[2023-03-16 14:50:25,347] [INFO] DFAST_QC pipeline started.
[2023-03-16 14:50:25,347] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 14:50:25,348] [INFO] DQC Reference Directory: /var/lib/cwl/stg84c87cf7-7422-4074-9047-9ad996dec6e9/dqc_reference
[2023-03-16 14:50:26,691] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 14:50:26,692] [INFO] Task started: Prodigal
[2023-03-16 14:50:26,692] [INFO] Running command: cat /var/lib/cwl/stg3fd24df3-1418-441d-9130-80936f0e7b22/OceanDNA-b20096.fa | prodigal -d OceanDNA-b20096/cds.fna -a OceanDNA-b20096/protein.faa -g 11 -q > /dev/null
[2023-03-16 14:50:32,497] [INFO] Task succeeded: Prodigal
[2023-03-16 14:50:32,498] [INFO] Task started: HMMsearch
[2023-03-16 14:50:32,498] [INFO] Running command: hmmsearch --tblout OceanDNA-b20096/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84c87cf7-7422-4074-9047-9ad996dec6e9/dqc_reference/reference_markers.hmm OceanDNA-b20096/protein.faa > /dev/null
[2023-03-16 14:50:32,631] [INFO] Task succeeded: HMMsearch
[2023-03-16 14:50:32,632] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg3fd24df3-1418-441d-9130-80936f0e7b22/OceanDNA-b20096.fa]
[2023-03-16 14:50:32,643] [INFO] Query marker FASTA was written to OceanDNA-b20096/markers.fasta
[2023-03-16 14:50:32,643] [INFO] Task started: Blastn
[2023-03-16 14:50:32,643] [INFO] Running command: blastn -query OceanDNA-b20096/markers.fasta -db /var/lib/cwl/stg84c87cf7-7422-4074-9047-9ad996dec6e9/dqc_reference/reference_markers.fasta -out OceanDNA-b20096/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 14:50:33,131] [INFO] Task succeeded: Blastn
[2023-03-16 14:50:33,131] [INFO] Selected 0 target genomes.
[2023-03-16 14:50:33,132] [INFO] Target genome list was writen to OceanDNA-b20096/target_genomes.txt
[2023-03-16 14:50:33,132] [ERROR] File is empty. [OceanDNA-b20096/target_genomes.txt]
[2023-03-16 14:50:33,132] [ERROR] Task failed. No target genome found.
[2023-03-16 14:50:33,132] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 14:50:33,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84c87cf7-7422-4074-9047-9ad996dec6e9/dqc_reference/checkm_data
[2023-03-16 14:50:33,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 14:50:33,327] [INFO] Task started: CheckM
[2023-03-16 14:50:33,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20096/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20096/checkm_input OceanDNA-b20096/checkm_result
[2023-03-16 14:51:06,382] [INFO] Task succeeded: CheckM
[2023-03-16 14:51:06,382] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.18%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 14:51:06,384] [INFO] ===== Completeness check finished =====
[2023-03-16 14:51:06,384] [INFO] ===== Start GTDB Search =====
[2023-03-16 14:51:06,385] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20096/markers.fasta)
[2023-03-16 14:51:06,386] [INFO] Task started: Blastn
[2023-03-16 14:51:06,386] [INFO] Running command: blastn -query OceanDNA-b20096/markers.fasta -db /var/lib/cwl/stg84c87cf7-7422-4074-9047-9ad996dec6e9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20096/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 14:51:09,055] [INFO] Task succeeded: Blastn
[2023-03-16 14:51:09,056] [INFO] Selected 7 target genomes.
[2023-03-16 14:51:09,056] [INFO] Target genome list was writen to OceanDNA-b20096/target_genomes_gtdb.txt
[2023-03-16 14:51:09,543] [INFO] Task started: fastANI
[2023-03-16 14:51:09,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fd24df3-1418-441d-9130-80936f0e7b22/OceanDNA-b20096.fa --refList OceanDNA-b20096/target_genomes_gtdb.txt --output OceanDNA-b20096/fastani_result_gtdb.tsv --threads 1
[2023-03-16 14:51:13,048] [INFO] Task succeeded: fastANI
[2023-03-16 14:51:13,051] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 14:51:13,051] [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_002169695.1	s__TMED80 sp002169695	80.8806	121	355	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__TMED80	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713885.1	s__TMED80 sp002713885	78.5844	120	355	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__TMED80	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 14:51:13,052] [INFO] GTDB search result was written to OceanDNA-b20096/result_gtdb.tsv
[2023-03-16 14:51:13,052] [INFO] ===== GTDB Search completed =====
[2023-03-16 14:51:13,052] [INFO] DFAST_QC result json was written to OceanDNA-b20096/dqc_result.json
[2023-03-16 14:51:13,052] [INFO] DFAST_QC completed!
[2023-03-16 14:51:13,052] [INFO] Total running time: 0h0m48s