[2023-06-30 12:04:39,997] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:04:40,001] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:04:40,002] [INFO] DQC Reference Directory: /var/lib/cwl/stgf70a7d80-7d25-4f89-a898-9cff477357e9/dqc_reference
[2023-06-30 12:04:41,290] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:04:41,291] [INFO] Task started: Prodigal
[2023-06-30 12:04:41,291] [INFO] Running command: gunzip -c /var/lib/cwl/stg831eeaa2-f131-4af9-b452-b659f23ace71/GCA_025994975.1_ASM2599497v1_genomic.fna.gz | prodigal -d GCA_025994975.1_ASM2599497v1_genomic.fna/cds.fna -a GCA_025994975.1_ASM2599497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:04:43,233] [INFO] Task succeeded: Prodigal
[2023-06-30 12:04:43,234] [INFO] Task started: HMMsearch
[2023-06-30 12:04:43,234] [INFO] Running command: hmmsearch --tblout GCA_025994975.1_ASM2599497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf70a7d80-7d25-4f89-a898-9cff477357e9/dqc_reference/reference_markers.hmm GCA_025994975.1_ASM2599497v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:04:43,427] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:04:43,429] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg831eeaa2-f131-4af9-b452-b659f23ace71/GCA_025994975.1_ASM2599497v1_genomic.fna.gz]
[2023-06-30 12:04:43,445] [INFO] Query marker FASTA was written to GCA_025994975.1_ASM2599497v1_genomic.fna/markers.fasta
[2023-06-30 12:04:43,445] [INFO] Task started: Blastn
[2023-06-30 12:04:43,445] [INFO] Running command: blastn -query GCA_025994975.1_ASM2599497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf70a7d80-7d25-4f89-a898-9cff477357e9/dqc_reference/reference_markers.fasta -out GCA_025994975.1_ASM2599497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:04:43,938] [INFO] Task succeeded: Blastn
[2023-06-30 12:04:43,943] [INFO] Selected 9 target genomes.
[2023-06-30 12:04:43,944] [INFO] Target genome list was writen to GCA_025994975.1_ASM2599497v1_genomic.fna/target_genomes.txt
[2023-06-30 12:04:43,948] [INFO] Task started: fastANI
[2023-06-30 12:04:43,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg831eeaa2-f131-4af9-b452-b659f23ace71/GCA_025994975.1_ASM2599497v1_genomic.fna.gz --refList GCA_025994975.1_ASM2599497v1_genomic.fna/target_genomes.txt --output GCA_025994975.1_ASM2599497v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:04:47,357] [INFO] Task succeeded: fastANI
[2023-06-30 12:04:47,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf70a7d80-7d25-4f89-a898-9cff477357e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:04:47,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf70a7d80-7d25-4f89-a898-9cff477357e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:04:47,364] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:04:47,364] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 12:04:47,365] [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
Candidatus Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	78.7729	136	209	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 12:04:47,367] [INFO] DFAST Taxonomy check result was written to GCA_025994975.1_ASM2599497v1_genomic.fna/tc_result.tsv
[2023-06-30 12:04:47,367] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:04:47,368] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:04:47,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf70a7d80-7d25-4f89-a898-9cff477357e9/dqc_reference/checkm_data
[2023-06-30 12:04:47,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:04:47,385] [INFO] Task started: CheckM
[2023-06-30 12:04:47,385] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025994975.1_ASM2599497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025994975.1_ASM2599497v1_genomic.fna/checkm_input GCA_025994975.1_ASM2599497v1_genomic.fna/checkm_result
[2023-06-30 12:05:00,289] [INFO] Task succeeded: CheckM
[2023-06-30 12:05:00,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 12:05:00,309] [INFO] ===== Completeness check finished =====
[2023-06-30 12:05:00,310] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:05:00,310] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025994975.1_ASM2599497v1_genomic.fna/markers.fasta)
[2023-06-30 12:05:00,310] [INFO] Task started: Blastn
[2023-06-30 12:05:00,310] [INFO] Running command: blastn -query GCA_025994975.1_ASM2599497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf70a7d80-7d25-4f89-a898-9cff477357e9/dqc_reference/reference_markers_gtdb.fasta -out GCA_025994975.1_ASM2599497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:05:00,844] [INFO] Task succeeded: Blastn
[2023-06-30 12:05:00,849] [INFO] Selected 9 target genomes.
[2023-06-30 12:05:00,850] [INFO] Target genome list was writen to GCA_025994975.1_ASM2599497v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:05:00,859] [INFO] Task started: fastANI
[2023-06-30 12:05:00,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg831eeaa2-f131-4af9-b452-b659f23ace71/GCA_025994975.1_ASM2599497v1_genomic.fna.gz --refList GCA_025994975.1_ASM2599497v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025994975.1_ASM2599497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:05:02,772] [INFO] Task succeeded: fastANI
[2023-06-30 12:05:02,780] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 12:05:02,780] [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_008638165.1	s__Pelagibacter sp008638165	98.8078	186	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.93	98.78	0.83	0.76	5	conclusive
GCF_900177485.1	s__Pelagibacter sp900177485	87.3857	193	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902571235.1	s__Pelagibacter sp902571235	81.0931	119	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520685.1	s__Pelagibacter sp902520685	81.0319	126	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622805.1	s__Pelagibacter sp902622805	80.8916	122	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.81	99.81	0.79	0.79	2	-
GCA_017880265.1	s__Pelagibacter sp017880265	79.4823	104	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.65	97.65	0.82	0.82	2	-
GCF_000155895.1	s__Pelagibacter sp000155895	79.184	139	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.42	95.11	0.93	0.90	6	-
GCA_902555655.1	s__Pelagibacter sp902555655	79.1676	108	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902569055.1	s__Pelagibacter sp902569055	78.9566	119	209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.72	99.72	0.75	0.75	2	-
--------------------------------------------------------------------------------
[2023-06-30 12:05:02,783] [INFO] GTDB search result was written to GCA_025994975.1_ASM2599497v1_genomic.fna/result_gtdb.tsv
[2023-06-30 12:05:02,783] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:05:02,786] [INFO] DFAST_QC result json was written to GCA_025994975.1_ASM2599497v1_genomic.fna/dqc_result.json
[2023-06-30 12:05:02,786] [INFO] DFAST_QC completed!
[2023-06-30 12:05:02,786] [INFO] Total running time: 0h0m23s