[2024-01-25 18:51:50,631] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:50,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:50,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg87bada62-89c0-4f15-9efc-a0c40a0da689/dqc_reference
[2024-01-25 18:51:51,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:51,763] [INFO] Task started: Prodigal
[2024-01-25 18:51:51,763] [INFO] Running command: gunzip -c /var/lib/cwl/stg2dc2bff7-9daf-4c59-a758-a794b7ee8438/GCF_015352985.1_ASM1535298v1_genomic.fna.gz | prodigal -d GCF_015352985.1_ASM1535298v1_genomic.fna/cds.fna -a GCF_015352985.1_ASM1535298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:13,876] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:13,876] [INFO] Task started: HMMsearch
[2024-01-25 18:52:13,876] [INFO] Running command: hmmsearch --tblout GCF_015352985.1_ASM1535298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87bada62-89c0-4f15-9efc-a0c40a0da689/dqc_reference/reference_markers.hmm GCF_015352985.1_ASM1535298v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:14,203] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:14,204] [INFO] Found 6/6 markers.
[2024-01-25 18:52:14,261] [INFO] Query marker FASTA was written to GCF_015352985.1_ASM1535298v1_genomic.fna/markers.fasta
[2024-01-25 18:52:14,261] [INFO] Task started: Blastn
[2024-01-25 18:52:14,261] [INFO] Running command: blastn -query GCF_015352985.1_ASM1535298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87bada62-89c0-4f15-9efc-a0c40a0da689/dqc_reference/reference_markers.fasta -out GCF_015352985.1_ASM1535298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:15,125] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:15,128] [INFO] Selected 13 target genomes.
[2024-01-25 18:52:15,129] [INFO] Target genome list was writen to GCF_015352985.1_ASM1535298v1_genomic.fna/target_genomes.txt
[2024-01-25 18:52:15,152] [INFO] Task started: fastANI
[2024-01-25 18:52:15,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dc2bff7-9daf-4c59-a758-a794b7ee8438/GCF_015352985.1_ASM1535298v1_genomic.fna.gz --refList GCF_015352985.1_ASM1535298v1_genomic.fna/target_genomes.txt --output GCF_015352985.1_ASM1535298v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:32,482] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:32,483] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87bada62-89c0-4f15-9efc-a0c40a0da689/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:32,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87bada62-89c0-4f15-9efc-a0c40a0da689/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:32,492] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:52:32,492] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:52:32,492] [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 malthae	strain=CC-AFH3	GCA_015352985.1	1260987	1260987	type	True	100.0	2626	2635	95	conclusive
Noviherbaspirillum aerium	strain=122213-3	GCA_008929045.1	2588497	2588497	type	True	86.7866	1642	2635	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	81.7334	828	2635	95	below_threshold
Noviherbaspirillum denitrificans	strain=TSA40	GCA_002211445.1	1968433	1968433	type	True	80.8649	814	2635	95	below_threshold
Noviherbaspirillum galbum	strain=17J57-3	GCA_010974945.1	2709383	2709383	type	True	80.7817	836	2635	95	below_threshold
Noviherbaspirillum humi	strain=U15	GCA_900188095.1	1688639	1688639	type	True	80.6615	779	2635	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	80.6201	853	2635	95	below_threshold
Noviherbaspirillum autotrophicum	strain=TSA66	GCA_000818395.1	709839	709839	type	True	80.1743	707	2635	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	80.1399	648	2635	95	below_threshold
Noviherbaspirillum pedocola	strain=DKR-6	GCA_016632335.1	2801341	2801341	type	True	79.4841	686	2635	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	79.4578	474	2635	95	below_threshold
Herbaspirillum rhizosphaerae	strain=UMS-37	GCA_001189965.1	346179	346179	type	True	79.0711	551	2635	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	78.9782	523	2635	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:32,494] [INFO] DFAST Taxonomy check result was written to GCF_015352985.1_ASM1535298v1_genomic.fna/tc_result.tsv
[2024-01-25 18:52:32,495] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:32,495] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:32,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87bada62-89c0-4f15-9efc-a0c40a0da689/dqc_reference/checkm_data
[2024-01-25 18:52:32,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:32,571] [INFO] Task started: CheckM
[2024-01-25 18:52:32,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015352985.1_ASM1535298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015352985.1_ASM1535298v1_genomic.fna/checkm_input GCF_015352985.1_ASM1535298v1_genomic.fna/checkm_result
[2024-01-25 18:53:37,731] [INFO] Task succeeded: CheckM
[2024-01-25 18:53:37,733] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:53:37,790] [INFO] ===== Completeness check finished =====
[2024-01-25 18:53:37,790] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:53:37,791] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015352985.1_ASM1535298v1_genomic.fna/markers.fasta)
[2024-01-25 18:53:37,791] [INFO] Task started: Blastn
[2024-01-25 18:53:37,791] [INFO] Running command: blastn -query GCF_015352985.1_ASM1535298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87bada62-89c0-4f15-9efc-a0c40a0da689/dqc_reference/reference_markers_gtdb.fasta -out GCF_015352985.1_ASM1535298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:39,475] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:39,478] [INFO] Selected 16 target genomes.
[2024-01-25 18:53:39,478] [INFO] Target genome list was writen to GCF_015352985.1_ASM1535298v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:53:39,498] [INFO] Task started: fastANI
[2024-01-25 18:53:39,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dc2bff7-9daf-4c59-a758-a794b7ee8438/GCF_015352985.1_ASM1535298v1_genomic.fna.gz --refList GCF_015352985.1_ASM1535298v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015352985.1_ASM1535298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:00,225] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:00,234] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:00,235] [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_015352985.1	s__Noviherbaspirillum malthae	100.0	2626	2635	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_008929045.1	s__Noviherbaspirillum aerium	86.7657	1645	2635	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	80.8416	818	2635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004570315.1	s__Noviherbaspirillum sp004570315	80.7847	643	2635	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	80.7756	837	2635	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	80.7504	725	2635	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	80.6782	778	2635	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	80.6098	856	2635	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	80.5686	901	2635	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	80.1545	710	2635	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	79.6719	701	2635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114705.1	s__Rugamonas rubra	79.1854	627	2635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	96.24	96.24	0.86	0.86	2	-
GCF_004563925.1	s__Herbaspirillum sp004563925	79.1839	541	2635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	100.00	99.99	0.98	0.95	4	-
GCF_001189965.1	s__Herbaspirillum rhizosphaerae	79.0823	552	2635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	75.2956	92	2635	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:54:00,236] [INFO] GTDB search result was written to GCF_015352985.1_ASM1535298v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:00,237] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:00,240] [INFO] DFAST_QC result json was written to GCF_015352985.1_ASM1535298v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:00,240] [INFO] DFAST_QC completed!
[2024-01-25 18:54:00,241] [INFO] Total running time: 0h2m10s