[2023-06-28 23:25:39,503] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:25:39,505] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:25:39,505] [INFO] DQC Reference Directory: /var/lib/cwl/stg06791372-50c7-45b6-b701-4fe1a802f6a0/dqc_reference
[2023-06-28 23:25:40,809] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:25:40,813] [INFO] Task started: Prodigal
[2023-06-28 23:25:40,816] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c9ea2b1-86bf-4370-bc7a-442481a83b3a/GCA_017607905.1_ASM1760790v1_genomic.fna.gz | prodigal -d GCA_017607905.1_ASM1760790v1_genomic.fna/cds.fna -a GCA_017607905.1_ASM1760790v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:25:42,847] [INFO] Task succeeded: Prodigal
[2023-06-28 23:25:42,847] [INFO] Task started: HMMsearch
[2023-06-28 23:25:42,847] [INFO] Running command: hmmsearch --tblout GCA_017607905.1_ASM1760790v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06791372-50c7-45b6-b701-4fe1a802f6a0/dqc_reference/reference_markers.hmm GCA_017607905.1_ASM1760790v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:25:43,073] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:25:43,074] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg9c9ea2b1-86bf-4370-bc7a-442481a83b3a/GCA_017607905.1_ASM1760790v1_genomic.fna.gz]
[2023-06-28 23:25:43,145] [INFO] Query marker FASTA was written to GCA_017607905.1_ASM1760790v1_genomic.fna/markers.fasta
[2023-06-28 23:25:43,145] [INFO] Task started: Blastn
[2023-06-28 23:25:43,145] [INFO] Running command: blastn -query GCA_017607905.1_ASM1760790v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06791372-50c7-45b6-b701-4fe1a802f6a0/dqc_reference/reference_markers.fasta -out GCA_017607905.1_ASM1760790v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:25:43,775] [INFO] Task succeeded: Blastn
[2023-06-28 23:25:43,778] [INFO] Selected 0 target genomes.
[2023-06-28 23:25:43,779] [INFO] Target genome list was writen to GCA_017607905.1_ASM1760790v1_genomic.fna/target_genomes.txt
[2023-06-28 23:25:43,779] [ERROR] File is empty. [GCA_017607905.1_ASM1760790v1_genomic.fna/target_genomes.txt]
[2023-06-28 23:25:43,779] [ERROR] Task failed. No target genome found.
[2023-06-28 23:25:43,779] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:25:43,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06791372-50c7-45b6-b701-4fe1a802f6a0/dqc_reference/checkm_data
[2023-06-28 23:25:43,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:25:43,794] [INFO] Task started: CheckM
[2023-06-28 23:25:43,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017607905.1_ASM1760790v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017607905.1_ASM1760790v1_genomic.fna/checkm_input GCA_017607905.1_ASM1760790v1_genomic.fna/checkm_result
[2023-06-28 23:26:00,771] [INFO] Task succeeded: CheckM
[2023-06-28 23:26:00,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.49%
Contamintation: 8.90%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:26:00,808] [INFO] ===== Completeness check finished =====
[2023-06-28 23:26:00,809] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:26:00,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017607905.1_ASM1760790v1_genomic.fna/markers.fasta)
[2023-06-28 23:26:00,810] [INFO] Task started: Blastn
[2023-06-28 23:26:00,810] [INFO] Running command: blastn -query GCA_017607905.1_ASM1760790v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06791372-50c7-45b6-b701-4fe1a802f6a0/dqc_reference/reference_markers_gtdb.fasta -out GCA_017607905.1_ASM1760790v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:26:01,355] [INFO] Task succeeded: Blastn
[2023-06-28 23:26:01,360] [INFO] Selected 1 target genomes.
[2023-06-28 23:26:01,360] [INFO] Target genome list was writen to GCA_017607905.1_ASM1760790v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:26:01,362] [INFO] Task started: fastANI
[2023-06-28 23:26:01,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c9ea2b1-86bf-4370-bc7a-442481a83b3a/GCA_017607905.1_ASM1760790v1_genomic.fna.gz --refList GCA_017607905.1_ASM1760790v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017607905.1_ASM1760790v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:26:01,649] [INFO] Task succeeded: fastANI
[2023-06-28 23:26:01,653] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 23:26:01,653] [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_017608575.1	s__JAFCFP01 sp017608575	99.3057	117	158	d__Archaea;p__Iainarchaeota;c__Iainarchaeia;o__Iainarchaeales;f__DTGL01;g__JAFCFP01	95.0	99.53	98.72	0.90	0.79	4	conclusive
--------------------------------------------------------------------------------
[2023-06-28 23:26:01,655] [INFO] GTDB search result was written to GCA_017607905.1_ASM1760790v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:26:01,656] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:26:01,659] [INFO] DFAST_QC result json was written to GCA_017607905.1_ASM1760790v1_genomic.fna/dqc_result.json
[2023-06-28 23:26:01,659] [INFO] DFAST_QC completed!
[2023-06-28 23:26:01,659] [INFO] Total running time: 0h0m22s