[2023-03-15 11:20:30,902] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:20:30,902] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:20:30,902] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbaeb206-b20e-4308-b994-c5ebf6bb8743/dqc_reference
[2023-03-15 11:20:32,030] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:20:32,030] [INFO] Task started: Prodigal
[2023-03-15 11:20:32,030] [INFO] Running command: cat /var/lib/cwl/stg0508a3d5-52d1-48c1-89b8-4843be2a2e22/OceanDNA-a4202.fa | prodigal -d OceanDNA-a4202/cds.fna -a OceanDNA-a4202/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:20:36,520] [INFO] Task succeeded: Prodigal
[2023-03-15 11:20:36,520] [INFO] Task started: HMMsearch
[2023-03-15 11:20:36,520] [INFO] Running command: hmmsearch --tblout OceanDNA-a4202/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbaeb206-b20e-4308-b994-c5ebf6bb8743/dqc_reference/reference_markers.hmm OceanDNA-a4202/protein.faa > /dev/null
[2023-03-15 11:20:36,642] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:20:36,643] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg0508a3d5-52d1-48c1-89b8-4843be2a2e22/OceanDNA-a4202.fa]
[2023-03-15 11:20:36,659] [INFO] Query marker FASTA was written to OceanDNA-a4202/markers.fasta
[2023-03-15 11:20:36,659] [INFO] Task started: Blastn
[2023-03-15 11:20:36,660] [INFO] Running command: blastn -query OceanDNA-a4202/markers.fasta -db /var/lib/cwl/stgbbaeb206-b20e-4308-b994-c5ebf6bb8743/dqc_reference/reference_markers.fasta -out OceanDNA-a4202/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:20:37,071] [INFO] Task succeeded: Blastn
[2023-03-15 11:20:37,079] [INFO] Selected 0 target genomes.
[2023-03-15 11:20:37,079] [INFO] Target genome list was writen to OceanDNA-a4202/target_genomes.txt
[2023-03-15 11:20:37,079] [ERROR] File is empty. [OceanDNA-a4202/target_genomes.txt]
[2023-03-15 11:20:37,079] [ERROR] Task failed. No target genome found.
[2023-03-15 11:20:37,079] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:20:37,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbaeb206-b20e-4308-b994-c5ebf6bb8743/dqc_reference/checkm_data
[2023-03-15 11:20:37,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:20:37,085] [INFO] Task started: CheckM
[2023-03-15 11:20:37,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4202/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4202/checkm_input OceanDNA-a4202/checkm_result
[2023-03-15 11:20:55,456] [INFO] Task succeeded: CheckM
[2023-03-15 11:20:55,456] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:20:55,471] [INFO] ===== Completeness check finished =====
[2023-03-15 11:20:55,471] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:20:55,471] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4202/markers.fasta)
[2023-03-15 11:20:55,473] [INFO] Task started: Blastn
[2023-03-15 11:20:55,473] [INFO] Running command: blastn -query OceanDNA-a4202/markers.fasta -db /var/lib/cwl/stgbbaeb206-b20e-4308-b994-c5ebf6bb8743/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4202/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:20:56,019] [INFO] Task succeeded: Blastn
[2023-03-15 11:20:56,022] [INFO] Selected 2 target genomes.
[2023-03-15 11:20:56,022] [INFO] Target genome list was writen to OceanDNA-a4202/target_genomes_gtdb.txt
[2023-03-15 11:20:56,025] [INFO] Task started: fastANI
[2023-03-15 11:20:56,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg0508a3d5-52d1-48c1-89b8-4843be2a2e22/OceanDNA-a4202.fa --refList OceanDNA-a4202/target_genomes_gtdb.txt --output OceanDNA-a4202/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:20:56,627] [INFO] Task succeeded: fastANI
[2023-03-15 11:20:56,630] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:20:56,630] [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_014239955.1	s__MGIIb-O3 sp014239955	91.4516	231	255	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195615.1	s__MGIIb-O3 sp004195615	91.2836	234	255	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.94	99.91	0.95	0.93	3	-
--------------------------------------------------------------------------------
[2023-03-15 11:20:56,632] [INFO] GTDB search result was written to OceanDNA-a4202/result_gtdb.tsv
[2023-03-15 11:20:56,634] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:20:56,637] [INFO] DFAST_QC result json was written to OceanDNA-a4202/dqc_result.json
[2023-03-15 11:20:56,637] [INFO] DFAST_QC completed!
[2023-03-15 11:20:56,637] [INFO] Total running time: 0h0m26s