[2024-01-24 15:18:47,938] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:47,940] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:47,941] [INFO] DQC Reference Directory: /var/lib/cwl/stge1a6976b-a746-4b4d-8590-6e24ed0019bf/dqc_reference
[2024-01-24 15:18:51,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:51,763] [INFO] Task started: Prodigal
[2024-01-24 15:18:51,764] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1cdfbd2-5210-4607-824d-b3f522043dc3/GCF_004766045.1_ASM476604v1_genomic.fna.gz | prodigal -d GCF_004766045.1_ASM476604v1_genomic.fna/cds.fna -a GCF_004766045.1_ASM476604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:05,168] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:05,169] [INFO] Task started: HMMsearch
[2024-01-24 15:19:05,169] [INFO] Running command: hmmsearch --tblout GCF_004766045.1_ASM476604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1a6976b-a746-4b4d-8590-6e24ed0019bf/dqc_reference/reference_markers.hmm GCF_004766045.1_ASM476604v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:05,652] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:05,654] [INFO] Found 6/6 markers.
[2024-01-24 15:19:05,707] [INFO] Query marker FASTA was written to GCF_004766045.1_ASM476604v1_genomic.fna/markers.fasta
[2024-01-24 15:19:05,707] [INFO] Task started: Blastn
[2024-01-24 15:19:05,707] [INFO] Running command: blastn -query GCF_004766045.1_ASM476604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1a6976b-a746-4b4d-8590-6e24ed0019bf/dqc_reference/reference_markers.fasta -out GCF_004766045.1_ASM476604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:06,280] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:06,285] [INFO] Selected 18 target genomes.
[2024-01-24 15:19:06,286] [INFO] Target genome list was writen to GCF_004766045.1_ASM476604v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:06,393] [INFO] Task started: fastANI
[2024-01-24 15:19:06,394] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1cdfbd2-5210-4607-824d-b3f522043dc3/GCF_004766045.1_ASM476604v1_genomic.fna.gz --refList GCF_004766045.1_ASM476604v1_genomic.fna/target_genomes.txt --output GCF_004766045.1_ASM476604v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:21,065] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:21,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1a6976b-a746-4b4d-8590-6e24ed0019bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:21,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1a6976b-a746-4b4d-8590-6e24ed0019bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:21,077] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:21,077] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:21,077] [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
Desulfosporosinus fructosivorans	strain=63.6F	GCA_004766045.1	2018669	2018669	type	True	100.0	2015	2019	95	conclusive
Desulfosporosinus lacus	strain=DSM 15449	GCA_900129935.1	329936	329936	type	True	80.5618	670	2019	95	below_threshold
Desulfosporosinus metallidurans	strain=OL	GCA_001936615.1	1888891	1888891	type	True	79.6908	602	2019	95	below_threshold
Desulfosporosinus hippei	strain=DSM 8344	GCA_900100785.1	569859	569859	type	True	78.7232	405	2019	95	below_threshold
Desulfosporosinus meridiei	strain=DSM 13257	GCA_000231385.3	79209	79209	type	True	78.6698	398	2019	95	below_threshold
Desulfosporosinus youngiae	strain=DSM 17734	GCA_000244895.1	339862	339862	type	True	78.3601	459	2019	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:21,079] [INFO] DFAST Taxonomy check result was written to GCF_004766045.1_ASM476604v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:21,080] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:21,080] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:21,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1a6976b-a746-4b4d-8590-6e24ed0019bf/dqc_reference/checkm_data
[2024-01-24 15:19:21,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:21,142] [INFO] Task started: CheckM
[2024-01-24 15:19:21,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004766045.1_ASM476604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004766045.1_ASM476604v1_genomic.fna/checkm_input GCF_004766045.1_ASM476604v1_genomic.fna/checkm_result
[2024-01-24 15:20:03,914] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:03,916] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.25%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 15:20:03,942] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:03,942] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:03,943] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004766045.1_ASM476604v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:03,943] [INFO] Task started: Blastn
[2024-01-24 15:20:03,943] [INFO] Running command: blastn -query GCF_004766045.1_ASM476604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1a6976b-a746-4b4d-8590-6e24ed0019bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_004766045.1_ASM476604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:04,701] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:04,705] [INFO] Selected 10 target genomes.
[2024-01-24 15:20:04,705] [INFO] Target genome list was writen to GCF_004766045.1_ASM476604v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:04,713] [INFO] Task started: fastANI
[2024-01-24 15:20:04,713] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1cdfbd2-5210-4607-824d-b3f522043dc3/GCF_004766045.1_ASM476604v1_genomic.fna.gz --refList GCF_004766045.1_ASM476604v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004766045.1_ASM476604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:12,620] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:12,627] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:12,628] [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_004766045.1	s__Desulfosporosinus fructosivorans	100.0	2015	2019	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003132105.1	s__Desulfosporosinus sp003132105	82.7668	440	2019	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001516045.1	s__Desulfosporosinus sp001516045	81.725	787	2019	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000770645.1	s__Desulfosporosinus sp000770645	81.4753	418	2019	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	99.63	99.30	0.85	0.80	5	-
GCA_002413075.1	s__Desulfosporosinus sp002413075	80.42	546	2019	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	99.37	99.29	0.84	0.83	3	-
GCA_002404215.1	s__Desulfosporosinus sp002404215	80.4074	483	2019	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001707885.1	s__Desulfosporosinus sp001707885	79.5224	633	2019	d__Bacteria;p__Firmicutes_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfosporosinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:12,629] [INFO] GTDB search result was written to GCF_004766045.1_ASM476604v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:12,630] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:12,633] [INFO] DFAST_QC result json was written to GCF_004766045.1_ASM476604v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:12,633] [INFO] DFAST_QC completed!
[2024-01-24 15:20:12,633] [INFO] Total running time: 0h1m25s