[2023-03-16 11:37:45,257] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:37:45,257] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:37:45,258] [INFO] DQC Reference Directory: /var/lib/cwl/stgafefb57c-5adc-4dd6-9459-436565f04d41/dqc_reference
[2023-03-16 11:37:49,398] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:37:49,398] [INFO] Task started: Prodigal
[2023-03-16 11:37:49,399] [INFO] Running command: cat /var/lib/cwl/stgaf93eba0-7421-47b2-a3fd-2fcd96c23d8a/OceanDNA-b24173.fa | prodigal -d OceanDNA-b24173/cds.fna -a OceanDNA-b24173/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:37:52,375] [INFO] Task succeeded: Prodigal
[2023-03-16 11:37:52,376] [INFO] Task started: HMMsearch
[2023-03-16 11:37:52,376] [INFO] Running command: hmmsearch --tblout OceanDNA-b24173/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafefb57c-5adc-4dd6-9459-436565f04d41/dqc_reference/reference_markers.hmm OceanDNA-b24173/protein.faa > /dev/null
[2023-03-16 11:37:52,582] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:37:52,582] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgaf93eba0-7421-47b2-a3fd-2fcd96c23d8a/OceanDNA-b24173.fa]
[2023-03-16 11:37:52,586] [INFO] Query marker FASTA was written to OceanDNA-b24173/markers.fasta
[2023-03-16 11:37:52,587] [INFO] Task started: Blastn
[2023-03-16 11:37:52,587] [INFO] Running command: blastn -query OceanDNA-b24173/markers.fasta -db /var/lib/cwl/stgafefb57c-5adc-4dd6-9459-436565f04d41/dqc_reference/reference_markers.fasta -out OceanDNA-b24173/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:37:53,393] [INFO] Task succeeded: Blastn
[2023-03-16 11:37:53,394] [INFO] Selected 0 target genomes.
[2023-03-16 11:37:53,394] [INFO] Target genome list was writen to OceanDNA-b24173/target_genomes.txt
[2023-03-16 11:37:53,394] [ERROR] File is empty. [OceanDNA-b24173/target_genomes.txt]
[2023-03-16 11:37:53,394] [ERROR] Task failed. No target genome found.
[2023-03-16 11:37:53,395] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:37:53,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafefb57c-5adc-4dd6-9459-436565f04d41/dqc_reference/checkm_data
[2023-03-16 11:37:53,598] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:37:53,600] [INFO] Task started: CheckM
[2023-03-16 11:37:53,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24173/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24173/checkm_input OceanDNA-b24173/checkm_result
[2023-03-16 11:38:19,704] [INFO] Task succeeded: CheckM
[2023-03-16 11:38:19,704] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:38:19,705] [INFO] ===== Completeness check finished =====
[2023-03-16 11:38:19,705] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:38:19,706] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24173/markers.fasta)
[2023-03-16 11:38:19,707] [INFO] Task started: Blastn
[2023-03-16 11:38:19,707] [INFO] Running command: blastn -query OceanDNA-b24173/markers.fasta -db /var/lib/cwl/stgafefb57c-5adc-4dd6-9459-436565f04d41/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24173/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:38:20,628] [INFO] Task succeeded: Blastn
[2023-03-16 11:38:20,629] [INFO] Selected 10 target genomes.
[2023-03-16 11:38:20,629] [INFO] Target genome list was writen to OceanDNA-b24173/target_genomes_gtdb.txt
[2023-03-16 11:38:21,163] [INFO] Task started: fastANI
[2023-03-16 11:38:21,163] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf93eba0-7421-47b2-a3fd-2fcd96c23d8a/OceanDNA-b24173.fa --refList OceanDNA-b24173/target_genomes_gtdb.txt --output OceanDNA-b24173/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:38:23,783] [INFO] Task succeeded: fastANI
[2023-03-16 11:38:23,783] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 11:38:23,784] [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
--------------------------------------------------------------------------------
[2023-03-16 11:38:23,784] [INFO] GTDB search result was written to OceanDNA-b24173/result_gtdb.tsv
[2023-03-16 11:38:23,784] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:38:23,784] [INFO] DFAST_QC result json was written to OceanDNA-b24173/dqc_result.json
[2023-03-16 11:38:23,784] [INFO] DFAST_QC completed!
[2023-03-16 11:38:23,784] [INFO] Total running time: 0h0m39s