[2023-03-16 06:54:59,030] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:54:59,030] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:54:59,030] [INFO] DQC Reference Directory: /var/lib/cwl/stg05a596e5-0158-44d6-b1e1-a28424c6bf01/dqc_reference
[2023-03-16 06:55:00,111] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:55:00,111] [INFO] Task started: Prodigal
[2023-03-16 06:55:00,111] [INFO] Running command: cat /var/lib/cwl/stgfae71c3c-27ab-4d7b-b4ef-044b2eef23f5/OceanDNA-a3160.fa | prodigal -d OceanDNA-a3160/cds.fna -a OceanDNA-a3160/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:55:09,770] [INFO] Task succeeded: Prodigal
[2023-03-16 06:55:09,771] [INFO] Task started: HMMsearch
[2023-03-16 06:55:09,771] [INFO] Running command: hmmsearch --tblout OceanDNA-a3160/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05a596e5-0158-44d6-b1e1-a28424c6bf01/dqc_reference/reference_markers.hmm OceanDNA-a3160/protein.faa > /dev/null
[2023-03-16 06:55:09,931] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:55:09,932] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgfae71c3c-27ab-4d7b-b4ef-044b2eef23f5/OceanDNA-a3160.fa]
[2023-03-16 06:55:09,946] [INFO] Query marker FASTA was written to OceanDNA-a3160/markers.fasta
[2023-03-16 06:55:09,948] [INFO] Task started: Blastn
[2023-03-16 06:55:09,949] [INFO] Running command: blastn -query OceanDNA-a3160/markers.fasta -db /var/lib/cwl/stg05a596e5-0158-44d6-b1e1-a28424c6bf01/dqc_reference/reference_markers.fasta -out OceanDNA-a3160/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:55:10,374] [INFO] Task succeeded: Blastn
[2023-03-16 06:55:10,376] [INFO] Selected 0 target genomes.
[2023-03-16 06:55:10,376] [INFO] Target genome list was writen to OceanDNA-a3160/target_genomes.txt
[2023-03-16 06:55:10,376] [ERROR] File is empty. [OceanDNA-a3160/target_genomes.txt]
[2023-03-16 06:55:10,376] [ERROR] Task failed. No target genome found.
[2023-03-16 06:55:10,376] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:55:10,376] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05a596e5-0158-44d6-b1e1-a28424c6bf01/dqc_reference/checkm_data
[2023-03-16 06:55:10,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:55:10,437] [INFO] Task started: CheckM
[2023-03-16 06:55:10,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3160/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3160/checkm_input OceanDNA-a3160/checkm_result
[2023-03-16 06:55:39,847] [INFO] Task succeeded: CheckM
[2023-03-16 06:55:39,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:55:39,886] [INFO] ===== Completeness check finished =====
[2023-03-16 06:55:39,886] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:55:39,887] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3160/markers.fasta)
[2023-03-16 06:55:39,888] [INFO] Task started: Blastn
[2023-03-16 06:55:39,888] [INFO] Running command: blastn -query OceanDNA-a3160/markers.fasta -db /var/lib/cwl/stg05a596e5-0158-44d6-b1e1-a28424c6bf01/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3160/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:55:40,317] [INFO] Task succeeded: Blastn
[2023-03-16 06:55:40,321] [INFO] Selected 10 target genomes.
[2023-03-16 06:55:40,322] [INFO] Target genome list was writen to OceanDNA-a3160/target_genomes_gtdb.txt
[2023-03-16 06:55:40,332] [INFO] Task started: fastANI
[2023-03-16 06:55:40,332] [INFO] Running command: fastANI --query /var/lib/cwl/stgfae71c3c-27ab-4d7b-b4ef-044b2eef23f5/OceanDNA-a3160.fa --refList OceanDNA-a3160/target_genomes_gtdb.txt --output OceanDNA-a3160/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:55:43,073] [INFO] Task succeeded: fastANI
[2023-03-16 06:55:43,076] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:55:43,076] [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_002505935.1	s__UBA226 sp002505935	99.0189	365	524	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__UBA226	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002719475.1	s__UBA226 sp002719475	93.5235	444	524	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__UBA226	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:55:43,077] [INFO] GTDB search result was written to OceanDNA-a3160/result_gtdb.tsv
[2023-03-16 06:55:43,079] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:55:43,081] [INFO] DFAST_QC result json was written to OceanDNA-a3160/dqc_result.json
[2023-03-16 06:55:43,081] [INFO] DFAST_QC completed!
[2023-03-16 06:55:43,081] [INFO] Total running time: 0h0m44s