[2024-01-25 17:47:50,754] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:47:50,756] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:47:50,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg8cf81d4e-47a9-413a-a4da-06cef415ba8b/dqc_reference
[2024-01-25 17:47:51,927] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:47:51,927] [INFO] Task started: Prodigal
[2024-01-25 17:47:51,928] [INFO] Running command: gunzip -c /var/lib/cwl/stg9db448a6-11e7-43d5-9dab-12afb7bf3139/GCF_000300975.2_HFRIS_v2_genomic.fna.gz | prodigal -d GCF_000300975.2_HFRIS_v2_genomic.fna/cds.fna -a GCF_000300975.2_HFRIS_v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:07,175] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:07,175] [INFO] Task started: HMMsearch
[2024-01-25 17:48:07,175] [INFO] Running command: hmmsearch --tblout GCF_000300975.2_HFRIS_v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8cf81d4e-47a9-413a-a4da-06cef415ba8b/dqc_reference/reference_markers.hmm GCF_000300975.2_HFRIS_v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:07,460] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:07,461] [INFO] Found 6/6 markers.
[2024-01-25 17:48:07,504] [INFO] Query marker FASTA was written to GCF_000300975.2_HFRIS_v2_genomic.fna/markers.fasta
[2024-01-25 17:48:07,504] [INFO] Task started: Blastn
[2024-01-25 17:48:07,505] [INFO] Running command: blastn -query GCF_000300975.2_HFRIS_v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cf81d4e-47a9-413a-a4da-06cef415ba8b/dqc_reference/reference_markers.fasta -out GCF_000300975.2_HFRIS_v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:08,499] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:08,502] [INFO] Selected 12 target genomes.
[2024-01-25 17:48:08,503] [INFO] Target genome list was writen to GCF_000300975.2_HFRIS_v2_genomic.fna/target_genomes.txt
[2024-01-25 17:48:08,507] [INFO] Task started: fastANI
[2024-01-25 17:48:08,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg9db448a6-11e7-43d5-9dab-12afb7bf3139/GCF_000300975.2_HFRIS_v2_genomic.fna.gz --refList GCF_000300975.2_HFRIS_v2_genomic.fna/target_genomes.txt --output GCF_000300975.2_HFRIS_v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:24,033] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:24,033] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8cf81d4e-47a9-413a-a4da-06cef415ba8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:24,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8cf81d4e-47a9-413a-a4da-06cef415ba8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:24,047] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:48:24,047] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:48:24,048] [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
Herbaspirillum frisingense	strain=GSF30	GCA_000300975.2	92645	92645	type	True	100.0	1753	1757	95	conclusive
Herbaspirillum aquaticum	strain=IEH 4430	GCA_002213425.1	568783	568783	type	True	87.8035	1386	1757	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_001040945.1	964	964	type	True	87.6206	1327	1757	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_013180375.1	964	964	type	True	87.6141	1306	1757	95	below_threshold
Herbaspirillum huttiense subsp. putei	strain=IAM 15032	GCA_000478365.1	230311	863372	type	True	87.5677	1361	1757	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	87.4844	1306	1757	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=DSM 11543	GCA_003719195.1	80842	80842	type	True	87.4541	1318	1757	95	below_threshold
Herbaspirillum rubrisubalbicans	strain=NBRC 102523	GCA_001591225.1	80842	80842	type	True	87.4478	1284	1757	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	81.7423	744	1757	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	79.7384	486	1757	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	79.3211	553	1757	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	78.6146	379	1757	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:24,051] [INFO] DFAST Taxonomy check result was written to GCF_000300975.2_HFRIS_v2_genomic.fna/tc_result.tsv
[2024-01-25 17:48:24,051] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:24,051] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:24,051] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8cf81d4e-47a9-413a-a4da-06cef415ba8b/dqc_reference/checkm_data
[2024-01-25 17:48:24,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:48:24,113] [INFO] Task started: CheckM
[2024-01-25 17:48:24,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000300975.2_HFRIS_v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000300975.2_HFRIS_v2_genomic.fna/checkm_input GCF_000300975.2_HFRIS_v2_genomic.fna/checkm_result
[2024-01-25 17:49:13,241] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:13,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:13,257] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:13,257] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:13,258] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000300975.2_HFRIS_v2_genomic.fna/markers.fasta)
[2024-01-25 17:49:13,258] [INFO] Task started: Blastn
[2024-01-25 17:49:13,258] [INFO] Running command: blastn -query GCF_000300975.2_HFRIS_v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cf81d4e-47a9-413a-a4da-06cef415ba8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000300975.2_HFRIS_v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:15,315] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:15,317] [INFO] Selected 9 target genomes.
[2024-01-25 17:49:15,317] [INFO] Target genome list was writen to GCF_000300975.2_HFRIS_v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:15,324] [INFO] Task started: fastANI
[2024-01-25 17:49:15,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg9db448a6-11e7-43d5-9dab-12afb7bf3139/GCF_000300975.2_HFRIS_v2_genomic.fna.gz --refList GCF_000300975.2_HFRIS_v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000300975.2_HFRIS_v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:27,916] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:27,922] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:49:27,922] [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_000300975.2	s__Herbaspirillum frisingense	100.0	1753	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.59	97.42	0.92	0.89	5	conclusive
GCF_015767275.1	s__Herbaspirillum sp013426985	94.1842	1555	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016429215.1	s__Herbaspirillum sp016429215	87.9809	1315	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002213425.1	s__Herbaspirillum aquaticum	87.8101	1385	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.01	95.53	0.89	0.85	3	-
GCA_019233085.1	s__Herbaspirillum sp019233085	87.7481	995	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004367745.1	s__Herbaspirillum huttiense	87.6968	1350	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.45	97.06	0.87	0.86	14	-
GCF_001040945.1	s__Herbaspirillum seropedicae	87.6206	1328	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.53	96.09	0.94	0.89	6	-
GCF_003719195.1	s__Herbaspirillum rubrisubalbicans	87.4397	1321	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.49	96.58	0.87	0.83	8	-
GCF_000261365.1	s__Herbaspirillum sp000261365	87.4185	1332	1757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.65	98.65	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:49:27,923] [INFO] GTDB search result was written to GCF_000300975.2_HFRIS_v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:27,924] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:27,928] [INFO] DFAST_QC result json was written to GCF_000300975.2_HFRIS_v2_genomic.fna/dqc_result.json
[2024-01-25 17:49:27,928] [INFO] DFAST_QC completed!
[2024-01-25 17:49:27,928] [INFO] Total running time: 0h1m37s