[2023-03-14 12:25:41,518] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:25:41,518] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:25:41,519] [INFO] DQC Reference Directory: /var/lib/cwl/stged0ca495-765f-490c-9617-3e0f54ae16e3/dqc_reference
[2023-03-14 12:25:42,664] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:25:42,664] [INFO] Task started: Prodigal
[2023-03-14 12:25:42,665] [INFO] Running command: cat /var/lib/cwl/stg05791291-dba8-4b0e-a8d7-e3e2055d2d53/OceanDNA-a1189.fa | prodigal -d OceanDNA-a1189/cds.fna -a OceanDNA-a1189/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:25:45,403] [INFO] Task succeeded: Prodigal
[2023-03-14 12:25:45,404] [INFO] Task started: HMMsearch
[2023-03-14 12:25:45,404] [INFO] Running command: hmmsearch --tblout OceanDNA-a1189/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged0ca495-765f-490c-9617-3e0f54ae16e3/dqc_reference/reference_markers.hmm OceanDNA-a1189/protein.faa > /dev/null
[2023-03-14 12:25:45,527] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:25:45,527] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg05791291-dba8-4b0e-a8d7-e3e2055d2d53/OceanDNA-a1189.fa]
[2023-03-14 12:25:45,532] [INFO] Query marker FASTA was written to OceanDNA-a1189/markers.fasta
[2023-03-14 12:25:45,534] [INFO] Task started: Blastn
[2023-03-14 12:25:45,534] [INFO] Running command: blastn -query OceanDNA-a1189/markers.fasta -db /var/lib/cwl/stged0ca495-765f-490c-9617-3e0f54ae16e3/dqc_reference/reference_markers.fasta -out OceanDNA-a1189/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:25:45,981] [INFO] Task succeeded: Blastn
[2023-03-14 12:25:45,982] [INFO] Selected 0 target genomes.
[2023-03-14 12:25:45,982] [INFO] Target genome list was writen to OceanDNA-a1189/target_genomes.txt
[2023-03-14 12:25:45,982] [ERROR] File is empty. [OceanDNA-a1189/target_genomes.txt]
[2023-03-14 12:25:45,982] [ERROR] Task failed. No target genome found.
[2023-03-14 12:25:45,983] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:25:45,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged0ca495-765f-490c-9617-3e0f54ae16e3/dqc_reference/checkm_data
[2023-03-14 12:25:45,993] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:25:45,995] [INFO] Task started: CheckM
[2023-03-14 12:25:45,995] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1189/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1189/checkm_input OceanDNA-a1189/checkm_result
[2023-03-14 12:26:00,338] [INFO] Task succeeded: CheckM
[2023-03-14 12:26:00,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:26:00,340] [INFO] ===== Completeness check finished =====
[2023-03-14 12:26:00,340] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:26:00,340] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1189/markers.fasta)
[2023-03-14 12:26:00,342] [INFO] Task started: Blastn
[2023-03-14 12:26:00,342] [INFO] Running command: blastn -query OceanDNA-a1189/markers.fasta -db /var/lib/cwl/stged0ca495-765f-490c-9617-3e0f54ae16e3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1189/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:26:00,888] [INFO] Task succeeded: Blastn
[2023-03-14 12:26:00,889] [INFO] Selected 5 target genomes.
[2023-03-14 12:26:00,889] [INFO] Target genome list was writen to OceanDNA-a1189/target_genomes_gtdb.txt
[2023-03-14 12:26:00,897] [INFO] Task started: fastANI
[2023-03-14 12:26:00,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg05791291-dba8-4b0e-a8d7-e3e2055d2d53/OceanDNA-a1189.fa --refList OceanDNA-a1189/target_genomes_gtdb.txt --output OceanDNA-a1189/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:26:01,977] [INFO] Task succeeded: fastANI
[2023-03-14 12:26:01,979] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:26:01,979] [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_002688355.1	s__GCA-2688355 sp002688355	99.9596	182	187	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__SCGC-AAA011-G17;f__GW2011-AR20;g__GCA-2688355	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-14 12:26:01,980] [INFO] GTDB search result was written to OceanDNA-a1189/result_gtdb.tsv
[2023-03-14 12:26:01,980] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:26:01,980] [INFO] DFAST_QC result json was written to OceanDNA-a1189/dqc_result.json
[2023-03-14 12:26:01,980] [INFO] DFAST_QC completed!
[2023-03-14 12:26:01,980] [INFO] Total running time: 0h0m20s