[2023-03-19 02:59:38,371] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:59:38,372] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:59:38,372] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a76a82a-ef22-4727-8481-8745467a589c/dqc_reference
[2023-03-19 02:59:39,430] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:59:39,431] [INFO] Task started: Prodigal
[2023-03-19 02:59:39,431] [INFO] Running command: cat /var/lib/cwl/stg1cfd1678-28fe-4fb5-817c-6d3936dc86e3/OceanDNA-a3280.fa | prodigal -d OceanDNA-a3280/cds.fna -a OceanDNA-a3280/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:59:47,531] [INFO] Task succeeded: Prodigal
[2023-03-19 02:59:47,532] [INFO] Task started: HMMsearch
[2023-03-19 02:59:47,532] [INFO] Running command: hmmsearch --tblout OceanDNA-a3280/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a76a82a-ef22-4727-8481-8745467a589c/dqc_reference/reference_markers.hmm OceanDNA-a3280/protein.faa > /dev/null
[2023-03-19 02:59:47,694] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:59:47,695] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1cfd1678-28fe-4fb5-817c-6d3936dc86e3/OceanDNA-a3280.fa]
[2023-03-19 02:59:47,708] [INFO] Query marker FASTA was written to OceanDNA-a3280/markers.fasta
[2023-03-19 02:59:47,708] [INFO] Task started: Blastn
[2023-03-19 02:59:47,708] [INFO] Running command: blastn -query OceanDNA-a3280/markers.fasta -db /var/lib/cwl/stg1a76a82a-ef22-4727-8481-8745467a589c/dqc_reference/reference_markers.fasta -out OceanDNA-a3280/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:59:48,128] [INFO] Task succeeded: Blastn
[2023-03-19 02:59:48,130] [INFO] Selected 0 target genomes.
[2023-03-19 02:59:48,130] [INFO] Target genome list was writen to OceanDNA-a3280/target_genomes.txt
[2023-03-19 02:59:48,130] [ERROR] File is empty. [OceanDNA-a3280/target_genomes.txt]
[2023-03-19 02:59:48,131] [ERROR] Task failed. No target genome found.
[2023-03-19 02:59:48,131] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:59:48,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a76a82a-ef22-4727-8481-8745467a589c/dqc_reference/checkm_data
[2023-03-19 02:59:48,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:59:48,137] [INFO] Task started: CheckM
[2023-03-19 02:59:48,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3280/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3280/checkm_input OceanDNA-a3280/checkm_result
[2023-03-19 03:00:13,632] [INFO] Task succeeded: CheckM
[2023-03-19 03:00:13,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:00:13,636] [INFO] ===== Completeness check finished =====
[2023-03-19 03:00:13,636] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:00:13,636] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3280/markers.fasta)
[2023-03-19 03:00:13,637] [INFO] Task started: Blastn
[2023-03-19 03:00:13,637] [INFO] Running command: blastn -query OceanDNA-a3280/markers.fasta -db /var/lib/cwl/stg1a76a82a-ef22-4727-8481-8745467a589c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3280/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:00:14,060] [INFO] Task succeeded: Blastn
[2023-03-19 03:00:14,062] [INFO] Selected 5 target genomes.
[2023-03-19 03:00:14,062] [INFO] Target genome list was writen to OceanDNA-a3280/target_genomes_gtdb.txt
[2023-03-19 03:00:14,068] [INFO] Task started: fastANI
[2023-03-19 03:00:14,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cfd1678-28fe-4fb5-817c-6d3936dc86e3/OceanDNA-a3280.fa --refList OceanDNA-a3280/target_genomes_gtdb.txt --output OceanDNA-a3280/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:00:15,419] [INFO] Task succeeded: fastANI
[2023-03-19 03:00:15,421] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:00:15,421] [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_002499585.1	s__MGIIb-N1 sp002499585	99.7943	416	452	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	99.69	99.19	0.92	0.84	12	conclusive
GCA_002495675.1	s__MGIIb-N1 sp002495675	78.1165	70	452	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:00:15,422] [INFO] GTDB search result was written to OceanDNA-a3280/result_gtdb.tsv
[2023-03-19 03:00:15,423] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:00:15,424] [INFO] DFAST_QC result json was written to OceanDNA-a3280/dqc_result.json
[2023-03-19 03:00:15,424] [INFO] DFAST_QC completed!
[2023-03-19 03:00:15,424] [INFO] Total running time: 0h0m37s