[2023-03-15 12:44:24,470] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:44:24,470] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:44:24,470] [INFO] DQC Reference Directory: /var/lib/cwl/stg86b34182-40bb-45e3-b6bb-6bcbb55b7ec0/dqc_reference
[2023-03-15 12:44:26,207] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:44:26,207] [INFO] Task started: Prodigal
[2023-03-15 12:44:26,207] [INFO] Running command: cat /var/lib/cwl/stgaf66275e-e0ef-4b21-8959-83f655da4619/OceanDNA-a1280.fa | prodigal -d OceanDNA-a1280/cds.fna -a OceanDNA-a1280/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:44:27,973] [INFO] Task succeeded: Prodigal
[2023-03-15 12:44:27,973] [INFO] Task started: HMMsearch
[2023-03-15 12:44:27,973] [INFO] Running command: hmmsearch --tblout OceanDNA-a1280/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86b34182-40bb-45e3-b6bb-6bcbb55b7ec0/dqc_reference/reference_markers.hmm OceanDNA-a1280/protein.faa > /dev/null
[2023-03-15 12:44:28,124] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:44:28,125] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgaf66275e-e0ef-4b21-8959-83f655da4619/OceanDNA-a1280.fa]
[2023-03-15 12:44:28,129] [INFO] Query marker FASTA was written to OceanDNA-a1280/markers.fasta
[2023-03-15 12:44:28,131] [INFO] Task started: Blastn
[2023-03-15 12:44:28,131] [INFO] Running command: blastn -query OceanDNA-a1280/markers.fasta -db /var/lib/cwl/stg86b34182-40bb-45e3-b6bb-6bcbb55b7ec0/dqc_reference/reference_markers.fasta -out OceanDNA-a1280/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:30,620] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:30,621] [INFO] Selected 0 target genomes.
[2023-03-15 12:44:30,621] [INFO] Target genome list was writen to OceanDNA-a1280/target_genomes.txt
[2023-03-15 12:44:30,621] [ERROR] File is empty. [OceanDNA-a1280/target_genomes.txt]
[2023-03-15 12:44:30,621] [ERROR] Task failed. No target genome found.
[2023-03-15 12:44:30,621] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:44:30,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86b34182-40bb-45e3-b6bb-6bcbb55b7ec0/dqc_reference/checkm_data
[2023-03-15 12:44:30,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:44:30,681] [INFO] Task started: CheckM
[2023-03-15 12:44:30,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1280/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1280/checkm_input OceanDNA-a1280/checkm_result
[2023-03-15 12:44:45,274] [INFO] Task succeeded: CheckM
[2023-03-15 12:44:45,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.41%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:44:45,276] [INFO] ===== Completeness check finished =====
[2023-03-15 12:44:45,276] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:44:45,276] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1280/markers.fasta)
[2023-03-15 12:44:45,278] [INFO] Task started: Blastn
[2023-03-15 12:44:45,278] [INFO] Running command: blastn -query OceanDNA-a1280/markers.fasta -db /var/lib/cwl/stg86b34182-40bb-45e3-b6bb-6bcbb55b7ec0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1280/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:45,882] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:45,882] [INFO] Selected 2 target genomes.
[2023-03-15 12:44:45,883] [INFO] Target genome list was writen to OceanDNA-a1280/target_genomes_gtdb.txt
[2023-03-15 12:44:45,926] [INFO] Task started: fastANI
[2023-03-15 12:44:45,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf66275e-e0ef-4b21-8959-83f655da4619/OceanDNA-a1280.fa --refList OceanDNA-a1280/target_genomes_gtdb.txt --output OceanDNA-a1280/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:44:46,178] [INFO] Task succeeded: fastANI
[2023-03-15 12:44:46,181] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:44:46,181] [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_014240455.1	s__JAAZWY01 sp014240455	90.2015	85	99	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__UBA10117;f__ARS21;g__JAAZWY01	95.0	98.17	98.17	0.91	0.91	2	-
GCA_018698915.1	s__JAAZWY01 sp018698915	82.606	81	99	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__UBA10117;f__ARS21;g__JAAZWY01	95.0	99.92	99.92	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-15 12:44:46,181] [INFO] GTDB search result was written to OceanDNA-a1280/result_gtdb.tsv
[2023-03-15 12:44:46,181] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:44:46,182] [INFO] DFAST_QC result json was written to OceanDNA-a1280/dqc_result.json
[2023-03-15 12:44:46,182] [INFO] DFAST_QC completed!
[2023-03-15 12:44:46,182] [INFO] Total running time: 0h0m22s