[2023-06-27 06:26:37,122] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:26:37,124] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:26:37,124] [INFO] DQC Reference Directory: /var/lib/cwl/stgd823fb17-5880-4bab-acec-ab89cb0b6f4e/dqc_reference
[2023-06-27 06:26:38,388] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:26:38,389] [INFO] Task started: Prodigal
[2023-06-27 06:26:38,389] [INFO] Running command: gunzip -c /var/lib/cwl/stg2dfd7814-c476-47ba-bb79-405f05cd4293/GCA_026225455.1_ASM2622545v1_genomic.fna.gz | prodigal -d GCA_026225455.1_ASM2622545v1_genomic.fna/cds.fna -a GCA_026225455.1_ASM2622545v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:26:48,416] [INFO] Task succeeded: Prodigal
[2023-06-27 06:26:48,417] [INFO] Task started: HMMsearch
[2023-06-27 06:26:48,417] [INFO] Running command: hmmsearch --tblout GCA_026225455.1_ASM2622545v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd823fb17-5880-4bab-acec-ab89cb0b6f4e/dqc_reference/reference_markers.hmm GCA_026225455.1_ASM2622545v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:26:48,675] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:26:48,676] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg2dfd7814-c476-47ba-bb79-405f05cd4293/GCA_026225455.1_ASM2622545v1_genomic.fna.gz]
[2023-06-27 06:26:48,719] [INFO] Query marker FASTA was written to GCA_026225455.1_ASM2622545v1_genomic.fna/markers.fasta
[2023-06-27 06:26:48,720] [INFO] Task started: Blastn
[2023-06-27 06:26:48,720] [INFO] Running command: blastn -query GCA_026225455.1_ASM2622545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd823fb17-5880-4bab-acec-ab89cb0b6f4e/dqc_reference/reference_markers.fasta -out GCA_026225455.1_ASM2622545v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:26:49,311] [INFO] Task succeeded: Blastn
[2023-06-27 06:26:49,316] [INFO] Selected 10 target genomes.
[2023-06-27 06:26:49,317] [INFO] Target genome list was writen to GCA_026225455.1_ASM2622545v1_genomic.fna/target_genomes.txt
[2023-06-27 06:26:49,323] [INFO] Task started: fastANI
[2023-06-27 06:26:49,323] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dfd7814-c476-47ba-bb79-405f05cd4293/GCA_026225455.1_ASM2622545v1_genomic.fna.gz --refList GCA_026225455.1_ASM2622545v1_genomic.fna/target_genomes.txt --output GCA_026225455.1_ASM2622545v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:27:00,608] [INFO] Task succeeded: fastANI
[2023-06-27 06:27:00,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd823fb17-5880-4bab-acec-ab89cb0b6f4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:27:00,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd823fb17-5880-4bab-acec-ab89cb0b6f4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:27:00,623] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:27:00,623] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 06:27:00,624] [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
Paraburkholderia domus	strain=LMG 31832	GCA_905220705.1	2793075	2793075	type	True	77.2275	220	1023	95	below_threshold
Paraburkholderia terricola	strain=LMG 20594	GCA_902833815.1	169427	169427	type	True	77.0896	249	1023	95	below_threshold
Paraburkholderia terricola	strain=LMG 20594	GCA_900142195.1	169427	169427	type	True	77.0622	248	1023	95	below_threshold
Paraburkholderia elongata	strain=5N	GCA_013177735.1	2675747	2675747	type	True	77.0508	225	1023	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	77.037	208	1023	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	77.0135	202	1023	95	below_threshold
Paraburkholderia nemoris	strain=LMG 31836	GCA_905221015.1	2793076	2793076	type	True	76.9364	253	1023	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	76.8857	201	1023	95	below_threshold
Paraburkholderia megapolitana	strain=LMG 23650	GCA_007556815.1	420953	420953	type	True	76.7751	218	1023	95	below_threshold
Paraburkholderia megapolitana	strain=LMG 23650	GCA_900113825.1	420953	420953	type	True	76.7548	220	1023	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 06:27:00,626] [INFO] DFAST Taxonomy check result was written to GCA_026225455.1_ASM2622545v1_genomic.fna/tc_result.tsv
[2023-06-27 06:27:00,627] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:27:00,627] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:27:00,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd823fb17-5880-4bab-acec-ab89cb0b6f4e/dqc_reference/checkm_data
[2023-06-27 06:27:00,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:27:00,666] [INFO] Task started: CheckM
[2023-06-27 06:27:00,667] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026225455.1_ASM2622545v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026225455.1_ASM2622545v1_genomic.fna/checkm_input GCA_026225455.1_ASM2622545v1_genomic.fna/checkm_result
[2023-06-27 06:27:33,568] [INFO] Task succeeded: CheckM
[2023-06-27 06:27:33,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:27:33,591] [INFO] ===== Completeness check finished =====
[2023-06-27 06:27:33,591] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:27:33,591] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026225455.1_ASM2622545v1_genomic.fna/markers.fasta)
[2023-06-27 06:27:33,592] [INFO] Task started: Blastn
[2023-06-27 06:27:33,592] [INFO] Running command: blastn -query GCA_026225455.1_ASM2622545v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd823fb17-5880-4bab-acec-ab89cb0b6f4e/dqc_reference/reference_markers_gtdb.fasta -out GCA_026225455.1_ASM2622545v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:27:34,320] [INFO] Task succeeded: Blastn
[2023-06-27 06:27:34,324] [INFO] Selected 10 target genomes.
[2023-06-27 06:27:34,325] [INFO] Target genome list was writen to GCA_026225455.1_ASM2622545v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:27:34,342] [INFO] Task started: fastANI
[2023-06-27 06:27:34,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dfd7814-c476-47ba-bb79-405f05cd4293/GCA_026225455.1_ASM2622545v1_genomic.fna.gz --refList GCA_026225455.1_ASM2622545v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026225455.1_ASM2622545v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:27:46,310] [INFO] Task succeeded: fastANI
[2023-06-27 06:27:46,326] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 06:27:46,326] [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_009765705.1	s__LMUX01 sp009765705	78.3447	318	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__LMUX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177725.1	s__Paraburkholderia susongensis	77.1164	216	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142195.1	s__Paraburkholderia terricola	77.0838	247	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.26	98.60	0.95	0.92	6	-
GCF_013177735.1	s__Paraburkholderia sp013177735	77.0508	225	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002278075.1	s__Paraburkholderia aromaticivorans	76.9905	253	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900019265.1	s__Paraburkholderia ribeironis	76.9744	232	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859875.1	s__Paraburkholderia solisilvae	76.9503	204	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011752995.1	s__Paraburkholderia sp011752995	76.9484	225	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.23	99.21	0.92	0.90	4	-
GCF_007556815.1	s__Paraburkholderia megapolitana	76.7751	218	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.99	99.99	1.00	1.00	2	-
GCA_000173575.1	s__Paraburkholderia sp000173575	76.759	205	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 06:27:46,345] [INFO] GTDB search result was written to GCA_026225455.1_ASM2622545v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:27:46,346] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:27:46,350] [INFO] DFAST_QC result json was written to GCA_026225455.1_ASM2622545v1_genomic.fna/dqc_result.json
[2023-06-27 06:27:46,351] [INFO] DFAST_QC completed!
[2023-06-27 06:27:46,351] [INFO] Total running time: 0h1m9s