[2024-01-24 13:01:24,313] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:24,315] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:24,315] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0e25cb0-c1de-42c6-a4f6-1e00484088af/dqc_reference
[2024-01-24 13:01:25,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:25,720] [INFO] Task started: Prodigal
[2024-01-24 13:01:25,721] [INFO] Running command: gunzip -c /var/lib/cwl/stg8469c98d-2f50-4389-961c-7581316878bd/GCF_008929045.1_ASM892904v1_genomic.fna.gz | prodigal -d GCF_008929045.1_ASM892904v1_genomic.fna/cds.fna -a GCF_008929045.1_ASM892904v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:47,456] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:47,456] [INFO] Task started: HMMsearch
[2024-01-24 13:01:47,457] [INFO] Running command: hmmsearch --tblout GCF_008929045.1_ASM892904v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0e25cb0-c1de-42c6-a4f6-1e00484088af/dqc_reference/reference_markers.hmm GCF_008929045.1_ASM892904v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:47,815] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:47,817] [INFO] Found 6/6 markers.
[2024-01-24 13:01:47,877] [INFO] Query marker FASTA was written to GCF_008929045.1_ASM892904v1_genomic.fna/markers.fasta
[2024-01-24 13:01:47,877] [INFO] Task started: Blastn
[2024-01-24 13:01:47,877] [INFO] Running command: blastn -query GCF_008929045.1_ASM892904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0e25cb0-c1de-42c6-a4f6-1e00484088af/dqc_reference/reference_markers.fasta -out GCF_008929045.1_ASM892904v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:48,652] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:48,654] [INFO] Selected 14 target genomes.
[2024-01-24 13:01:48,655] [INFO] Target genome list was writen to GCF_008929045.1_ASM892904v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:48,659] [INFO] Task started: fastANI
[2024-01-24 13:01:48,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg8469c98d-2f50-4389-961c-7581316878bd/GCF_008929045.1_ASM892904v1_genomic.fna.gz --refList GCF_008929045.1_ASM892904v1_genomic.fna/target_genomes.txt --output GCF_008929045.1_ASM892904v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:05,634] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:05,635] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0e25cb0-c1de-42c6-a4f6-1e00484088af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:05,635] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0e25cb0-c1de-42c6-a4f6-1e00484088af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:05,648] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:05,649] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:05,649] [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
Noviherbaspirillum aerium	strain=122213-3	GCA_008929045.1	2588497	2588497	type	True	100.0	2219	2222	95	conclusive
Noviherbaspirillum malthae	strain=CC-AFH3	GCA_015352985.1	1260987	1260987	type	True	86.7611	1630	2222	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	81.2884	796	2222	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	80.5945	828	2222	95	below_threshold
Noviherbaspirillum denitrificans	strain=TSA40	GCA_002211445.1	1968433	1968433	type	True	80.5872	733	2222	95	below_threshold
Noviherbaspirillum humi	strain=U15	GCA_900188095.1	1688639	1688639	type	True	80.5344	717	2222	95	below_threshold
Noviherbaspirillum galbum	strain=17J57-3	GCA_010974945.1	2709383	2709383	type	True	80.4749	793	2222	95	below_threshold
Noviherbaspirillum autotrophicum	strain=TSA66	GCA_000818395.1	709839	709839	type	True	80.2226	645	2222	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	80.1093	603	2222	95	below_threshold
Noviherbaspirillum massiliense	strain=JC206	GCA_000312045.1	1465823	1465823	type	True	79.5317	580	2222	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	79.268	436	2222	95	below_threshold
Herbaspirillum rhizosphaerae	strain=UMS-37	GCA_001189965.1	346179	346179	type	True	79.0414	476	2222	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	78.8057	482	2222	95	below_threshold
Janthinobacterium psychrotolerans	strain=S3-2	GCA_001677885.1	1747903	1747903	type	True	78.2845	467	2222	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:05,650] [INFO] DFAST Taxonomy check result was written to GCF_008929045.1_ASM892904v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:05,651] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:05,651] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:05,651] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0e25cb0-c1de-42c6-a4f6-1e00484088af/dqc_reference/checkm_data
[2024-01-24 13:02:05,653] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:05,717] [INFO] Task started: CheckM
[2024-01-24 13:02:05,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008929045.1_ASM892904v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008929045.1_ASM892904v1_genomic.fna/checkm_input GCF_008929045.1_ASM892904v1_genomic.fna/checkm_result
[2024-01-24 13:03:08,932] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:08,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:08,959] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:08,959] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:08,960] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008929045.1_ASM892904v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:08,960] [INFO] Task started: Blastn
[2024-01-24 13:03:08,960] [INFO] Running command: blastn -query GCF_008929045.1_ASM892904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0e25cb0-c1de-42c6-a4f6-1e00484088af/dqc_reference/reference_markers_gtdb.fasta -out GCF_008929045.1_ASM892904v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:10,240] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:10,244] [INFO] Selected 14 target genomes.
[2024-01-24 13:03:10,245] [INFO] Target genome list was writen to GCF_008929045.1_ASM892904v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:10,256] [INFO] Task started: fastANI
[2024-01-24 13:03:10,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg8469c98d-2f50-4389-961c-7581316878bd/GCF_008929045.1_ASM892904v1_genomic.fna.gz --refList GCF_008929045.1_ASM892904v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008929045.1_ASM892904v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:27,635] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:27,653] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:27,653] [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_008929045.1	s__Noviherbaspirillum aerium	100.0	2219	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015352985.1	s__Noviherbaspirillum malthae	86.7477	1632	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211445.1	s__Noviherbaspirillum denitrificans	80.6357	728	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003591035.1	s__Noviherbaspirillum sp003591035	80.5879	828	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188095.1	s__Noviherbaspirillum humi	80.5254	720	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007874125.1	s__Noviherbaspirillum sp007874125	80.5043	680	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428545.1	s__Noviherbaspirillum sp001428545	80.499	842	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010974945.1	s__Noviherbaspirillum galbum	80.4539	795	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000818395.1	s__Noviherbaspirillum autotrophicum	80.2442	643	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804275.1	s__Noviherbaspirillum sp004804275	79.7991	649	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312045.1	s__Noviherbaspirillum massiliense	79.5406	579	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003537575.1	s__Paucimonas sp003537575	79.3066	454	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004563925.1	s__Herbaspirillum sp004563925	78.9611	502	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	100.00	99.99	0.98	0.95	4	-
GCF_000221045.1	s__Collimonas fungivorans_A	78.9113	469	2222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	95.12	95.12	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:27,655] [INFO] GTDB search result was written to GCF_008929045.1_ASM892904v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:27,655] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:27,658] [INFO] DFAST_QC result json was written to GCF_008929045.1_ASM892904v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:27,659] [INFO] DFAST_QC completed!
[2024-01-24 13:03:27,659] [INFO] Total running time: 0h2m3s