[2023-06-13 19:15:47,967] [INFO] DFAST_QC pipeline started.
[2023-06-13 19:15:47,969] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 19:15:47,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg14b373c9-fa8c-4f0b-af6f-887a055383f0/dqc_reference
[2023-06-13 19:15:49,166] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 19:15:49,166] [INFO] Task started: Prodigal
[2023-06-13 19:15:49,167] [INFO] Running command: gunzip -c /var/lib/cwl/stg2deeb002-0955-49ee-95a7-29a9940f3bf5/GCA_022425245.1_ASM2242524v1_genomic.fna.gz | prodigal -d GCA_022425245.1_ASM2242524v1_genomic.fna/cds.fna -a GCA_022425245.1_ASM2242524v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 19:15:52,691] [INFO] Task succeeded: Prodigal
[2023-06-13 19:15:52,691] [INFO] Task started: HMMsearch
[2023-06-13 19:15:52,691] [INFO] Running command: hmmsearch --tblout GCA_022425245.1_ASM2242524v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14b373c9-fa8c-4f0b-af6f-887a055383f0/dqc_reference/reference_markers.hmm GCA_022425245.1_ASM2242524v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 19:15:52,850] [INFO] Task succeeded: HMMsearch
[2023-06-13 19:15:52,851] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2deeb002-0955-49ee-95a7-29a9940f3bf5/GCA_022425245.1_ASM2242524v1_genomic.fna.gz]
[2023-06-13 19:15:52,875] [INFO] Query marker FASTA was written to GCA_022425245.1_ASM2242524v1_genomic.fna/markers.fasta
[2023-06-13 19:15:52,876] [INFO] Task started: Blastn
[2023-06-13 19:15:52,876] [INFO] Running command: blastn -query GCA_022425245.1_ASM2242524v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14b373c9-fa8c-4f0b-af6f-887a055383f0/dqc_reference/reference_markers.fasta -out GCA_022425245.1_ASM2242524v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:15:53,668] [INFO] Task succeeded: Blastn
[2023-06-13 19:15:53,671] [INFO] Selected 29 target genomes.
[2023-06-13 19:15:53,672] [INFO] Target genome list was writen to GCA_022425245.1_ASM2242524v1_genomic.fna/target_genomes.txt
[2023-06-13 19:15:53,678] [INFO] Task started: fastANI
[2023-06-13 19:15:53,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg2deeb002-0955-49ee-95a7-29a9940f3bf5/GCA_022425245.1_ASM2242524v1_genomic.fna.gz --refList GCA_022425245.1_ASM2242524v1_genomic.fna/target_genomes.txt --output GCA_022425245.1_ASM2242524v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 19:16:16,660] [INFO] Task succeeded: fastANI
[2023-06-13 19:16:16,661] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14b373c9-fa8c-4f0b-af6f-887a055383f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 19:16:16,661] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14b373c9-fa8c-4f0b-af6f-887a055383f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 19:16:16,663] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 19:16:16,663] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 19:16:16,663] [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
--------------------------------------------------------------------------------
[2023-06-13 19:16:16,665] [INFO] DFAST Taxonomy check result was written to GCA_022425245.1_ASM2242524v1_genomic.fna/tc_result.tsv
[2023-06-13 19:16:16,666] [INFO] ===== Taxonomy check completed =====
[2023-06-13 19:16:16,666] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 19:16:16,666] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14b373c9-fa8c-4f0b-af6f-887a055383f0/dqc_reference/checkm_data
[2023-06-13 19:16:16,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 19:16:16,685] [INFO] Task started: CheckM
[2023-06-13 19:16:16,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022425245.1_ASM2242524v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022425245.1_ASM2242524v1_genomic.fna/checkm_input GCA_022425245.1_ASM2242524v1_genomic.fna/checkm_result
[2023-06-13 19:16:33,933] [INFO] Task succeeded: CheckM
[2023-06-13 19:16:33,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.64%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 19:16:33,961] [INFO] ===== Completeness check finished =====
[2023-06-13 19:16:33,962] [INFO] ===== Start GTDB Search =====
[2023-06-13 19:16:33,962] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022425245.1_ASM2242524v1_genomic.fna/markers.fasta)
[2023-06-13 19:16:33,962] [INFO] Task started: Blastn
[2023-06-13 19:16:33,962] [INFO] Running command: blastn -query GCA_022425245.1_ASM2242524v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14b373c9-fa8c-4f0b-af6f-887a055383f0/dqc_reference/reference_markers_gtdb.fasta -out GCA_022425245.1_ASM2242524v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:16:35,170] [INFO] Task succeeded: Blastn
[2023-06-13 19:16:35,176] [INFO] Selected 8 target genomes.
[2023-06-13 19:16:35,176] [INFO] Target genome list was writen to GCA_022425245.1_ASM2242524v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 19:16:35,181] [INFO] Task started: fastANI
[2023-06-13 19:16:35,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg2deeb002-0955-49ee-95a7-29a9940f3bf5/GCA_022425245.1_ASM2242524v1_genomic.fna.gz --refList GCA_022425245.1_ASM2242524v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022425245.1_ASM2242524v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 19:16:38,708] [INFO] Task succeeded: fastANI
[2023-06-13 19:16:38,715] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 19:16:38,715] [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_012103605.1	s__S36-B12 sp012103605	98.4346	284	321	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	95.57	95.57	0.76	0.76	2	conclusive
GCA_010029945.1	s__S36-B12 sp010029945	93.93	244	321	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	98.25	98.18	0.79	0.75	5	-
GCA_002728915.1	s__S36-B12 sp002728915	93.0924	263	321	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	99.13	98.99	0.85	0.80	4	-
GCA_002694095.1	s__S36-B12 sp002694095	92.0371	270	321	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	97.65	97.49	0.82	0.80	3	-
GCA_002729215.1	s__S36-B12 sp002729215	90.5176	275	321	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	98.32	97.43	0.87	0.81	12	-
GCA_018402235.1	s__S36-B12 sp018402235	77.1548	81	321	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 19:16:38,717] [INFO] GTDB search result was written to GCA_022425245.1_ASM2242524v1_genomic.fna/result_gtdb.tsv
[2023-06-13 19:16:38,718] [INFO] ===== GTDB Search completed =====
[2023-06-13 19:16:38,722] [INFO] DFAST_QC result json was written to GCA_022425245.1_ASM2242524v1_genomic.fna/dqc_result.json
[2023-06-13 19:16:38,722] [INFO] DFAST_QC completed!
[2023-06-13 19:16:38,722] [INFO] Total running time: 0h0m51s