[2023-06-29 20:24:33,283] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:24:33,286] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:24:33,286] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf126eb0-5a74-4069-858a-c7ccf4904bcd/dqc_reference
[2023-06-29 20:24:35,553] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:24:35,554] [INFO] Task started: Prodigal
[2023-06-29 20:24:35,555] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd59ceb0-dfa8-44c1-b098-3a680a6654a1/GCA_023539655.1_ASM2353965v1_genomic.fna.gz | prodigal -d GCA_023539655.1_ASM2353965v1_genomic.fna/cds.fna -a GCA_023539655.1_ASM2353965v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:24:40,307] [INFO] Task succeeded: Prodigal
[2023-06-29 20:24:40,308] [INFO] Task started: HMMsearch
[2023-06-29 20:24:40,308] [INFO] Running command: hmmsearch --tblout GCA_023539655.1_ASM2353965v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf126eb0-5a74-4069-858a-c7ccf4904bcd/dqc_reference/reference_markers.hmm GCA_023539655.1_ASM2353965v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:24:40,530] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:24:40,531] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgdd59ceb0-dfa8-44c1-b098-3a680a6654a1/GCA_023539655.1_ASM2353965v1_genomic.fna.gz]
[2023-06-29 20:24:40,549] [INFO] Query marker FASTA was written to GCA_023539655.1_ASM2353965v1_genomic.fna/markers.fasta
[2023-06-29 20:24:40,550] [INFO] Task started: Blastn
[2023-06-29 20:24:40,550] [INFO] Running command: blastn -query GCA_023539655.1_ASM2353965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf126eb0-5a74-4069-858a-c7ccf4904bcd/dqc_reference/reference_markers.fasta -out GCA_023539655.1_ASM2353965v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:24:41,017] [INFO] Task succeeded: Blastn
[2023-06-29 20:24:41,022] [INFO] Selected 0 target genomes.
[2023-06-29 20:24:41,022] [INFO] Target genome list was writen to GCA_023539655.1_ASM2353965v1_genomic.fna/target_genomes.txt
[2023-06-29 20:24:41,022] [ERROR] File is empty. [GCA_023539655.1_ASM2353965v1_genomic.fna/target_genomes.txt]
[2023-06-29 20:24:41,023] [ERROR] Task failed. No target genome found.
[2023-06-29 20:24:41,023] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:24:41,024] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf126eb0-5a74-4069-858a-c7ccf4904bcd/dqc_reference/checkm_data
[2023-06-29 20:24:41,028] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:24:41,042] [INFO] Task started: CheckM
[2023-06-29 20:24:41,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023539655.1_ASM2353965v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023539655.1_ASM2353965v1_genomic.fna/checkm_input GCA_023539655.1_ASM2353965v1_genomic.fna/checkm_result
[2023-06-29 20:25:00,465] [INFO] Task succeeded: CheckM
[2023-06-29 20:25:00,467] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:25:00,486] [INFO] ===== Completeness check finished =====
[2023-06-29 20:25:00,487] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:25:00,487] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023539655.1_ASM2353965v1_genomic.fna/markers.fasta)
[2023-06-29 20:25:00,488] [INFO] Task started: Blastn
[2023-06-29 20:25:00,488] [INFO] Running command: blastn -query GCA_023539655.1_ASM2353965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf126eb0-5a74-4069-858a-c7ccf4904bcd/dqc_reference/reference_markers_gtdb.fasta -out GCA_023539655.1_ASM2353965v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:25:00,939] [INFO] Task succeeded: Blastn
[2023-06-29 20:25:00,943] [INFO] Selected 3 target genomes.
[2023-06-29 20:25:00,943] [INFO] Target genome list was writen to GCA_023539655.1_ASM2353965v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:25:00,945] [INFO] Task started: fastANI
[2023-06-29 20:25:00,945] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd59ceb0-dfa8-44c1-b098-3a680a6654a1/GCA_023539655.1_ASM2353965v1_genomic.fna.gz --refList GCA_023539655.1_ASM2353965v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023539655.1_ASM2353965v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:25:01,746] [INFO] Task succeeded: fastANI
[2023-06-29 20:25:01,755] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:25:01,755] [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_011363045.1	s__NZ13-MG1 sp011363045	88.2672	329	351	d__Archaea;p__Thermoproteota;c__Nitrososphaeria_A;o__Caldarchaeales;f__NZ13-MGT;g__NZ13-MG1	95.0	99.62	99.51	0.90	0.82	4	-
GCA_011364235.1	s__NZ13-MG1 sp011364235	80.6052	284	351	d__Archaea;p__Thermoproteota;c__Nitrososphaeria_A;o__Caldarchaeales;f__NZ13-MGT;g__NZ13-MG1	95.0	99.98	99.98	0.99	0.99	2	-
GCA_003056285.1	s__NZ13-MG1 sp003056285	77.0667	144	351	d__Archaea;p__Thermoproteota;c__Nitrososphaeria_A;o__Caldarchaeales;f__NZ13-MGT;g__NZ13-MG1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:25:01,758] [INFO] GTDB search result was written to GCA_023539655.1_ASM2353965v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:25:01,758] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:25:01,762] [INFO] DFAST_QC result json was written to GCA_023539655.1_ASM2353965v1_genomic.fna/dqc_result.json
[2023-06-29 20:25:01,763] [INFO] DFAST_QC completed!
[2023-06-29 20:25:01,763] [INFO] Total running time: 0h0m28s