[2023-06-27 11:34:14,345] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:34:14,348] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:34:14,348] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb53208a-de2e-4163-b163-57cb1b12c5ec/dqc_reference
[2023-06-27 11:34:15,870] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:34:15,871] [INFO] Task started: Prodigal
[2023-06-27 11:34:15,871] [INFO] Running command: gunzip -c /var/lib/cwl/stgf12f1387-e90a-4baf-97af-cd3d970a9a21/GCA_026393045.1_ASM2639304v1_genomic.fna.gz | prodigal -d GCA_026393045.1_ASM2639304v1_genomic.fna/cds.fna -a GCA_026393045.1_ASM2639304v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:34:19,145] [INFO] Task succeeded: Prodigal
[2023-06-27 11:34:19,146] [INFO] Task started: HMMsearch
[2023-06-27 11:34:19,146] [INFO] Running command: hmmsearch --tblout GCA_026393045.1_ASM2639304v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb53208a-de2e-4163-b163-57cb1b12c5ec/dqc_reference/reference_markers.hmm GCA_026393045.1_ASM2639304v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:34:19,372] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:34:19,374] [INFO] Found 6/6 markers.
[2023-06-27 11:34:19,410] [INFO] Query marker FASTA was written to GCA_026393045.1_ASM2639304v1_genomic.fna/markers.fasta
[2023-06-27 11:34:19,411] [INFO] Task started: Blastn
[2023-06-27 11:34:19,411] [INFO] Running command: blastn -query GCA_026393045.1_ASM2639304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb53208a-de2e-4163-b163-57cb1b12c5ec/dqc_reference/reference_markers.fasta -out GCA_026393045.1_ASM2639304v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:34:20,945] [INFO] Task succeeded: Blastn
[2023-06-27 11:34:20,952] [INFO] Selected 25 target genomes.
[2023-06-27 11:34:20,952] [INFO] Target genome list was writen to GCA_026393045.1_ASM2639304v1_genomic.fna/target_genomes.txt
[2023-06-27 11:34:20,957] [INFO] Task started: fastANI
[2023-06-27 11:34:20,957] [INFO] Running command: fastANI --query /var/lib/cwl/stgf12f1387-e90a-4baf-97af-cd3d970a9a21/GCA_026393045.1_ASM2639304v1_genomic.fna.gz --refList GCA_026393045.1_ASM2639304v1_genomic.fna/target_genomes.txt --output GCA_026393045.1_ASM2639304v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:34:32,229] [INFO] Task succeeded: fastANI
[2023-06-27 11:34:32,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb53208a-de2e-4163-b163-57cb1b12c5ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:34:32,230] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb53208a-de2e-4163-b163-57cb1b12c5ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:34:32,231] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:34:32,231] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 11:34:32,231] [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
--------------------------------------------------------------------------------
[2023-06-27 11:34:32,233] [INFO] DFAST Taxonomy check result was written to GCA_026393045.1_ASM2639304v1_genomic.fna/tc_result.tsv
[2023-06-27 11:34:32,234] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:34:32,234] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:34:32,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb53208a-de2e-4163-b163-57cb1b12c5ec/dqc_reference/checkm_data
[2023-06-27 11:34:32,237] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:34:32,258] [INFO] Task started: CheckM
[2023-06-27 11:34:32,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026393045.1_ASM2639304v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026393045.1_ASM2639304v1_genomic.fna/checkm_input GCA_026393045.1_ASM2639304v1_genomic.fna/checkm_result
[2023-06-27 11:34:49,616] [INFO] Task succeeded: CheckM
[2023-06-27 11:34:49,617] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:34:49,639] [INFO] ===== Completeness check finished =====
[2023-06-27 11:34:49,639] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:34:49,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026393045.1_ASM2639304v1_genomic.fna/markers.fasta)
[2023-06-27 11:34:49,640] [INFO] Task started: Blastn
[2023-06-27 11:34:49,640] [INFO] Running command: blastn -query GCA_026393045.1_ASM2639304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb53208a-de2e-4163-b163-57cb1b12c5ec/dqc_reference/reference_markers_gtdb.fasta -out GCA_026393045.1_ASM2639304v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:34:50,694] [INFO] Task succeeded: Blastn
[2023-06-27 11:34:50,715] [INFO] Selected 14 target genomes.
[2023-06-27 11:34:50,715] [INFO] Target genome list was writen to GCA_026393045.1_ASM2639304v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:34:50,720] [INFO] Task started: fastANI
[2023-06-27 11:34:50,721] [INFO] Running command: fastANI --query /var/lib/cwl/stgf12f1387-e90a-4baf-97af-cd3d970a9a21/GCA_026393045.1_ASM2639304v1_genomic.fna.gz --refList GCA_026393045.1_ASM2639304v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026393045.1_ASM2639304v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:34:54,399] [INFO] Task succeeded: fastANI
[2023-06-27 11:34:54,417] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 11:34:54,417] [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_903842675.1	s__AAA044-D11 sp903842675	98.2899	309	408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	98.43	97.97	0.83	0.78	19	conclusive
GCA_903871555.1	s__AAA044-D11 sp903871555	78.8511	160	408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.45	99.05	0.90	0.84	22	-
GCA_000485495.1	s__AAA044-D11 sp000485495	78.8055	129	408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007280395.1	s__AAA044-D11 sp007280395	78.5456	119	408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903836945.1	s__AAA044-D11 sp903836945	78.3733	131	408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.73	99.63	0.93	0.90	11	-
GCA_002340925.1	s__AAA044-D11 sp002340925	78.1749	94	408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009726125.1	s__AAA044-D11 sp009726125	78.0979	130	408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.98	99.96	0.97	0.96	6	-
GCA_009698045.1	s__AAA044-D11 sp009698045	77.7187	62	408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.24	99.10	0.86	0.82	7	-
GCA_009701575.1	s__AAA044-D11 sp009701575	77.6948	125	408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009705075.1	s__AAA044-D11 sp009705075	77.6761	60	408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	98.34	98.34	0.77	0.77	2	-
GCA_009701525.1	s__AAA044-D11 sp009701525	77.5824	93	408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903898855.1	s__AAA044-D11 sp903898855	77.3348	57	408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 11:34:54,420] [INFO] GTDB search result was written to GCA_026393045.1_ASM2639304v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:34:54,421] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:34:54,451] [INFO] DFAST_QC result json was written to GCA_026393045.1_ASM2639304v1_genomic.fna/dqc_result.json
[2023-06-27 11:34:54,451] [INFO] DFAST_QC completed!
[2023-06-27 11:34:54,451] [INFO] Total running time: 0h0m40s