[2023-06-27 06:48:50,500] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:48:50,503] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:48:50,503] [INFO] DQC Reference Directory: /var/lib/cwl/stgce4c2f0b-d47d-4b97-b045-155170d6eafd/dqc_reference
[2023-06-27 06:48:51,746] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:48:51,747] [INFO] Task started: Prodigal
[2023-06-27 06:48:51,747] [INFO] Running command: gunzip -c /var/lib/cwl/stge8dfabff-a6aa-4a80-8b5a-1d9b7c6817ee/GCA_027372265.1_ASM2737226v1_genomic.fna.gz | prodigal -d GCA_027372265.1_ASM2737226v1_genomic.fna/cds.fna -a GCA_027372265.1_ASM2737226v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:48:56,706] [INFO] Task succeeded: Prodigal
[2023-06-27 06:48:56,707] [INFO] Task started: HMMsearch
[2023-06-27 06:48:56,707] [INFO] Running command: hmmsearch --tblout GCA_027372265.1_ASM2737226v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce4c2f0b-d47d-4b97-b045-155170d6eafd/dqc_reference/reference_markers.hmm GCA_027372265.1_ASM2737226v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:48:56,901] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:48:56,902] [WARNING] Found 2/6 markers. [/var/lib/cwl/stge8dfabff-a6aa-4a80-8b5a-1d9b7c6817ee/GCA_027372265.1_ASM2737226v1_genomic.fna.gz]
[2023-06-27 06:48:56,937] [INFO] Query marker FASTA was written to GCA_027372265.1_ASM2737226v1_genomic.fna/markers.fasta
[2023-06-27 06:48:56,938] [INFO] Task started: Blastn
[2023-06-27 06:48:56,938] [INFO] Running command: blastn -query GCA_027372265.1_ASM2737226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce4c2f0b-d47d-4b97-b045-155170d6eafd/dqc_reference/reference_markers.fasta -out GCA_027372265.1_ASM2737226v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:48:57,430] [INFO] Task succeeded: Blastn
[2023-06-27 06:48:57,433] [INFO] Selected 0 target genomes.
[2023-06-27 06:48:57,434] [INFO] Target genome list was writen to GCA_027372265.1_ASM2737226v1_genomic.fna/target_genomes.txt
[2023-06-27 06:48:57,434] [ERROR] File is empty. [GCA_027372265.1_ASM2737226v1_genomic.fna/target_genomes.txt]
[2023-06-27 06:48:57,434] [ERROR] Task failed. No target genome found.
[2023-06-27 06:48:57,434] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:48:57,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce4c2f0b-d47d-4b97-b045-155170d6eafd/dqc_reference/checkm_data
[2023-06-27 06:48:57,438] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:48:57,482] [INFO] Task started: CheckM
[2023-06-27 06:48:57,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027372265.1_ASM2737226v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027372265.1_ASM2737226v1_genomic.fna/checkm_input GCA_027372265.1_ASM2737226v1_genomic.fna/checkm_result
[2023-06-27 06:49:18,992] [INFO] Task succeeded: CheckM
[2023-06-27 06:49:18,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:49:19,021] [INFO] ===== Completeness check finished =====
[2023-06-27 06:49:19,021] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:49:19,021] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027372265.1_ASM2737226v1_genomic.fna/markers.fasta)
[2023-06-27 06:49:19,022] [INFO] Task started: Blastn
[2023-06-27 06:49:19,022] [INFO] Running command: blastn -query GCA_027372265.1_ASM2737226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce4c2f0b-d47d-4b97-b045-155170d6eafd/dqc_reference/reference_markers_gtdb.fasta -out GCA_027372265.1_ASM2737226v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:49:19,534] [INFO] Task succeeded: Blastn
[2023-06-27 06:49:19,538] [INFO] Selected 3 target genomes.
[2023-06-27 06:49:19,539] [INFO] Target genome list was writen to GCA_027372265.1_ASM2737226v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:49:19,542] [INFO] Task started: fastANI
[2023-06-27 06:49:19,542] [INFO] Running command: fastANI --query /var/lib/cwl/stge8dfabff-a6aa-4a80-8b5a-1d9b7c6817ee/GCA_027372265.1_ASM2737226v1_genomic.fna.gz --refList GCA_027372265.1_ASM2737226v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027372265.1_ASM2737226v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:49:21,682] [INFO] Task succeeded: fastANI
[2023-06-27 06:49:21,703] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 06:49:21,703] [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
--------------------------------------------------------------------------------
[2023-06-27 06:49:21,718] [INFO] GTDB search result was written to GCA_027372265.1_ASM2737226v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:49:21,719] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:49:21,727] [INFO] DFAST_QC result json was written to GCA_027372265.1_ASM2737226v1_genomic.fna/dqc_result.json
[2023-06-27 06:49:21,727] [INFO] DFAST_QC completed!
[2023-06-27 06:49:21,727] [INFO] Total running time: 0h0m31s