:55,595] [INFO] Selected 5 target genomes.
[2023-03-18 06:30:55,595] [INFO] Target genome list was writen to OceanDNA-a4089/target_genomes_gtdb.txt
[2023-03-18 06:30:55,708] [INFO] Task started: fastANI
[2023-03-18 06:30:55,709] [INFO] Running command: fastANI --query /var/lib/cwl/stga3b01a1c-a9d0-4fe7-bf01-d08938582e0e/OceanDNA-a4089.fa --refList OceanDNA-a4089/target_genomes_gtdb.txt --output OceanDNA-a4089/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:30:56,853] [INFO] Task succeeded: fastANI
[2023-03-18 06:30:56,856] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 06:30:56,856] [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_002716085.1	s__MGIIb-O3 sp002716085	82.0953	281	320	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_002725315.1	s__MGIIb-O3 sp002725315	76.3909	55	320	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.12	98.81	0.90	0.86	5	-
--------------------------------------------------------------------------------
[2023-03-18 06:30:56,858] [INFO] GTDB search result was written to OceanDNA-a4089/result_gtdb.tsv
[2023-03-18 06:30:56,858] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:30:56,860] [INFO] DFAST_QC result json was written to OceanDNA-a4089/dqc_result.json
[2023-03-18 06:30:56,860] [INFO] DFAST_QC completed!
[2023-03-18 06:30:56,860] [INFO] Total running time: 0h0m32s