[2024-01-24 13:01:24,602] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:24,604] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:24,604] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c40cbda-adc6-4f4b-ab6e-4ef7a8dcd14b/dqc_reference
[2024-01-24 13:01:25,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:25,944] [INFO] Task started: Prodigal
[2024-01-24 13:01:25,944] [INFO] Running command: gunzip -c /var/lib/cwl/stga9f798ad-3efe-4a85-bc2e-c029cd6a267a/GCF_002902945.1_ASM290294v1_genomic.fna.gz | prodigal -d GCF_002902945.1_ASM290294v1_genomic.fna/cds.fna -a GCF_002902945.1_ASM290294v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:55,068] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:55,069] [INFO] Task started: HMMsearch
[2024-01-24 13:01:55,069] [INFO] Running command: hmmsearch --tblout GCF_002902945.1_ASM290294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c40cbda-adc6-4f4b-ab6e-4ef7a8dcd14b/dqc_reference/reference_markers.hmm GCF_002902945.1_ASM290294v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:55,460] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:55,462] [INFO] Found 6/6 markers.
[2024-01-24 13:01:55,535] [INFO] Query marker FASTA was written to GCF_002902945.1_ASM290294v1_genomic.fna/markers.fasta
[2024-01-24 13:01:55,536] [INFO] Task started: Blastn
[2024-01-24 13:01:55,536] [INFO] Running command: blastn -query GCF_002902945.1_ASM290294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c40cbda-adc6-4f4b-ab6e-4ef7a8dcd14b/dqc_reference/reference_markers.fasta -out GCF_002902945.1_ASM290294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:56,455] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:56,459] [INFO] Selected 12 target genomes.
[2024-01-24 13:01:56,460] [INFO] Target genome list was writen to GCF_002902945.1_ASM290294v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:56,465] [INFO] Task started: fastANI
[2024-01-24 13:01:56,465] [INFO] Running command: fastANI --query /var/lib/cwl/stga9f798ad-3efe-4a85-bc2e-c029cd6a267a/GCF_002902945.1_ASM290294v1_genomic.fna.gz --refList GCF_002902945.1_ASM290294v1_genomic.fna/target_genomes.txt --output GCF_002902945.1_ASM290294v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:34,071] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:34,072] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c40cbda-adc6-4f4b-ab6e-4ef7a8dcd14b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:34,073] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c40cbda-adc6-4f4b-ab6e-4ef7a8dcd14b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:34,085] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:02:34,085] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:34,086] [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 caribensis	strain=DSM 13236	GCA_002902945.1	75105	75105	type	True	100.0	3008	3009	95	conclusive
Paraburkholderia caribensis	strain=MWAP64	GCA_001449005.1	75105	75105	type	True	99.9966	3008	3009	95	conclusive
Paraburkholderia caribensis	strain=LMG 18531	GCA_902833515.1	75105	75105	type	True	99.9798	2957	3009	95	conclusive
Paraburkholderia terrae	strain=DSM 17804	GCA_002902925.1	311230	311230	type	True	92.9154	2363	3009	95	below_threshold
Paraburkholderia terrae	strain=NBRC 100964	GCA_000739835.1	311230	311230	type	True	92.8905	2247	3009	95	below_threshold
Paraburkholderia hospita	strain=LMG 20598	GCA_902833685.1	169430	169430	type	True	92.8795	2347	3009	95	below_threshold
Paraburkholderia hospita	strain=DSM 17164	GCA_002902965.1	169430	169430	type	True	92.8417	2369	3009	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	87.8816	2206	3009	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	82.4932	1296	3009	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	82.4851	1201	3009	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	82.0138	1274	3009	95	below_threshold
Paraburkholderia kirstenboschensis	strain=KB15	GCA_001636975.1	1245436	1245436	type	True	81.5379	1116	3009	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:34,088] [INFO] DFAST Taxonomy check result was written to GCF_002902945.1_ASM290294v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:34,089] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:34,089] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:34,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c40cbda-adc6-4f4b-ab6e-4ef7a8dcd14b/dqc_reference/checkm_data
[2024-01-24 13:02:34,091] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:34,176] [INFO] Task started: CheckM
[2024-01-24 13:02:34,176] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902945.1_ASM290294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902945.1_ASM290294v1_genomic.fna/checkm_input GCF_002902945.1_ASM290294v1_genomic.fna/checkm_result
[2024-01-24 13:04:01,706] [INFO] Task succeeded: CheckM
[2024-01-24 13:04:01,707] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:04:01,731] [INFO] ===== Completeness check finished =====
[2024-01-24 13:04:01,731] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:04:01,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902945.1_ASM290294v1_genomic.fna/markers.fasta)
[2024-01-24 13:04:01,732] [INFO] Task started: Blastn
[2024-01-24 13:04:01,732] [INFO] Running command: blastn -query GCF_002902945.1_ASM290294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c40cbda-adc6-4f4b-ab6e-4ef7a8dcd14b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902945.1_ASM290294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:04:03,408] [INFO] Task succeeded: Blastn
[2024-01-24 13:04:03,412] [INFO] Selected 6 target genomes.
[2024-01-24 13:04:03,412] [INFO] Target genome list was writen to GCF_002902945.1_ASM290294v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:04:03,417] [INFO] Task started: fastANI
[2024-01-24 13:04:03,418] [INFO] Running command: fastANI --query /var/lib/cwl/stga9f798ad-3efe-4a85-bc2e-c029cd6a267a/GCF_002902945.1_ASM290294v1_genomic.fna.gz --refList GCF_002902945.1_ASM290294v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902945.1_ASM290294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:04:31,208] [INFO] Task succeeded: fastANI
[2024-01-24 13:04:31,220] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:04:31,220] [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_002902945.1	s__Paraburkholderia caribensis	100.0	3008	3009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	98.86	96.01	0.91	0.80	9	conclusive
GCF_002902925.1	s__Paraburkholderia terrae	92.9075	2364	3009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.2599	98.84	97.67	0.92	0.83	3	-
GCF_002902965.1	s__Paraburkholderia hospita	92.8154	2372	3009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.2599	98.45	97.70	0.87	0.82	14	-
GCF_013426915.1	s__Paraburkholderia sp013426915	92.551	2313	3009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013426895.1	s__Paraburkholderia sp013426895	92.0586	2361	3009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017104715.1	s__Paraburkholderia sp017104715	88.5471	2207	3009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:04:31,222] [INFO] GTDB search result was written to GCF_002902945.1_ASM290294v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:04:31,223] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:04:31,226] [INFO] DFAST_QC result json was written to GCF_002902945.1_ASM290294v1_genomic.fna/dqc_result.json
[2024-01-24 13:04:31,226] [INFO] DFAST_QC completed!
[2024-01-24 13:04:31,226] [INFO] Total running time: 0h3m7s