[2024-01-24 12:21:57,980] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:57,983] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:57,983] [INFO] DQC Reference Directory: /var/lib/cwl/stg451391ed-f5df-49ed-9160-4cfd42353b43/dqc_reference
[2024-01-24 12:21:59,660] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:59,661] [INFO] Task started: Prodigal
[2024-01-24 12:21:59,661] [INFO] Running command: gunzip -c /var/lib/cwl/stga39aae12-de6d-4313-9120-2727f6454c23/GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna.gz | prodigal -d GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/cds.fna -a GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:06,170] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:06,171] [INFO] Task started: HMMsearch
[2024-01-24 12:22:06,171] [INFO] Running command: hmmsearch --tblout GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg451391ed-f5df-49ed-9160-4cfd42353b43/dqc_reference/reference_markers.hmm GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:06,484] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:06,485] [INFO] Found 6/6 markers.
[2024-01-24 12:22:06,514] [INFO] Query marker FASTA was written to GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/markers.fasta
[2024-01-24 12:22:06,515] [INFO] Task started: Blastn
[2024-01-24 12:22:06,515] [INFO] Running command: blastn -query GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/markers.fasta -db /var/lib/cwl/stg451391ed-f5df-49ed-9160-4cfd42353b43/dqc_reference/reference_markers.fasta -out GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:07,111] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:07,115] [INFO] Selected 12 target genomes.
[2024-01-24 12:22:07,115] [INFO] Target genome list was writen to GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/target_genomes.txt
[2024-01-24 12:22:07,147] [INFO] Task started: fastANI
[2024-01-24 12:22:07,147] [INFO] Running command: fastANI --query /var/lib/cwl/stga39aae12-de6d-4313-9120-2727f6454c23/GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna.gz --refList GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/target_genomes.txt --output GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:12,427] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:12,428] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg451391ed-f5df-49ed-9160-4cfd42353b43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:12,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg451391ed-f5df-49ed-9160-4cfd42353b43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:12,432] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:12,432] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:12,432] [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
Syntrophomonas zehnderi	strain=OL-4	GCA_000983115.1	404335	404335	type	True	100.0	933	958	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:22:12,434] [INFO] DFAST Taxonomy check result was written to GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/tc_result.tsv
[2024-01-24 12:22:12,434] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:12,434] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:12,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg451391ed-f5df-49ed-9160-4cfd42353b43/dqc_reference/checkm_data
[2024-01-24 12:22:12,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:12,465] [INFO] Task started: CheckM
[2024-01-24 12:22:12,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/checkm_input GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/checkm_result
[2024-01-24 12:22:40,576] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:40,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 25.00%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:40,609] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:40,610] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:40,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/markers.fasta)
[2024-01-24 12:22:40,611] [INFO] Task started: Blastn
[2024-01-24 12:22:40,611] [INFO] Running command: blastn -query GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/markers.fasta -db /var/lib/cwl/stg451391ed-f5df-49ed-9160-4cfd42353b43/dqc_reference/reference_markers_gtdb.fasta -out GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:41,487] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:41,490] [INFO] Selected 22 target genomes.
[2024-01-24 12:22:41,490] [INFO] Target genome list was writen to GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:41,509] [INFO] Task started: fastANI
[2024-01-24 12:22:41,509] [INFO] Running command: fastANI --query /var/lib/cwl/stga39aae12-de6d-4313-9120-2727f6454c23/GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna.gz --refList GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/target_genomes_gtdb.txt --output GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:52,201] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:52,208] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:52,208] [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
GCF_000983115.1	s__Syntrophomonas_B zehnderi	100.0	933	958	d__Bacteria;p__Firmicutes_B;c__Syntrophomonadia;o__Syntrophomonadales;f__Syntrophomonadaceae;g__Syntrophomonas_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012729495.1	s__Syntrophomonas_B sp012729495	77.4114	106	958	d__Bacteria;p__Firmicutes_B;c__Syntrophomonadia;o__Syntrophomonadales;f__Syntrophomonadaceae;g__Syntrophomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840245.1	s__PHAA01 sp002840245	76.9519	65	958	d__Bacteria;p__Firmicutes_B;c__Syntrophomonadia;o__Syntrophomonadales;f__Syntrophomonadaceae;g__PHAA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002408445.1	s__UBA4851 sp002408445	76.5841	51	958	d__Bacteria;p__Firmicutes_B;c__Syntrophomonadia;o__Syntrophomonadales;f__Syntrophomonadaceae;g__UBA4851	95.0	99.19	98.86	0.79	0.72	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:52,210] [INFO] GTDB search result was written to GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:52,210] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:52,217] [INFO] DFAST_QC result json was written to GCF_000983115.1_Syntrophomonas_Zehnderi_OL-4_genomic.fna/dqc_result.json
[2024-01-24 12:22:52,218] [INFO] DFAST_QC completed!
[2024-01-24 12:22:52,218] [INFO] Total running time: 0h0m54s