[2023-06-28 13:27:06,276] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:27:06,283] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:27:06,284] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb2d8946-b02a-4075-bf9b-e56952b5a629/dqc_reference
[2023-06-28 13:27:07,536] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:27:07,537] [INFO] Task started: Prodigal
[2023-06-28 13:27:07,537] [INFO] Running command: gunzip -c /var/lib/cwl/stg322246ac-a1a3-4ab3-8547-dc3b749375ad/GCA_012517195.1_ASM1251719v1_genomic.fna.gz | prodigal -d GCA_012517195.1_ASM1251719v1_genomic.fna/cds.fna -a GCA_012517195.1_ASM1251719v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:27:10,171] [INFO] Task succeeded: Prodigal
[2023-06-28 13:27:10,171] [INFO] Task started: HMMsearch
[2023-06-28 13:27:10,171] [INFO] Running command: hmmsearch --tblout GCA_012517195.1_ASM1251719v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb2d8946-b02a-4075-bf9b-e56952b5a629/dqc_reference/reference_markers.hmm GCA_012517195.1_ASM1251719v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:27:10,322] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:27:10,323] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg322246ac-a1a3-4ab3-8547-dc3b749375ad/GCA_012517195.1_ASM1251719v1_genomic.fna.gz]
[2023-06-28 13:27:10,339] [INFO] Query marker FASTA was written to GCA_012517195.1_ASM1251719v1_genomic.fna/markers.fasta
[2023-06-28 13:27:10,339] [INFO] Task started: Blastn
[2023-06-28 13:27:10,339] [INFO] Running command: blastn -query GCA_012517195.1_ASM1251719v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb2d8946-b02a-4075-bf9b-e56952b5a629/dqc_reference/reference_markers.fasta -out GCA_012517195.1_ASM1251719v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:27:11,084] [INFO] Task succeeded: Blastn
[2023-06-28 13:27:11,090] [INFO] Selected 7 target genomes.
[2023-06-28 13:27:11,091] [INFO] Target genome list was writen to GCA_012517195.1_ASM1251719v1_genomic.fna/target_genomes.txt
[2023-06-28 13:27:11,157] [INFO] Task started: fastANI
[2023-06-28 13:27:11,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg322246ac-a1a3-4ab3-8547-dc3b749375ad/GCA_012517195.1_ASM1251719v1_genomic.fna.gz --refList GCA_012517195.1_ASM1251719v1_genomic.fna/target_genomes.txt --output GCA_012517195.1_ASM1251719v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:27:15,379] [INFO] Task succeeded: fastANI
[2023-06-28 13:27:15,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb2d8946-b02a-4075-bf9b-e56952b5a629/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:27:15,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb2d8946-b02a-4075-bf9b-e56952b5a629/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:27:15,380] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:27:15,380] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 13:27:15,381] [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 13:27:15,382] [INFO] DFAST Taxonomy check result was written to GCA_012517195.1_ASM1251719v1_genomic.fna/tc_result.tsv
[2023-06-28 13:27:15,382] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:27:15,383] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:27:15,383] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb2d8946-b02a-4075-bf9b-e56952b5a629/dqc_reference/checkm_data
[2023-06-28 13:27:15,385] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:27:15,400] [INFO] Task started: CheckM
[2023-06-28 13:27:15,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012517195.1_ASM1251719v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012517195.1_ASM1251719v1_genomic.fna/checkm_input GCA_012517195.1_ASM1251719v1_genomic.fna/checkm_result
[2023-06-28 13:27:29,809] [INFO] Task succeeded: CheckM
[2023-06-28 13:27:29,809] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:27:29,835] [INFO] ===== Completeness check finished =====
[2023-06-28 13:27:29,835] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:27:29,836] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012517195.1_ASM1251719v1_genomic.fna/markers.fasta)
[2023-06-28 13:27:29,836] [INFO] Task started: Blastn
[2023-06-28 13:27:29,836] [INFO] Running command: blastn -query GCA_012517195.1_ASM1251719v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeb2d8946-b02a-4075-bf9b-e56952b5a629/dqc_reference/reference_markers_gtdb.fasta -out GCA_012517195.1_ASM1251719v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:27:30,512] [INFO] Task succeeded: Blastn
[2023-06-28 13:27:30,514] [INFO] Selected 14 target genomes.
[2023-06-28 13:27:30,514] [INFO] Target genome list was writen to GCA_012517195.1_ASM1251719v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:27:30,532] [INFO] Task started: fastANI
[2023-06-28 13:27:30,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg322246ac-a1a3-4ab3-8547-dc3b749375ad/GCA_012517195.1_ASM1251719v1_genomic.fna.gz --refList GCA_012517195.1_ASM1251719v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012517195.1_ASM1251719v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:27:36,138] [INFO] Task succeeded: fastANI
[2023-06-28 13:27:36,143] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:27:36,143] [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_012517195.1	s__79-D21 sp012517195	99.9999	357	361	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__79-D21;g__79-D21	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000402835.1	s__79-D21 sp000402835	82.9641	146	361	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__79-D21;g__79-D21	95.0	98.35	98.35	0.73	0.73	2	-
GCA_015657435.1	s__79-D21 sp015657435	79.288	208	361	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__79-D21;g__79-D21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002436015.1	s__79-D21 sp002436015	78.7654	105	361	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__79-D21;g__79-D21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432945.1	s__79-D21 sp002432945	78.5749	118	361	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__79-D21;g__79-D21	95.0	98.86	98.71	0.86	0.82	3	-
--------------------------------------------------------------------------------
[2023-06-28 13:27:36,144] [INFO] GTDB search result was written to GCA_012517195.1_ASM1251719v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:27:36,145] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:27:36,149] [INFO] DFAST_QC result json was written to GCA_012517195.1_ASM1251719v1_genomic.fna/dqc_result.json
[2023-06-28 13:27:36,149] [INFO] DFAST_QC completed!
[2023-06-28 13:27:36,149] [INFO] Total running time: 0h0m30s