[2024-01-25 18:57:20,448] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:57:20,450] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:57:20,450] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f426091-99d1-4f1c-a72f-63ed5076ba14/dqc_reference
[2024-01-25 18:57:21,599] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:57:21,600] [INFO] Task started: Prodigal
[2024-01-25 18:57:21,600] [INFO] Running command: gunzip -c /var/lib/cwl/stg883a3add-f024-4569-89f2-11a1f09245c0/GCF_026343855.1_ASM2634385v1_genomic.fna.gz | prodigal -d GCF_026343855.1_ASM2634385v1_genomic.fna/cds.fna -a GCF_026343855.1_ASM2634385v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:57:34,483] [INFO] Task succeeded: Prodigal
[2024-01-25 18:57:34,484] [INFO] Task started: HMMsearch
[2024-01-25 18:57:34,484] [INFO] Running command: hmmsearch --tblout GCF_026343855.1_ASM2634385v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f426091-99d1-4f1c-a72f-63ed5076ba14/dqc_reference/reference_markers.hmm GCF_026343855.1_ASM2634385v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:57:34,769] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:57:34,771] [INFO] Found 6/6 markers.
[2024-01-25 18:57:34,819] [INFO] Query marker FASTA was written to GCF_026343855.1_ASM2634385v1_genomic.fna/markers.fasta
[2024-01-25 18:57:34,819] [INFO] Task started: Blastn
[2024-01-25 18:57:34,819] [INFO] Running command: blastn -query GCF_026343855.1_ASM2634385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f426091-99d1-4f1c-a72f-63ed5076ba14/dqc_reference/reference_markers.fasta -out GCF_026343855.1_ASM2634385v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:35,938] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:35,941] [INFO] Selected 16 target genomes.
[2024-01-25 18:57:35,942] [INFO] Target genome list was writen to GCF_026343855.1_ASM2634385v1_genomic.fna/target_genomes.txt
[2024-01-25 18:57:35,957] [INFO] Task started: fastANI
[2024-01-25 18:57:35,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg883a3add-f024-4569-89f2-11a1f09245c0/GCF_026343855.1_ASM2634385v1_genomic.fna.gz --refList GCF_026343855.1_ASM2634385v1_genomic.fna/target_genomes.txt --output GCF_026343855.1_ASM2634385v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:57:53,963] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:53,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f426091-99d1-4f1c-a72f-63ed5076ba14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:57:53,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f426091-99d1-4f1c-a72f-63ed5076ba14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:57:53,974] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:57:53,975] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:57:53,975] [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
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	86.8793	1251	1713	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	86.5113	1243	1713	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	81.4503	948	1713	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	80.4959	806	1713	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	78.4278	456	1713	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	78.3857	616	1713	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.2458	534	1713	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	78.2361	508	1713	95	below_threshold
Aminobacter aminovorans	strain=NCTC10684	GCA_900445235.1	83263	83263	type	True	78.0599	454	1713	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	78.0218	453	1713	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	78.012	394	1713	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.6796	499	1713	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	77.5799	439	1713	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	77.4673	310	1713	95	below_threshold
Breoghania corrubedonensis	strain=DSM 23382	GCA_003053845.1	665038	665038	type	True	77.3701	329	1713	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	77.3233	377	1713	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:57:53,977] [INFO] DFAST Taxonomy check result was written to GCF_026343855.1_ASM2634385v1_genomic.fna/tc_result.tsv
[2024-01-25 18:57:53,977] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:57:53,978] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:57:53,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f426091-99d1-4f1c-a72f-63ed5076ba14/dqc_reference/checkm_data
[2024-01-25 18:57:53,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:57:54,028] [INFO] Task started: CheckM
[2024-01-25 18:57:54,028] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026343855.1_ASM2634385v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026343855.1_ASM2634385v1_genomic.fna/checkm_input GCF_026343855.1_ASM2634385v1_genomic.fna/checkm_result
[2024-01-25 18:58:33,501] [INFO] Task succeeded: CheckM
[2024-01-25 18:58:33,503] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:58:33,523] [INFO] ===== Completeness check finished =====
[2024-01-25 18:58:33,523] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:58:33,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026343855.1_ASM2634385v1_genomic.fna/markers.fasta)
[2024-01-25 18:58:33,524] [INFO] Task started: Blastn
[2024-01-25 18:58:33,524] [INFO] Running command: blastn -query GCF_026343855.1_ASM2634385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f426091-99d1-4f1c-a72f-63ed5076ba14/dqc_reference/reference_markers_gtdb.fasta -out GCF_026343855.1_ASM2634385v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:35,764] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:35,766] [INFO] Selected 7 target genomes.
[2024-01-25 18:58:35,767] [INFO] Target genome list was writen to GCF_026343855.1_ASM2634385v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:58:35,773] [INFO] Task started: fastANI
[2024-01-25 18:58:35,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg883a3add-f024-4569-89f2-11a1f09245c0/GCF_026343855.1_ASM2634385v1_genomic.fna.gz --refList GCF_026343855.1_ASM2634385v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026343855.1_ASM2634385v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:58:44,637] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:44,643] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:58:44,643] [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_017305815.1	s__Kaistia sp017305815	98.2322	998	1713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016629525.1	s__Kaistia sp016629525	87.2463	1256	1713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423225.1	s__Kaistia adipata	86.9074	1248	1713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380505.1	s__Kaistia granuli	86.5192	1242	1713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307955.1	s__Kaistia sp017307955	81.6985	884	1713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196455.1	s__Kaistia hirudinis	81.4258	953	1713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	96.80	96.80	0.96	0.96	2	-
GCF_014199915.1	s__Prosthecomicrobium pneumaticum	80.3604	787	1713	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:58:44,644] [INFO] GTDB search result was written to GCF_026343855.1_ASM2634385v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:58:44,645] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:58:44,648] [INFO] DFAST_QC result json was written to GCF_026343855.1_ASM2634385v1_genomic.fna/dqc_result.json
[2024-01-25 18:58:44,648] [INFO] DFAST_QC completed!
[2024-01-25 18:58:44,648] [INFO] Total running time: 0h1m24s