[2023-06-27 11:53:28,307] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:53:28,309] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:53:28,309] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe386a59-752b-4d0a-8e02-ca463f047e6c/dqc_reference
[2023-06-27 11:53:29,574] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:53:29,575] [INFO] Task started: Prodigal
[2023-06-27 11:53:29,575] [INFO] Running command: gunzip -c /var/lib/cwl/stga0f5324d-e730-4c3a-bd0f-bfa5480930df/GCA_002170515.2_ASM217051v2_genomic.fna.gz | prodigal -d GCA_002170515.2_ASM217051v2_genomic.fna/cds.fna -a GCA_002170515.2_ASM217051v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:53:42,983] [INFO] Task succeeded: Prodigal
[2023-06-27 11:53:42,984] [INFO] Task started: HMMsearch
[2023-06-27 11:53:42,984] [INFO] Running command: hmmsearch --tblout GCA_002170515.2_ASM217051v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe386a59-752b-4d0a-8e02-ca463f047e6c/dqc_reference/reference_markers.hmm GCA_002170515.2_ASM217051v2_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:53:43,256] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:53:43,257] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga0f5324d-e730-4c3a-bd0f-bfa5480930df/GCA_002170515.2_ASM217051v2_genomic.fna.gz]
[2023-06-27 11:53:43,291] [INFO] Query marker FASTA was written to GCA_002170515.2_ASM217051v2_genomic.fna/markers.fasta
[2023-06-27 11:53:43,292] [INFO] Task started: Blastn
[2023-06-27 11:53:43,292] [INFO] Running command: blastn -query GCA_002170515.2_ASM217051v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe386a59-752b-4d0a-8e02-ca463f047e6c/dqc_reference/reference_markers.fasta -out GCA_002170515.2_ASM217051v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:53:43,813] [INFO] Task succeeded: Blastn
[2023-06-27 11:53:43,817] [INFO] Selected 0 target genomes.
[2023-06-27 11:53:43,817] [INFO] Target genome list was writen to GCA_002170515.2_ASM217051v2_genomic.fna/target_genomes.txt
[2023-06-27 11:53:43,817] [ERROR] File is empty. [GCA_002170515.2_ASM217051v2_genomic.fna/target_genomes.txt]
[2023-06-27 11:53:43,818] [ERROR] Task failed. No target genome found.
[2023-06-27 11:53:43,818] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:53:43,818] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe386a59-752b-4d0a-8e02-ca463f047e6c/dqc_reference/checkm_data
[2023-06-27 11:53:43,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:53:43,875] [INFO] Task started: CheckM
[2023-06-27 11:53:43,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002170515.2_ASM217051v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002170515.2_ASM217051v2_genomic.fna/checkm_input GCA_002170515.2_ASM217051v2_genomic.fna/checkm_result
[2023-06-27 11:54:24,853] [INFO] Task succeeded: CheckM
[2023-06-27 11:54:24,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.72%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:54:24,877] [INFO] ===== Completeness check finished =====
[2023-06-27 11:54:24,878] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:54:24,878] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002170515.2_ASM217051v2_genomic.fna/markers.fasta)
[2023-06-27 11:54:24,879] [INFO] Task started: Blastn
[2023-06-27 11:54:24,879] [INFO] Running command: blastn -query GCA_002170515.2_ASM217051v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe386a59-752b-4d0a-8e02-ca463f047e6c/dqc_reference/reference_markers_gtdb.fasta -out GCA_002170515.2_ASM217051v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:54:25,327] [INFO] Task succeeded: Blastn
[2023-06-27 11:54:25,349] [INFO] Selected 6 target genomes.
[2023-06-27 11:54:25,349] [INFO] Target genome list was writen to GCA_002170515.2_ASM217051v2_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:54:25,354] [INFO] Task started: fastANI
[2023-06-27 11:54:25,354] [INFO] Running command: fastANI --query /var/lib/cwl/stga0f5324d-e730-4c3a-bd0f-bfa5480930df/GCA_002170515.2_ASM217051v2_genomic.fna.gz --refList GCA_002170515.2_ASM217051v2_genomic.fna/target_genomes_gtdb.txt --output GCA_002170515.2_ASM217051v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:54:29,442] [INFO] Task succeeded: fastANI
[2023-06-27 11:54:29,453] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 11:54:29,454] [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_014529625.1	s__UBA5691 sp002420265	98.0996	781	811	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	96.17	95.09	0.91	0.87	4	conclusive
GCA_002420185.1	s__UBA5691 sp002420185	92.0137	634	811	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018700525.1	s__UBA5691 sp018700525	78.5166	92	811	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	99.68	99.65	0.95	0.94	5	-
GCA_002474325.1	s__UBA5691 sp002474325	77.4714	58	811	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	98.86	98.86	0.81	0.81	2	-
GCA_002694885.1	s__UBA5691 sp002694885	76.513	85	811	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA5691	95.0	99.79	99.79	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-27 11:54:29,457] [INFO] GTDB search result was written to GCA_002170515.2_ASM217051v2_genomic.fna/result_gtdb.tsv
[2023-06-27 11:54:29,457] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:54:29,460] [INFO] DFAST_QC result json was written to GCA_002170515.2_ASM217051v2_genomic.fna/dqc_result.json
[2023-06-27 11:54:29,460] [INFO] DFAST_QC completed!
[2023-06-27 11:54:29,460] [INFO] Total running time: 0h1m1s