[2023-06-27 15:01:15,795] [INFO] DFAST_QC pipeline started.
[2023-06-27 15:01:15,797] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 15:01:15,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg91ee9be2-9e0b-47c5-b14c-94c30ed7ad19/dqc_reference
[2023-06-27 15:01:17,119] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 15:01:17,120] [INFO] Task started: Prodigal
[2023-06-27 15:01:17,120] [INFO] Running command: gunzip -c /var/lib/cwl/stgb38e1ffe-7c85-4fbf-b240-c7bac95aa234/GCA_026015235.1_ASM2601523v1_genomic.fna.gz | prodigal -d GCA_026015235.1_ASM2601523v1_genomic.fna/cds.fna -a GCA_026015235.1_ASM2601523v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 15:01:23,023] [INFO] Task succeeded: Prodigal
[2023-06-27 15:01:23,024] [INFO] Task started: HMMsearch
[2023-06-27 15:01:23,024] [INFO] Running command: hmmsearch --tblout GCA_026015235.1_ASM2601523v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91ee9be2-9e0b-47c5-b14c-94c30ed7ad19/dqc_reference/reference_markers.hmm GCA_026015235.1_ASM2601523v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 15:01:23,143] [INFO] Task succeeded: HMMsearch
[2023-06-27 15:01:23,144] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgb38e1ffe-7c85-4fbf-b240-c7bac95aa234/GCA_026015235.1_ASM2601523v1_genomic.fna.gz]
[2023-06-27 15:01:23,164] [INFO] Query marker FASTA was written to GCA_026015235.1_ASM2601523v1_genomic.fna/markers.fasta
[2023-06-27 15:01:23,164] [INFO] Task started: Blastn
[2023-06-27 15:01:23,164] [INFO] Running command: blastn -query GCA_026015235.1_ASM2601523v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91ee9be2-9e0b-47c5-b14c-94c30ed7ad19/dqc_reference/reference_markers.fasta -out GCA_026015235.1_ASM2601523v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:01:23,614] [INFO] Task succeeded: Blastn
[2023-06-27 15:01:23,618] [INFO] Selected 0 target genomes.
[2023-06-27 15:01:23,619] [INFO] Target genome list was writen to GCA_026015235.1_ASM2601523v1_genomic.fna/target_genomes.txt
[2023-06-27 15:01:23,619] [ERROR] File is empty. [GCA_026015235.1_ASM2601523v1_genomic.fna/target_genomes.txt]
[2023-06-27 15:01:23,619] [ERROR] Task failed. No target genome found.
[2023-06-27 15:01:23,619] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 15:01:23,619] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91ee9be2-9e0b-47c5-b14c-94c30ed7ad19/dqc_reference/checkm_data
[2023-06-27 15:01:23,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 15:01:23,638] [INFO] Task started: CheckM
[2023-06-27 15:01:23,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026015235.1_ASM2601523v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026015235.1_ASM2601523v1_genomic.fna/checkm_input GCA_026015235.1_ASM2601523v1_genomic.fna/checkm_result
[2023-06-27 15:01:47,455] [INFO] Task succeeded: CheckM
[2023-06-27 15:01:47,457] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.94%
Contamintation: 3.12%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 15:01:47,480] [INFO] ===== Completeness check finished =====
[2023-06-27 15:01:47,481] [INFO] ===== Start GTDB Search =====
[2023-06-27 15:01:47,481] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026015235.1_ASM2601523v1_genomic.fna/markers.fasta)
[2023-06-27 15:01:47,481] [INFO] Task started: Blastn
[2023-06-27 15:01:47,481] [INFO] Running command: blastn -query GCA_026015235.1_ASM2601523v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91ee9be2-9e0b-47c5-b14c-94c30ed7ad19/dqc_reference/reference_markers_gtdb.fasta -out GCA_026015235.1_ASM2601523v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 15:01:47,859] [INFO] Task succeeded: Blastn
[2023-06-27 15:01:47,864] [INFO] Selected 5 target genomes.
[2023-06-27 15:01:47,864] [INFO] Target genome list was writen to GCA_026015235.1_ASM2601523v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 15:01:47,894] [INFO] Task started: fastANI
[2023-06-27 15:01:47,894] [INFO] Running command: fastANI --query /var/lib/cwl/stgb38e1ffe-7c85-4fbf-b240-c7bac95aa234/GCA_026015235.1_ASM2601523v1_genomic.fna.gz --refList GCA_026015235.1_ASM2601523v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026015235.1_ASM2601523v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 15:01:49,316] [INFO] Task succeeded: fastANI
[2023-06-27 15:01:49,321] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 15:01:49,321] [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_016783455.1	s__BS750m-G28 sp016783455	77.3525	74	260	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__TCS64;f__TCS64;g__BS750m-G28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016783485.1	s__GCA-2726865 sp014381835	77.0887	65	260	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__TCS64;f__TCS64;g__GCA-2726865	95.0	99.35	99.35	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2023-06-27 15:01:49,323] [INFO] GTDB search result was written to GCA_026015235.1_ASM2601523v1_genomic.fna/result_gtdb.tsv
[2023-06-27 15:01:49,324] [INFO] ===== GTDB Search completed =====
[2023-06-27 15:01:49,327] [INFO] DFAST_QC result json was written to GCA_026015235.1_ASM2601523v1_genomic.fna/dqc_result.json
[2023-06-27 15:01:49,327] [INFO] DFAST_QC completed!
[2023-06-27 15:01:49,327] [INFO] Total running time: 0h0m34s