[2023-03-16 08:50:58,977] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:50:58,977] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:50:58,977] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5046882-a9c3-42a0-8173-29be28ca8927/dqc_reference
[2023-03-16 08:51:00,069] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:51:00,071] [INFO] Task started: Prodigal
[2023-03-16 08:51:00,071] [INFO] Running command: cat /var/lib/cwl/stgb20e4c36-95fe-4222-a0a1-d4dd79fedddb/OceanDNA-a848.fa | prodigal -d OceanDNA-a848/cds.fna -a OceanDNA-a848/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:51:05,789] [INFO] Task succeeded: Prodigal
[2023-03-16 08:51:05,790] [INFO] Task started: HMMsearch
[2023-03-16 08:51:05,790] [INFO] Running command: hmmsearch --tblout OceanDNA-a848/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5046882-a9c3-42a0-8173-29be28ca8927/dqc_reference/reference_markers.hmm OceanDNA-a848/protein.faa > /dev/null
[2023-03-16 08:51:05,926] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:51:05,927] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgb20e4c36-95fe-4222-a0a1-d4dd79fedddb/OceanDNA-a848.fa]
[2023-03-16 08:51:05,941] [INFO] Query marker FASTA was written to OceanDNA-a848/markers.fasta
[2023-03-16 08:51:05,942] [INFO] Task started: Blastn
[2023-03-16 08:51:05,942] [INFO] Running command: blastn -query OceanDNA-a848/markers.fasta -db /var/lib/cwl/stgd5046882-a9c3-42a0-8173-29be28ca8927/dqc_reference/reference_markers.fasta -out OceanDNA-a848/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:51:06,374] [INFO] Task succeeded: Blastn
[2023-03-16 08:51:06,376] [INFO] Selected 0 target genomes.
[2023-03-16 08:51:06,376] [INFO] Target genome list was writen to OceanDNA-a848/target_genomes.txt
[2023-03-16 08:51:06,376] [ERROR] File is empty. [OceanDNA-a848/target_genomes.txt]
[2023-03-16 08:51:06,376] [ERROR] Task failed. No target genome found.
[2023-03-16 08:51:06,376] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:51:06,377] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5046882-a9c3-42a0-8173-29be28ca8927/dqc_reference/checkm_data
[2023-03-16 08:51:06,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:51:06,475] [INFO] Task started: CheckM
[2023-03-16 08:51:06,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a848/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a848/checkm_input OceanDNA-a848/checkm_result
[2023-03-16 08:51:26,297] [INFO] Task succeeded: CheckM
[2023-03-16 08:51:26,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:51:26,304] [INFO] ===== Completeness check finished =====
[2023-03-16 08:51:26,304] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:51:26,305] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a848/markers.fasta)
[2023-03-16 08:51:26,306] [INFO] Task started: Blastn
[2023-03-16 08:51:26,306] [INFO] Running command: blastn -query OceanDNA-a848/markers.fasta -db /var/lib/cwl/stgd5046882-a9c3-42a0-8173-29be28ca8927/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a848/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:51:26,765] [INFO] Task succeeded: Blastn
[2023-03-16 08:51:26,768] [INFO] Selected 2 target genomes.
[2023-03-16 08:51:26,768] [INFO] Target genome list was writen to OceanDNA-a848/target_genomes_gtdb.txt
[2023-03-16 08:51:26,771] [INFO] Task started: fastANI
[2023-03-16 08:51:26,771] [INFO] Running command: fastANI --query /var/lib/cwl/stgb20e4c36-95fe-4222-a0a1-d4dd79fedddb/OceanDNA-a848.fa --refList OceanDNA-a848/target_genomes_gtdb.txt --output OceanDNA-a848/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:51:27,376] [INFO] Task succeeded: fastANI
[2023-03-16 08:51:27,379] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 08:51:27,379] [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_002713325.1	s__UBA213 sp002713325	99.6099	284	344	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__UBA213;g__UBA213	95.0	98.35	97.23	0.79	0.76	3	conclusive
--------------------------------------------------------------------------------
[2023-03-16 08:51:27,380] [INFO] GTDB search result was written to OceanDNA-a848/result_gtdb.tsv
[2023-03-16 08:51:27,381] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:51:27,382] [INFO] DFAST_QC result json was written to OceanDNA-a848/dqc_result.json
[2023-03-16 08:51:27,383] [INFO] DFAST_QC completed!
[2023-03-16 08:51:27,383] [INFO] Total running time: 0h0m28s