[2023-03-19 05:19:33,811] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,811] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,812] [INFO] DQC Reference Directory: /var/lib/cwl/stg04c693ea-50c6-4820-a9dd-52c1d42a36c3/dqc_reference
[2023-03-19 05:19:35,410] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:35,410] [INFO] Task started: Prodigal
[2023-03-19 05:19:35,410] [INFO] Running command: cat /var/lib/cwl/stg94d941a2-6b0d-46b8-9420-046114173afe/OceanDNA-a1017.fa | prodigal -d OceanDNA-a1017/cds.fna -a OceanDNA-a1017/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:19:37,553] [INFO] Task succeeded: Prodigal
[2023-03-19 05:19:37,553] [INFO] Task started: HMMsearch
[2023-03-19 05:19:37,554] [INFO] Running command: hmmsearch --tblout OceanDNA-a1017/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04c693ea-50c6-4820-a9dd-52c1d42a36c3/dqc_reference/reference_markers.hmm OceanDNA-a1017/protein.faa > /dev/null
[2023-03-19 05:19:37,794] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:19:37,794] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg94d941a2-6b0d-46b8-9420-046114173afe/OceanDNA-a1017.fa]
[2023-03-19 05:19:37,801] [INFO] Query marker FASTA was written to OceanDNA-a1017/markers.fasta
[2023-03-19 05:19:37,801] [INFO] Task started: Blastn
[2023-03-19 05:19:37,801] [INFO] Running command: blastn -query OceanDNA-a1017/markers.fasta -db /var/lib/cwl/stg04c693ea-50c6-4820-a9dd-52c1d42a36c3/dqc_reference/reference_markers.fasta -out OceanDNA-a1017/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:38,359] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:38,360] [INFO] Selected 0 target genomes.
[2023-03-19 05:19:38,360] [INFO] Target genome list was writen to OceanDNA-a1017/target_genomes.txt
[2023-03-19 05:19:38,360] [ERROR] File is empty. [OceanDNA-a1017/target_genomes.txt]
[2023-03-19 05:19:38,360] [ERROR] Task failed. No target genome found.
[2023-03-19 05:19:38,361] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:19:38,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04c693ea-50c6-4820-a9dd-52c1d42a36c3/dqc_reference/checkm_data
[2023-03-19 05:19:38,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:19:38,413] [INFO] Task started: CheckM
[2023-03-19 05:19:38,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1017/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1017/checkm_input OceanDNA-a1017/checkm_result
[2023-03-19 05:19:55,171] [INFO] Task succeeded: CheckM
[2023-03-19 05:19:55,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:19:55,173] [INFO] ===== Completeness check finished =====
[2023-03-19 05:19:55,173] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:19:55,173] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1017/markers.fasta)
[2023-03-19 05:19:55,175] [INFO] Task started: Blastn
[2023-03-19 05:19:55,175] [INFO] Running command: blastn -query OceanDNA-a1017/markers.fasta -db /var/lib/cwl/stg04c693ea-50c6-4820-a9dd-52c1d42a36c3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1017/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:55,896] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:55,897] [INFO] Selected 3 target genomes.
[2023-03-19 05:19:55,897] [INFO] Target genome list was writen to OceanDNA-a1017/target_genomes_gtdb.txt
[2023-03-19 05:19:55,949] [INFO] Task started: fastANI
[2023-03-19 05:19:55,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg94d941a2-6b0d-46b8-9420-046114173afe/OceanDNA-a1017.fa --refList OceanDNA-a1017/target_genomes_gtdb.txt --output OceanDNA-a1017/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:19:56,395] [INFO] Task succeeded: fastANI
[2023-03-19 05:19:56,397] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:19:56,397] [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_018691995.1	s__JABIDZ01 sp018691995	99.5923	77	96	d__Archaea;p__Iainarchaeota;c__Iainarchaeia;o__Iainarchaeales;f__JAAZKV01;g__JABIDZ01	95.0	99.60	99.60	0.90	0.90	2	conclusive
--------------------------------------------------------------------------------
[2023-03-19 05:19:56,397] [INFO] GTDB search result was written to OceanDNA-a1017/result_gtdb.tsv
[2023-03-19 05:19:56,397] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:19:56,398] [INFO] DFAST_QC result json was written to OceanDNA-a1017/dqc_result.json
[2023-03-19 05:19:56,398] [INFO] DFAST_QC completed!
[2023-03-19 05:19:56,398] [INFO] Total running time: 0h0m23s