[2023-06-18 19:52:00,408] [INFO] DFAST_QC pipeline started.
[2023-06-18 19:52:00,413] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 19:52:00,413] [INFO] DQC Reference Directory: /var/lib/cwl/stg81b15eaf-9ab3-4804-81b8-dbb8f98800b2/dqc_reference
[2023-06-18 19:52:01,961] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 19:52:01,962] [INFO] Task started: Prodigal
[2023-06-18 19:52:01,962] [INFO] Running command: gunzip -c /var/lib/cwl/stg47409d23-992b-4bd2-b75c-28b2d64229c3/GCA_018433595.1_SV1_genomic.fna.gz | prodigal -d GCA_018433595.1_SV1_genomic.fna/cds.fna -a GCA_018433595.1_SV1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 19:52:08,009] [INFO] Task succeeded: Prodigal
[2023-06-18 19:52:08,010] [INFO] Task started: HMMsearch
[2023-06-18 19:52:08,011] [INFO] Running command: hmmsearch --tblout GCA_018433595.1_SV1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81b15eaf-9ab3-4804-81b8-dbb8f98800b2/dqc_reference/reference_markers.hmm GCA_018433595.1_SV1_genomic.fna/protein.faa > /dev/null
[2023-06-18 19:52:08,258] [INFO] Task succeeded: HMMsearch
[2023-06-18 19:52:08,259] [INFO] Found 6/6 markers.
[2023-06-18 19:52:08,287] [INFO] Query marker FASTA was written to GCA_018433595.1_SV1_genomic.fna/markers.fasta
[2023-06-18 19:52:08,288] [INFO] Task started: Blastn
[2023-06-18 19:52:08,288] [INFO] Running command: blastn -query GCA_018433595.1_SV1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81b15eaf-9ab3-4804-81b8-dbb8f98800b2/dqc_reference/reference_markers.fasta -out GCA_018433595.1_SV1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:52:08,922] [INFO] Task succeeded: Blastn
[2023-06-18 19:52:08,931] [INFO] Selected 25 target genomes.
[2023-06-18 19:52:08,932] [INFO] Target genome list was writen to GCA_018433595.1_SV1_genomic.fna/target_genomes.txt
[2023-06-18 19:52:08,935] [INFO] Task started: fastANI
[2023-06-18 19:52:08,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg47409d23-992b-4bd2-b75c-28b2d64229c3/GCA_018433595.1_SV1_genomic.fna.gz --refList GCA_018433595.1_SV1_genomic.fna/target_genomes.txt --output GCA_018433595.1_SV1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 19:52:21,642] [INFO] Task succeeded: fastANI
[2023-06-18 19:52:21,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81b15eaf-9ab3-4804-81b8-dbb8f98800b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 19:52:21,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81b15eaf-9ab3-4804-81b8-dbb8f98800b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 19:52:21,651] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 19:52:21,652] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 19:52:21,652] [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
Aminomonas paucivorans	strain=DSM 12260	GCA_000165795.1	81412	81412	type	True	77.0132	98	808	95	below_threshold
Aminiphilus circumscriptus	strain=DSM 16581	GCA_000526375.1	290732	290732	type	True	76.8889	65	808	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 19:52:21,654] [INFO] DFAST Taxonomy check result was written to GCA_018433595.1_SV1_genomic.fna/tc_result.tsv
[2023-06-18 19:52:21,655] [INFO] ===== Taxonomy check completed =====
[2023-06-18 19:52:21,656] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 19:52:21,656] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81b15eaf-9ab3-4804-81b8-dbb8f98800b2/dqc_reference/checkm_data
[2023-06-18 19:52:21,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 19:52:21,691] [INFO] Task started: CheckM
[2023-06-18 19:52:21,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018433595.1_SV1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018433595.1_SV1_genomic.fna/checkm_input GCA_018433595.1_SV1_genomic.fna/checkm_result
[2023-06-18 19:52:46,085] [INFO] Task succeeded: CheckM
[2023-06-18 19:52:46,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 19:52:46,110] [INFO] ===== Completeness check finished =====
[2023-06-18 19:52:46,110] [INFO] ===== Start GTDB Search =====
[2023-06-18 19:52:46,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018433595.1_SV1_genomic.fna/markers.fasta)
[2023-06-18 19:52:46,111] [INFO] Task started: Blastn
[2023-06-18 19:52:46,111] [INFO] Running command: blastn -query GCA_018433595.1_SV1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81b15eaf-9ab3-4804-81b8-dbb8f98800b2/dqc_reference/reference_markers_gtdb.fasta -out GCA_018433595.1_SV1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:52:46,999] [INFO] Task succeeded: Blastn
[2023-06-18 19:52:47,004] [INFO] Selected 17 target genomes.
[2023-06-18 19:52:47,004] [INFO] Target genome list was writen to GCA_018433595.1_SV1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 19:52:47,012] [INFO] Task started: fastANI
[2023-06-18 19:52:47,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg47409d23-992b-4bd2-b75c-28b2d64229c3/GCA_018433595.1_SV1_genomic.fna.gz --refList GCA_018433595.1_SV1_genomic.fna/target_genomes_gtdb.txt --output GCA_018433595.1_SV1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 19:52:56,134] [INFO] Task succeeded: fastANI
[2023-06-18 19:52:56,147] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 19:52:56,147] [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_018433595.1	s__SV1-B22 sp018433595	100.0	804	808	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__SV1-B22;g__SV1-B22	95.0	98.92	97.17	0.90	0.86	7	conclusive
GCA_016756725.1	s__SV1-B22 sp016756725	82.6902	463	808	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__SV1-B22;g__SV1-B22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018398915.1	s__SV1-B22 sp018398915	81.7024	476	808	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__SV1-B22;g__SV1-B22	95.0	99.20	99.20	0.94	0.94	2	-
GCA_002425685.1	s__Aminiphilus sp002425685	77.0357	64	808	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminiphilaceae;g__Aminiphilus	95.0	98.97	98.23	0.86	0.86	3	-
GCF_000165795.1	s__Aminomonas paucivorans	77.0102	99	808	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Synergistaceae;g__Aminomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526375.1	s__Aminiphilus circumscriptus	76.8889	65	808	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminiphilaceae;g__Aminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018436725.1	s__JAAYLU01 sp018436725	76.4482	66	808	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Aminobacteriaceae;g__JAAYLU01	95.0	98.42	97.96	0.92	0.90	4	-
--------------------------------------------------------------------------------
[2023-06-18 19:52:56,149] [INFO] GTDB search result was written to GCA_018433595.1_SV1_genomic.fna/result_gtdb.tsv
[2023-06-18 19:52:56,149] [INFO] ===== GTDB Search completed =====
[2023-06-18 19:52:56,152] [INFO] DFAST_QC result json was written to GCA_018433595.1_SV1_genomic.fna/dqc_result.json
[2023-06-18 19:52:56,152] [INFO] DFAST_QC completed!
[2023-06-18 19:52:56,152] [INFO] Total running time: 0h0m56s