[2023-03-15 08:59:47,029] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:59:47,029] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:59:47,029] [INFO] DQC Reference Directory: /var/lib/cwl/stg02c58e52-0941-4caf-bf3b-0462afd6f668/dqc_reference
[2023-03-15 08:59:48,103] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:59:48,104] [INFO] Task started: Prodigal
[2023-03-15 08:59:48,104] [INFO] Running command: cat /var/lib/cwl/stg79ec218d-df14-44c1-9540-f50303b82730/OceanDNA-a3770.fa | prodigal -d OceanDNA-a3770/cds.fna -a OceanDNA-a3770/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:59:53,015] [INFO] Task succeeded: Prodigal
[2023-03-15 08:59:53,016] [INFO] Task started: HMMsearch
[2023-03-15 08:59:53,016] [INFO] Running command: hmmsearch --tblout OceanDNA-a3770/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02c58e52-0941-4caf-bf3b-0462afd6f668/dqc_reference/reference_markers.hmm OceanDNA-a3770/protein.faa > /dev/null
[2023-03-15 08:59:53,121] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:59:53,121] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg79ec218d-df14-44c1-9540-f50303b82730/OceanDNA-a3770.fa]
[2023-03-15 08:59:53,128] [INFO] Query marker FASTA was written to OceanDNA-a3770/markers.fasta
[2023-03-15 08:59:53,128] [INFO] Task started: Blastn
[2023-03-15 08:59:53,128] [INFO] Running command: blastn -query OceanDNA-a3770/markers.fasta -db /var/lib/cwl/stg02c58e52-0941-4caf-bf3b-0462afd6f668/dqc_reference/reference_markers.fasta -out OceanDNA-a3770/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:59:53,533] [INFO] Task succeeded: Blastn
[2023-03-15 08:59:53,533] [INFO] Selected 0 target genomes.
[2023-03-15 08:59:53,534] [INFO] Target genome list was writen to OceanDNA-a3770/target_genomes.txt
[2023-03-15 08:59:53,534] [ERROR] File is empty. [OceanDNA-a3770/target_genomes.txt]
[2023-03-15 08:59:53,534] [ERROR] Task failed. No target genome found.
[2023-03-15 08:59:53,534] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:59:53,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02c58e52-0941-4caf-bf3b-0462afd6f668/dqc_reference/checkm_data
[2023-03-15 08:59:53,546] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:59:53,548] [INFO] Task started: CheckM
[2023-03-15 08:59:53,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3770/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3770/checkm_input OceanDNA-a3770/checkm_result
[2023-03-15 09:00:15,601] [INFO] Task succeeded: CheckM
[2023-03-15 09:00:15,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:00:15,603] [INFO] ===== Completeness check finished =====
[2023-03-15 09:00:15,603] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:00:15,603] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3770/markers.fasta)
[2023-03-15 09:00:15,605] [INFO] Task started: Blastn
[2023-03-15 09:00:15,605] [INFO] Running command: blastn -query OceanDNA-a3770/markers.fasta -db /var/lib/cwl/stg02c58e52-0941-4caf-bf3b-0462afd6f668/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3770/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:00:16,923] [INFO] Task succeeded: Blastn
[2023-03-15 09:00:16,924] [INFO] Selected 2 target genomes.
[2023-03-15 09:00:16,924] [INFO] Target genome list was writen to OceanDNA-a3770/target_genomes_gtdb.txt
[2023-03-15 09:00:16,930] [INFO] Task started: fastANI
[2023-03-15 09:00:16,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg79ec218d-df14-44c1-9540-f50303b82730/OceanDNA-a3770.fa --refList OceanDNA-a3770/target_genomes_gtdb.txt --output OceanDNA-a3770/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:00:17,414] [INFO] Task succeeded: fastANI
[2023-03-15 09:00:17,417] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:00:17,417] [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_002504905.1	s__MGIIb-O2 sp002504905	79.372	204	298	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	99.85	99.68	0.95	0.91	6	-
GCA_902514485.1	s__MGIIb-O2 sp902514485	77.6183	72	298	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	98.21	98.21	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2023-03-15 09:00:17,417] [INFO] GTDB search result was written to OceanDNA-a3770/result_gtdb.tsv
[2023-03-15 09:00:17,417] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:00:17,418] [INFO] DFAST_QC result json was written to OceanDNA-a3770/dqc_result.json
[2023-03-15 09:00:17,418] [INFO] DFAST_QC completed!
[2023-03-15 09:00:17,418] [INFO] Total running time: 0h0m30s