[2023-06-17 01:07:51,517] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:07:51,527] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:07:51,527] [INFO] DQC Reference Directory: /var/lib/cwl/stg05128a36-665e-4a78-b363-15100455bde3/dqc_reference
[2023-06-17 01:07:52,935] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:07:52,936] [INFO] Task started: Prodigal
[2023-06-17 01:07:52,937] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d467301-5afc-43ea-b832-ef6549f864af/GCA_009700835.1_ASM970083v1_genomic.fna.gz | prodigal -d GCA_009700835.1_ASM970083v1_genomic.fna/cds.fna -a GCA_009700835.1_ASM970083v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:07:57,532] [INFO] Task succeeded: Prodigal
[2023-06-17 01:07:57,533] [INFO] Task started: HMMsearch
[2023-06-17 01:07:57,533] [INFO] Running command: hmmsearch --tblout GCA_009700835.1_ASM970083v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05128a36-665e-4a78-b363-15100455bde3/dqc_reference/reference_markers.hmm GCA_009700835.1_ASM970083v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:07:57,782] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:07:57,783] [INFO] Found 6/6 markers.
[2023-06-17 01:07:57,810] [INFO] Query marker FASTA was written to GCA_009700835.1_ASM970083v1_genomic.fna/markers.fasta
[2023-06-17 01:07:57,810] [INFO] Task started: Blastn
[2023-06-17 01:07:57,810] [INFO] Running command: blastn -query GCA_009700835.1_ASM970083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05128a36-665e-4a78-b363-15100455bde3/dqc_reference/reference_markers.fasta -out GCA_009700835.1_ASM970083v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:07:58,435] [INFO] Task succeeded: Blastn
[2023-06-17 01:07:58,444] [INFO] Selected 30 target genomes.
[2023-06-17 01:07:58,444] [INFO] Target genome list was writen to GCA_009700835.1_ASM970083v1_genomic.fna/target_genomes.txt
[2023-06-17 01:07:58,455] [INFO] Task started: fastANI
[2023-06-17 01:07:58,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d467301-5afc-43ea-b832-ef6549f864af/GCA_009700835.1_ASM970083v1_genomic.fna.gz --refList GCA_009700835.1_ASM970083v1_genomic.fna/target_genomes.txt --output GCA_009700835.1_ASM970083v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 01:08:18,291] [INFO] Task succeeded: fastANI
[2023-06-17 01:08:18,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05128a36-665e-4a78-b363-15100455bde3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 01:08:18,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05128a36-665e-4a78-b363-15100455bde3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 01:08:18,294] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 01:08:18,294] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 01:08:18,294] [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
--------------------------------------------------------------------------------
[2023-06-17 01:08:18,296] [INFO] DFAST Taxonomy check result was written to GCA_009700835.1_ASM970083v1_genomic.fna/tc_result.tsv
[2023-06-17 01:08:18,297] [INFO] ===== Taxonomy check completed =====
[2023-06-17 01:08:18,297] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:08:18,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05128a36-665e-4a78-b363-15100455bde3/dqc_reference/checkm_data
[2023-06-17 01:08:18,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:08:18,326] [INFO] Task started: CheckM
[2023-06-17 01:08:18,326] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009700835.1_ASM970083v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009700835.1_ASM970083v1_genomic.fna/checkm_input GCA_009700835.1_ASM970083v1_genomic.fna/checkm_result
[2023-06-17 01:08:38,933] [INFO] Task succeeded: CheckM
[2023-06-17 01:08:38,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 01:08:38,955] [INFO] ===== Completeness check finished =====
[2023-06-17 01:08:38,956] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:08:38,956] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009700835.1_ASM970083v1_genomic.fna/markers.fasta)
[2023-06-17 01:08:38,956] [INFO] Task started: Blastn
[2023-06-17 01:08:38,956] [INFO] Running command: blastn -query GCA_009700835.1_ASM970083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05128a36-665e-4a78-b363-15100455bde3/dqc_reference/reference_markers_gtdb.fasta -out GCA_009700835.1_ASM970083v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:08:39,708] [INFO] Task succeeded: Blastn
[2023-06-17 01:08:39,713] [INFO] Selected 13 target genomes.
[2023-06-17 01:08:39,713] [INFO] Target genome list was writen to GCA_009700835.1_ASM970083v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:08:39,721] [INFO] Task started: fastANI
[2023-06-17 01:08:39,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d467301-5afc-43ea-b832-ef6549f864af/GCA_009700835.1_ASM970083v1_genomic.fna.gz --refList GCA_009700835.1_ASM970083v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009700835.1_ASM970083v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:08:44,403] [INFO] Task succeeded: fastANI
[2023-06-17 01:08:44,414] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 01:08:44,414] [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_009698575.1	s__UBA5976 sp009698575	99.9444	527	583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA5976;g__UBA5976	95.0	99.89	99.66	0.97	0.94	7	conclusive
GCA_009702945.1	s__UBA5976 sp009702945	80.3534	176	583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA5976;g__UBA5976	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009918005.1	s__UBA5976 sp009918005	80.1029	191	583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA5976;g__UBA5976	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903925705.1	s__UBA5976 sp903925705	79.6733	194	583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA5976;g__UBA5976	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002430405.1	s__UBA5976 sp002430405	78.8775	135	583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA5976;g__UBA5976	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903951185.1	s__UBA5976 sp903951185	77.6676	72	583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA5976;g__UBA5976	95.0	99.15	99.15	0.83	0.83	2	-
GCA_903892635.1	s__UBA5976 sp903892635	77.0988	76	583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__UBA5976;g__UBA5976	95.0	99.72	99.72	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-17 01:08:44,416] [INFO] GTDB search result was written to GCA_009700835.1_ASM970083v1_genomic.fna/result_gtdb.tsv
[2023-06-17 01:08:44,417] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:08:44,421] [INFO] DFAST_QC result json was written to GCA_009700835.1_ASM970083v1_genomic.fna/dqc_result.json
[2023-06-17 01:08:44,421] [INFO] DFAST_QC completed!
[2023-06-17 01:08:44,422] [INFO] Total running time: 0h0m53s