[2023-03-15 11:54:50,854] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:54:50,854] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:54:50,854] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fee98dc-a376-4f7b-955a-25398db23b4c/dqc_reference
[2023-03-15 11:54:51,937] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:54:51,937] [INFO] Task started: Prodigal
[2023-03-15 11:54:51,938] [INFO] Running command: cat /var/lib/cwl/stga4cd7ea5-f2e3-48e1-9341-66761ef403c2/OceanDNA-a1024.fa | prodigal -d OceanDNA-a1024/cds.fna -a OceanDNA-a1024/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:54:57,622] [INFO] Task succeeded: Prodigal
[2023-03-15 11:54:57,622] [INFO] Task started: HMMsearch
[2023-03-15 11:54:57,622] [INFO] Running command: hmmsearch --tblout OceanDNA-a1024/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fee98dc-a376-4f7b-955a-25398db23b4c/dqc_reference/reference_markers.hmm OceanDNA-a1024/protein.faa > /dev/null
[2023-03-15 11:54:57,768] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:54:57,769] [WARNING] Found 2/6 markers. [/var/lib/cwl/stga4cd7ea5-f2e3-48e1-9341-66761ef403c2/OceanDNA-a1024.fa]
[2023-03-15 11:54:57,777] [INFO] Query marker FASTA was written to OceanDNA-a1024/markers.fasta
[2023-03-15 11:54:57,778] [INFO] Task started: Blastn
[2023-03-15 11:54:57,779] [INFO] Running command: blastn -query OceanDNA-a1024/markers.fasta -db /var/lib/cwl/stg8fee98dc-a376-4f7b-955a-25398db23b4c/dqc_reference/reference_markers.fasta -out OceanDNA-a1024/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:54:58,215] [INFO] Task succeeded: Blastn
[2023-03-15 11:54:58,217] [INFO] Selected 0 target genomes.
[2023-03-15 11:54:58,217] [INFO] Target genome list was writen to OceanDNA-a1024/target_genomes.txt
[2023-03-15 11:54:58,217] [ERROR] File is empty. [OceanDNA-a1024/target_genomes.txt]
[2023-03-15 11:54:58,217] [ERROR] Task failed. No target genome found.
[2023-03-15 11:54:58,217] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:54:58,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fee98dc-a376-4f7b-955a-25398db23b4c/dqc_reference/checkm_data
[2023-03-15 11:54:58,220] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:54:58,223] [INFO] Task started: CheckM
[2023-03-15 11:54:58,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1024/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1024/checkm_input OceanDNA-a1024/checkm_result
[2023-03-15 11:55:17,898] [INFO] Task succeeded: CheckM
[2023-03-15 11:55:17,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:55:17,925] [INFO] ===== Completeness check finished =====
[2023-03-15 11:55:17,925] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:55:17,925] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1024/markers.fasta)
[2023-03-15 11:55:17,926] [INFO] Task started: Blastn
[2023-03-15 11:55:17,926] [INFO] Running command: blastn -query OceanDNA-a1024/markers.fasta -db /var/lib/cwl/stg8fee98dc-a376-4f7b-955a-25398db23b4c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1024/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:55:18,385] [INFO] Task succeeded: Blastn
[2023-03-15 11:55:18,389] [INFO] Selected 2 target genomes.
[2023-03-15 11:55:18,389] [INFO] Target genome list was writen to OceanDNA-a1024/target_genomes_gtdb.txt
[2023-03-15 11:55:18,392] [INFO] Task started: fastANI
[2023-03-15 11:55:18,392] [INFO] Running command: fastANI --query /var/lib/cwl/stga4cd7ea5-f2e3-48e1-9341-66761ef403c2/OceanDNA-a1024.fa --refList OceanDNA-a1024/target_genomes_gtdb.txt --output OceanDNA-a1024/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:55:18,865] [INFO] Task succeeded: fastANI
[2023-03-15 11:55:18,867] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:55:18,867] [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_002688035.1	s__GCA-2688035 sp002688035	99.7937	216	310	d__Archaea;p__Iainarchaeota;c__Iainarchaeia;o__Iainarchaeales;f__GCA-2688035;g__GCA-2688035	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-15 11:55:18,906] [INFO] GTDB search result was written to OceanDNA-a1024/result_gtdb.tsv
[2023-03-15 11:55:18,909] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:55:18,911] [INFO] DFAST_QC result json was written to OceanDNA-a1024/dqc_result.json
[2023-03-15 11:55:18,911] [INFO] DFAST_QC completed!
[2023-03-15 11:55:18,911] [INFO] Total running time: 0h0m28s