[2024-01-24 13:49:55,323] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:55,325] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:55,325] [INFO] DQC Reference Directory: /var/lib/cwl/stg43d8e59e-a02f-4057-9226-718cdf1a2dce/dqc_reference
[2024-01-24 13:49:56,681] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:56,682] [INFO] Task started: Prodigal
[2024-01-24 13:49:56,682] [INFO] Running command: gunzip -c /var/lib/cwl/stg5320ab66-3878-4dd5-b02a-e92151d7e2d5/GCF_010974945.1_ASM1097494v1_genomic.fna.gz | prodigal -d GCF_010974945.1_ASM1097494v1_genomic.fna/cds.fna -a GCF_010974945.1_ASM1097494v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:16,610] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:16,611] [INFO] Task started: HMMsearch
[2024-01-24 13:50:16,611] [INFO] Running command: hmmsearch --tblout GCF_010974945.1_ASM1097494v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43d8e59e-a02f-4057-9226-718cdf1a2dce/dqc_reference/reference_markers.hmm GCF_010974945.1_ASM1097494v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:16,921] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:16,923] [INFO] Found 6/6 markers.
[2024-01-24 13:50:16,973] [INFO] Query marker FASTA was written to GCF_010974945.1_ASM1097494v1_genomic.fna/markers.fasta
[2024-01-24 13:50:16,973] [INFO] Task started: Blastn
[2024-01-24 13:50:16,973] [INFO] Running command: blastn -query GCF_010974945.1_ASM1097494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43d8e59e-a02f-4057-9226-718cdf1a2dce/dqc_reference/reference_markers.fasta -out GCF_010974945.1_ASM1097494v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:18,015] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:18,018] [INFO] Selected 16 target genomes.
[2024-01-24 13:50:18,019] [INFO] Target genome list was writen to GCF_010974945.1_ASM1097494v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:18,025] [INFO] Task started: fastANI
[2024-01-24 13:50:18,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg5320ab66-3878-4dd5-b02a-e92151d7e2d5/GCF_010974945.1_ASM1097494v1_genomic.fna.gz --refList GCF_010974945.1_ASM1097494v1_genomic.fna/target_genomes.txt --output GCF_010974945.1_ASM1097494v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:35,757] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:35,758] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43d8e59e-a02f-4057-9226-718cdf1a2dce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:35,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43d8e59e-a02f-4057-9226-718cdf1a2dce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:35,776] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:35,776] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:35,776] [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 galbum	strain=17J57-3	GCA_010974945.1	2709383	2709383	type	True	100.0	1993	1997	95	conclusive
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	81.4024	732	1997	95	below_threshold
Noviherbaspirillum humi	strain=U15	GCA_900188095.1	1688639	1688639	type	True	81.018	744	1997	95	below_threshold
Noviherbaspirillum malthae	strain=CC-AFH3	GCA_015352985.1	1260987	1260987	type	True	80.7194	840	1997	95	below_threshold
Noviherbaspirillum denitrificans	strain=TSA40	GCA_002211445.1	1968433	1968433	type	True	80.5049	747	1997	95	below_threshold
Noviherbaspirillum aerium	strain=122213-3	GCA_008929045.1	2588497	2588497	type	True	80.4826	791	1997	95	below_threshold
Herbaspirillum robiniae	strain=HZ10	GCA_002213415.1	2014887	2014887	type	True	80.1392	607	1997	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_001040945.1	964	964	type	True	79.7376	523	1997	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_013180375.1	964	964	type	True	79.6539	515	1997	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	79.5497	530	1997	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	79.5294	452	1997	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	79.487	563	1997	95	below_threshold
Herbaspirillum huttiense subsp. putei	strain=IAM 15032	GCA_000478365.1	230311	863372	type	True	79.3376	529	1997	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	79.2336	453	1997	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	79.1863	581	1997	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	79.0987	604	1997	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:35,778] [INFO] DFAST Taxonomy check result was written to GCF_010974945.1_ASM1097494v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:35,778] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:35,778] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:35,778] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43d8e59e-a02f-4057-9226-718cdf1a2dce/dqc_reference/checkm_data
[2024-01-24 13:50:35,779] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:35,836] [INFO] Task started: CheckM
[2024-01-24 13:50:35,837] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010974945.1_ASM1097494v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010974945.1_ASM1097494v1_genomic.fna/checkm_input GCF_010974945.1_ASM1097494v1_genomic.fna/checkm_result
[2024-01-24 13:51:32,039] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:32,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:32,063] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:32,063] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:32,063] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010974945.1_ASM1097494v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:32,064] [INFO] Task started: Blastn
[2024-01-24 13:51:32,064] [INFO] Running command: blastn -query GCF_010974945.1_ASM1097494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43d8e59e-a02f-4057-9226-718cdf1a2dce/dqc_reference/reference_markers_gtdb.fasta -out GCF_010974945.1_ASM1097494v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:34,125] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:34,130] [INFO] Selected 18 target genomes.
[2024-01-24 13:51:34,131] [INFO] Target genome list was writen to GCF_010974945.1_ASM1097494v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:34,190] [INFO] Task started: fastANI
[2024-01-24 13:51:34,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg5320ab66-3878-4dd5-b02a-e92151d7e2d5/GCF_010974945.1_ASM1097494v1_genomic.fna.gz --refList GCF_010974945.1_ASM1097494v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010974945.1_ASM1097494v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:55,241] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:55,269] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:55,269] [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_010974945.1	s__Noviherbaspirillum galbum	100.0	1993	1997	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004570315.1	s__Noviherbaspirillum sp004570315	81.0984	692	1997	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	81.0149	743	1997	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015352985.1	s__Noviherbaspirillum malthae	80.6873	843	1997	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	80.5618	716	1997	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	80.5092	746	1997	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008929045.1	s__Noviherbaspirillum aerium	80.4904	790	1997	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744395.1	s__Herbaspirillum sp017744395	80.4127	559	1997	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002213415.1	s__Herbaspirillum robiniae	80.1389	607	1997	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.55	98.54	0.93	0.92	3	-
GCF_017814915.1	s__Herbaspirillum sp017814915	80.1196	562	1997	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715495.1	s__Herbaspirillum sp006715495	80.1143	536	1997	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	99.71	99.15	0.99	0.96	4	-
GCA_009914615.1	s__Herbaspirillum frisingense_B	80.0952	506	1997	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000818395.1	s__Noviherbaspirillum autotrophicum	79.982	649	1997	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015352955.1	s__Noviherbaspirillum_A soli	79.9808	665	1997	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001040945.1	s__Herbaspirillum seropedicae	79.7387	522	1997	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.53	96.09	0.94	0.89	6	-
GCF_003590875.1	s__Noviherbaspirillum sp003590875	79.5184	558	1997	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003537575.1	s__Paucimonas sp003537575	79.4874	471	1997	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004367745.1	s__Herbaspirillum huttiense	79.3698	530	1997	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.45	97.06	0.87	0.86	14	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:55,271] [INFO] GTDB search result was written to GCF_010974945.1_ASM1097494v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:55,272] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:55,275] [INFO] DFAST_QC result json was written to GCF_010974945.1_ASM1097494v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:55,276] [INFO] DFAST_QC completed!
[2024-01-24 13:51:55,276] [INFO] Total running time: 0h1m60s