[2023-06-27 16:00:36,156] [INFO] DFAST_QC pipeline started.
[2023-06-27 16:00:36,158] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 16:00:36,158] [INFO] DQC Reference Directory: /var/lib/cwl/stgc94bde00-b0fa-48fb-80aa-2dc9e317cfed/dqc_reference
[2023-06-27 16:00:37,336] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 16:00:37,337] [INFO] Task started: Prodigal
[2023-06-27 16:00:37,337] [INFO] Running command: gunzip -c /var/lib/cwl/stg31259ac9-09c3-4927-b83f-b8a674a8d649/GCA_002686355.1_ASM268635v1_genomic.fna.gz | prodigal -d GCA_002686355.1_ASM268635v1_genomic.fna/cds.fna -a GCA_002686355.1_ASM268635v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 16:00:38,869] [INFO] Task succeeded: Prodigal
[2023-06-27 16:00:38,869] [INFO] Task started: HMMsearch
[2023-06-27 16:00:38,869] [INFO] Running command: hmmsearch --tblout GCA_002686355.1_ASM268635v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc94bde00-b0fa-48fb-80aa-2dc9e317cfed/dqc_reference/reference_markers.hmm GCA_002686355.1_ASM268635v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 16:00:38,978] [INFO] Task succeeded: HMMsearch
[2023-06-27 16:00:38,979] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg31259ac9-09c3-4927-b83f-b8a674a8d649/GCA_002686355.1_ASM268635v1_genomic.fna.gz]
[2023-06-27 16:00:38,995] [INFO] Query marker FASTA was written to GCA_002686355.1_ASM268635v1_genomic.fna/markers.fasta
[2023-06-27 16:00:38,995] [INFO] Task started: Blastn
[2023-06-27 16:00:38,995] [INFO] Running command: blastn -query GCA_002686355.1_ASM268635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc94bde00-b0fa-48fb-80aa-2dc9e317cfed/dqc_reference/reference_markers.fasta -out GCA_002686355.1_ASM268635v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 16:00:39,482] [INFO] Task succeeded: Blastn
[2023-06-27 16:00:39,486] [INFO] Selected 0 target genomes.
[2023-06-27 16:00:39,486] [INFO] Target genome list was writen to GCA_002686355.1_ASM268635v1_genomic.fna/target_genomes.txt
[2023-06-27 16:00:39,486] [ERROR] File is empty. [GCA_002686355.1_ASM268635v1_genomic.fna/target_genomes.txt]
[2023-06-27 16:00:39,486] [ERROR] Task failed. No target genome found.
[2023-06-27 16:00:39,486] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 16:00:39,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc94bde00-b0fa-48fb-80aa-2dc9e317cfed/dqc_reference/checkm_data
[2023-06-27 16:00:39,490] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 16:00:39,499] [INFO] Task started: CheckM
[2023-06-27 16:00:39,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002686355.1_ASM268635v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002686355.1_ASM268635v1_genomic.fna/checkm_input GCA_002686355.1_ASM268635v1_genomic.fna/checkm_result
[2023-06-27 16:00:51,836] [INFO] Task succeeded: CheckM
[2023-06-27 16:00:51,837] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 16:00:51,861] [INFO] ===== Completeness check finished =====
[2023-06-27 16:00:51,861] [INFO] ===== Start GTDB Search =====
[2023-06-27 16:00:51,862] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002686355.1_ASM268635v1_genomic.fna/markers.fasta)
[2023-06-27 16:00:51,862] [INFO] Task started: Blastn
[2023-06-27 16:00:51,862] [INFO] Running command: blastn -query GCA_002686355.1_ASM268635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc94bde00-b0fa-48fb-80aa-2dc9e317cfed/dqc_reference/reference_markers_gtdb.fasta -out GCA_002686355.1_ASM268635v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 16:00:52,340] [INFO] Task succeeded: Blastn
[2023-06-27 16:00:52,344] [INFO] Selected 4 target genomes.
[2023-06-27 16:00:52,344] [INFO] Target genome list was writen to GCA_002686355.1_ASM268635v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 16:00:52,347] [INFO] Task started: fastANI
[2023-06-27 16:00:52,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg31259ac9-09c3-4927-b83f-b8a674a8d649/GCA_002686355.1_ASM268635v1_genomic.fna.gz --refList GCA_002686355.1_ASM268635v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002686355.1_ASM268635v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 16:00:52,948] [INFO] Task succeeded: fastANI
[2023-06-27 16:00:52,952] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 16:00:52,952] [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_002686355.1	s__ARS1301 sp002686355	100.0	130	131	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__ARS1301	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-27 16:00:52,954] [INFO] GTDB search result was written to GCA_002686355.1_ASM268635v1_genomic.fna/result_gtdb.tsv
[2023-06-27 16:00:52,955] [INFO] ===== GTDB Search completed =====
[2023-06-27 16:00:52,957] [INFO] DFAST_QC result json was written to GCA_002686355.1_ASM268635v1_genomic.fna/dqc_result.json
[2023-06-27 16:00:52,957] [INFO] DFAST_QC completed!
[2023-06-27 16:00:52,957] [INFO] Total running time: 0h0m17s