[2023-03-17 05:26:45,808] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:26:45,809] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:26:45,809] [INFO] DQC Reference Directory: /var/lib/cwl/stga479c55b-00d1-4c2c-b44b-6cd4e88723a0/dqc_reference
[2023-03-17 05:26:46,920] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:26:46,920] [INFO] Task started: Prodigal
[2023-03-17 05:26:46,920] [INFO] Running command: cat /var/lib/cwl/stg1ed56d6c-6d0d-40cd-b8b8-eec6b99e224b/OceanDNA-a1276.fa | prodigal -d OceanDNA-a1276/cds.fna -a OceanDNA-a1276/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:26:49,260] [INFO] Task succeeded: Prodigal
[2023-03-17 05:26:49,260] [INFO] Task started: HMMsearch
[2023-03-17 05:26:49,260] [INFO] Running command: hmmsearch --tblout OceanDNA-a1276/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga479c55b-00d1-4c2c-b44b-6cd4e88723a0/dqc_reference/reference_markers.hmm OceanDNA-a1276/protein.faa > /dev/null
[2023-03-17 05:26:49,367] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:26:49,368] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg1ed56d6c-6d0d-40cd-b8b8-eec6b99e224b/OceanDNA-a1276.fa]
[2023-03-17 05:26:49,373] [INFO] Query marker FASTA was written to OceanDNA-a1276/markers.fasta
[2023-03-17 05:26:49,374] [INFO] Task started: Blastn
[2023-03-17 05:26:49,374] [INFO] Running command: blastn -query OceanDNA-a1276/markers.fasta -db /var/lib/cwl/stga479c55b-00d1-4c2c-b44b-6cd4e88723a0/dqc_reference/reference_markers.fasta -out OceanDNA-a1276/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:26:49,879] [INFO] Task succeeded: Blastn
[2023-03-17 05:26:49,880] [INFO] Selected 0 target genomes.
[2023-03-17 05:26:49,880] [INFO] Target genome list was writen to OceanDNA-a1276/target_genomes.txt
[2023-03-17 05:26:49,880] [ERROR] File is empty. [OceanDNA-a1276/target_genomes.txt]
[2023-03-17 05:26:49,880] [ERROR] Task failed. No target genome found.
[2023-03-17 05:26:49,880] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:26:49,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga479c55b-00d1-4c2c-b44b-6cd4e88723a0/dqc_reference/checkm_data
[2023-03-17 05:26:49,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:26:49,982] [INFO] Task started: CheckM
[2023-03-17 05:26:49,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1276/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1276/checkm_input OceanDNA-a1276/checkm_result
[2023-03-17 05:27:05,828] [INFO] Task succeeded: CheckM
[2023-03-17 05:27:05,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.53%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:27:05,830] [INFO] ===== Completeness check finished =====
[2023-03-17 05:27:05,830] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:27:05,830] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1276/markers.fasta)
[2023-03-17 05:27:05,832] [INFO] Task started: Blastn
[2023-03-17 05:27:05,832] [INFO] Running command: blastn -query OceanDNA-a1276/markers.fasta -db /var/lib/cwl/stga479c55b-00d1-4c2c-b44b-6cd4e88723a0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1276/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:27:06,376] [INFO] Task succeeded: Blastn
[2023-03-17 05:27:06,376] [INFO] Selected 2 target genomes.
[2023-03-17 05:27:06,376] [INFO] Target genome list was writen to OceanDNA-a1276/target_genomes_gtdb.txt
[2023-03-17 05:27:06,453] [INFO] Task started: fastANI
[2023-03-17 05:27:06,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ed56d6c-6d0d-40cd-b8b8-eec6b99e224b/OceanDNA-a1276.fa --refList OceanDNA-a1276/target_genomes_gtdb.txt --output OceanDNA-a1276/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:27:06,837] [INFO] Task succeeded: fastANI
[2023-03-17 05:27:06,839] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:27:06,839] [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_018652045.1	s__JABICX01 sp018652045	99.858	140	148	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__UBA10117;f__JABICX01;g__JABICX01	95.0	99.84	99.82	0.90	0.89	3	conclusive
--------------------------------------------------------------------------------
[2023-03-17 05:27:06,839] [INFO] GTDB search result was written to OceanDNA-a1276/result_gtdb.tsv
[2023-03-17 05:27:06,839] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:27:06,840] [INFO] DFAST_QC result json was written to OceanDNA-a1276/dqc_result.json
[2023-03-17 05:27:06,840] [INFO] DFAST_QC completed!
[2023-03-17 05:27:06,840] [INFO] Total running time: 0h0m21s