[2023-06-28 20:07:08,143] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:07:08,147] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:07:08,147] [INFO] DQC Reference Directory: /var/lib/cwl/stg03a95683-30f9-4e61-a8b9-8ee19e9172cb/dqc_reference
[2023-06-28 20:07:09,559] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:07:09,560] [INFO] Task started: Prodigal
[2023-06-28 20:07:09,560] [INFO] Running command: gunzip -c /var/lib/cwl/stge0c24780-f29d-4f0e-a4a4-070cb3ebf60b/GCA_027377445.1_ASM2737744v1_genomic.fna.gz | prodigal -d GCA_027377445.1_ASM2737744v1_genomic.fna/cds.fna -a GCA_027377445.1_ASM2737744v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:07:15,362] [INFO] Task succeeded: Prodigal
[2023-06-28 20:07:15,363] [INFO] Task started: HMMsearch
[2023-06-28 20:07:15,363] [INFO] Running command: hmmsearch --tblout GCA_027377445.1_ASM2737744v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03a95683-30f9-4e61-a8b9-8ee19e9172cb/dqc_reference/reference_markers.hmm GCA_027377445.1_ASM2737744v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:07:15,571] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:07:15,573] [WARNING] Found 2/6 markers. [/var/lib/cwl/stge0c24780-f29d-4f0e-a4a4-070cb3ebf60b/GCA_027377445.1_ASM2737744v1_genomic.fna.gz]
[2023-06-28 20:07:15,600] [INFO] Query marker FASTA was written to GCA_027377445.1_ASM2737744v1_genomic.fna/markers.fasta
[2023-06-28 20:07:15,601] [INFO] Task started: Blastn
[2023-06-28 20:07:15,601] [INFO] Running command: blastn -query GCA_027377445.1_ASM2737744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03a95683-30f9-4e61-a8b9-8ee19e9172cb/dqc_reference/reference_markers.fasta -out GCA_027377445.1_ASM2737744v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:07:16,200] [INFO] Task succeeded: Blastn
[2023-06-28 20:07:16,204] [INFO] Selected 5 target genomes.
[2023-06-28 20:07:16,205] [INFO] Target genome list was writen to GCA_027377445.1_ASM2737744v1_genomic.fna/target_genomes.txt
[2023-06-28 20:07:16,208] [INFO] Task started: fastANI
[2023-06-28 20:07:16,208] [INFO] Running command: fastANI --query /var/lib/cwl/stge0c24780-f29d-4f0e-a4a4-070cb3ebf60b/GCA_027377445.1_ASM2737744v1_genomic.fna.gz --refList GCA_027377445.1_ASM2737744v1_genomic.fna/target_genomes.txt --output GCA_027377445.1_ASM2737744v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:07:21,488] [INFO] Task succeeded: fastANI
[2023-06-28 20:07:21,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03a95683-30f9-4e61-a8b9-8ee19e9172cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:07:21,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03a95683-30f9-4e61-a8b9-8ee19e9172cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:07:21,492] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:07:21,493] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 20:07:21,493] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-28 20:07:21,496] [INFO] DFAST Taxonomy check result was written to GCA_027377445.1_ASM2737744v1_genomic.fna/tc_result.tsv
[2023-06-28 20:07:21,496] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:07:21,497] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:07:21,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03a95683-30f9-4e61-a8b9-8ee19e9172cb/dqc_reference/checkm_data
[2023-06-28 20:07:21,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:07:21,517] [INFO] Task started: CheckM
[2023-06-28 20:07:21,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027377445.1_ASM2737744v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027377445.1_ASM2737744v1_genomic.fna/checkm_input GCA_027377445.1_ASM2737744v1_genomic.fna/checkm_result
[2023-06-28 20:07:43,657] [INFO] Task succeeded: CheckM
[2023-06-28 20:07:43,660] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.30%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 20:07:43,683] [INFO] ===== Completeness check finished =====
[2023-06-28 20:07:43,684] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:07:43,684] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027377445.1_ASM2737744v1_genomic.fna/markers.fasta)
[2023-06-28 20:07:43,685] [INFO] Task started: Blastn
[2023-06-28 20:07:43,685] [INFO] Running command: blastn -query GCA_027377445.1_ASM2737744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03a95683-30f9-4e61-a8b9-8ee19e9172cb/dqc_reference/reference_markers_gtdb.fasta -out GCA_027377445.1_ASM2737744v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:07:44,393] [INFO] Task succeeded: Blastn
[2023-06-28 20:07:44,397] [INFO] Selected 4 target genomes.
[2023-06-28 20:07:44,397] [INFO] Target genome list was writen to GCA_027377445.1_ASM2737744v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:07:44,398] [INFO] Task started: fastANI
[2023-06-28 20:07:44,398] [INFO] Running command: fastANI --query /var/lib/cwl/stge0c24780-f29d-4f0e-a4a4-070cb3ebf60b/GCA_027377445.1_ASM2737744v1_genomic.fna.gz --refList GCA_027377445.1_ASM2737744v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027377445.1_ASM2737744v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:07:45,795] [INFO] Task succeeded: fastANI
[2023-06-28 20:07:45,803] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 20:07:45,803] [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_002495185.1	s__UBA184 sp002495185	78.6899	141	371	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002503985.1	s__UBA184 sp002503985	78.4842	148	371	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013290045.1	s__UBA184 sp013290045	77.5522	98	371	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013044425.1	s__UBA184 sp013044425	77.1626	74	371	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__UBA184;f__UBA184;g__UBA184	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 20:07:45,805] [INFO] GTDB search result was written to GCA_027377445.1_ASM2737744v1_genomic.fna/result_gtdb.tsv
[2023-06-28 20:07:45,806] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:07:45,809] [INFO] DFAST_QC result json was written to GCA_027377445.1_ASM2737744v1_genomic.fna/dqc_result.json
[2023-06-28 20:07:45,809] [INFO] DFAST_QC completed!
[2023-06-28 20:07:45,809] [INFO] Total running time: 0h0m38s