[2023-06-27 01:35:31,292] [INFO] DFAST_QC pipeline started.
[2023-06-27 01:35:31,295] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 01:35:31,296] [INFO] DQC Reference Directory: /var/lib/cwl/stg8050ec24-85bd-4018-a30a-445314a522e3/dqc_reference
[2023-06-27 01:35:32,704] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 01:35:32,705] [INFO] Task started: Prodigal
[2023-06-27 01:35:32,705] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e1d69f0-ac99-4556-a162-18970264b8f1/GCA_026014585.1_ASM2601458v1_genomic.fna.gz | prodigal -d GCA_026014585.1_ASM2601458v1_genomic.fna/cds.fna -a GCA_026014585.1_ASM2601458v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 01:35:38,576] [INFO] Task succeeded: Prodigal
[2023-06-27 01:35:38,576] [INFO] Task started: HMMsearch
[2023-06-27 01:35:38,576] [INFO] Running command: hmmsearch --tblout GCA_026014585.1_ASM2601458v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8050ec24-85bd-4018-a30a-445314a522e3/dqc_reference/reference_markers.hmm GCA_026014585.1_ASM2601458v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 01:35:38,799] [INFO] Task succeeded: HMMsearch
[2023-06-27 01:35:38,800] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg1e1d69f0-ac99-4556-a162-18970264b8f1/GCA_026014585.1_ASM2601458v1_genomic.fna.gz]
[2023-06-27 01:35:38,826] [INFO] Query marker FASTA was written to GCA_026014585.1_ASM2601458v1_genomic.fna/markers.fasta
[2023-06-27 01:35:38,826] [INFO] Task started: Blastn
[2023-06-27 01:35:38,826] [INFO] Running command: blastn -query GCA_026014585.1_ASM2601458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8050ec24-85bd-4018-a30a-445314a522e3/dqc_reference/reference_markers.fasta -out GCA_026014585.1_ASM2601458v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:35:39,340] [INFO] Task succeeded: Blastn
[2023-06-27 01:35:39,343] [INFO] Selected 0 target genomes.
[2023-06-27 01:35:39,344] [INFO] Target genome list was writen to GCA_026014585.1_ASM2601458v1_genomic.fna/target_genomes.txt
[2023-06-27 01:35:39,344] [ERROR] File is empty. [GCA_026014585.1_ASM2601458v1_genomic.fna/target_genomes.txt]
[2023-06-27 01:35:39,344] [ERROR] Task failed. No target genome found.
[2023-06-27 01:35:39,344] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 01:35:39,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8050ec24-85bd-4018-a30a-445314a522e3/dqc_reference/checkm_data
[2023-06-27 01:35:39,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 01:35:39,374] [INFO] Task started: CheckM
[2023-06-27 01:35:39,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026014585.1_ASM2601458v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026014585.1_ASM2601458v1_genomic.fna/checkm_input GCA_026014585.1_ASM2601458v1_genomic.fna/checkm_result
[2023-06-27 01:36:04,584] [INFO] Task succeeded: CheckM
[2023-06-27 01:36:04,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 01:36:04,610] [INFO] ===== Completeness check finished =====
[2023-06-27 01:36:04,610] [INFO] ===== Start GTDB Search =====
[2023-06-27 01:36:04,611] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026014585.1_ASM2601458v1_genomic.fna/markers.fasta)
[2023-06-27 01:36:04,611] [INFO] Task started: Blastn
[2023-06-27 01:36:04,611] [INFO] Running command: blastn -query GCA_026014585.1_ASM2601458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8050ec24-85bd-4018-a30a-445314a522e3/dqc_reference/reference_markers_gtdb.fasta -out GCA_026014585.1_ASM2601458v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 01:36:05,137] [INFO] Task succeeded: Blastn
[2023-06-27 01:36:05,166] [INFO] Selected 3 target genomes.
[2023-06-27 01:36:05,166] [INFO] Target genome list was writen to GCA_026014585.1_ASM2601458v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 01:36:05,170] [INFO] Task started: fastANI
[2023-06-27 01:36:05,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e1d69f0-ac99-4556-a162-18970264b8f1/GCA_026014585.1_ASM2601458v1_genomic.fna.gz --refList GCA_026014585.1_ASM2601458v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026014585.1_ASM2601458v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 01:36:06,604] [INFO] Task succeeded: fastANI
[2023-06-27 01:36:06,608] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 01:36:06,608] [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_003151735.1	s__PALSA-986 sp003151735	76.5679	108	758	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__B26-1;f__UBA233;g__PALSA-986	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133625.1	s__PALSA-986 sp003133625	76.5166	93	758	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__B26-1;f__UBA233;g__PALSA-986	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 01:36:06,611] [INFO] GTDB search result was written to GCA_026014585.1_ASM2601458v1_genomic.fna/result_gtdb.tsv
[2023-06-27 01:36:06,611] [INFO] ===== GTDB Search completed =====
[2023-06-27 01:36:06,614] [INFO] DFAST_QC result json was written to GCA_026014585.1_ASM2601458v1_genomic.fna/dqc_result.json
[2023-06-27 01:36:06,614] [INFO] DFAST_QC completed!
[2023-06-27 01:36:06,614] [INFO] Total running time: 0h0m35s