[2024-01-24 11:35:11,806] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,808] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,808] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2f44a54-4b7e-4b46-ad2e-da2000223ffb/dqc_reference
[2024-01-24 11:35:13,044] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:13,045] [INFO] Task started: Prodigal
[2024-01-24 11:35:13,045] [INFO] Running command: gunzip -c /var/lib/cwl/stgd959245a-f05a-48bd-a97a-09e1c638b7b3/GCF_019132845.1_ASM1913284v1_genomic.fna.gz | prodigal -d GCF_019132845.1_ASM1913284v1_genomic.fna/cds.fna -a GCF_019132845.1_ASM1913284v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:22,216] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:22,216] [INFO] Task started: HMMsearch
[2024-01-24 11:35:22,216] [INFO] Running command: hmmsearch --tblout GCF_019132845.1_ASM1913284v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2f44a54-4b7e-4b46-ad2e-da2000223ffb/dqc_reference/reference_markers.hmm GCF_019132845.1_ASM1913284v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:22,490] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:22,491] [INFO] Found 6/6 markers.
[2024-01-24 11:35:22,522] [INFO] Query marker FASTA was written to GCF_019132845.1_ASM1913284v1_genomic.fna/markers.fasta
[2024-01-24 11:35:22,522] [INFO] Task started: Blastn
[2024-01-24 11:35:22,523] [INFO] Running command: blastn -query GCF_019132845.1_ASM1913284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2f44a54-4b7e-4b46-ad2e-da2000223ffb/dqc_reference/reference_markers.fasta -out GCF_019132845.1_ASM1913284v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:23,192] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:23,194] [INFO] Selected 18 target genomes.
[2024-01-24 11:35:23,195] [INFO] Target genome list was writen to GCF_019132845.1_ASM1913284v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:23,216] [INFO] Task started: fastANI
[2024-01-24 11:35:23,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgd959245a-f05a-48bd-a97a-09e1c638b7b3/GCF_019132845.1_ASM1913284v1_genomic.fna.gz --refList GCF_019132845.1_ASM1913284v1_genomic.fna/target_genomes.txt --output GCF_019132845.1_ASM1913284v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:38,332] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:38,333] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2f44a54-4b7e-4b46-ad2e-da2000223ffb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:38,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2f44a54-4b7e-4b46-ad2e-da2000223ffb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:38,341] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:38,341] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:38,341] [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
Advenella alkanexedens	strain=LAM0050	GCA_019132845.1	1481665	1481665	type	True	100.0	985	986	95	conclusive
Advenella faeciporci	strain=KCTC 23732	GCA_014652395.1	797535	797535	type	True	90.267	825	986	95	below_threshold
Advenella mandrilli	strain=WQ 585	GCA_016595155.1	2800330	2800330	type	True	87.22	819	986	95	below_threshold
Achromobacter mucicolens	strain=LMG 26685	GCA_902859725.1	1389922	1389922	type	True	78.2526	62	986	95	below_threshold
Pusillimonas minor	strain=YC-7-48	GCA_014237865.1	2697024	2697024	type	True	77.8669	86	986	95	below_threshold
Advenella mimigardefordensis	strain=DPN7	GCA_000521505.1	302406	302406	type	True	77.4088	171	986	95	below_threshold
Advenella incenata	strain=DSM 23814	GCA_004217095.1	267800	267800	type	True	77.3044	126	986	95	below_threshold
Advenella kashmirensis	strain=WT001	GCA_000219915.3	310575	310575	type	True	76.9077	145	986	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:38,343] [INFO] DFAST Taxonomy check result was written to GCF_019132845.1_ASM1913284v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:38,343] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:38,344] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:38,344] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2f44a54-4b7e-4b46-ad2e-da2000223ffb/dqc_reference/checkm_data
[2024-01-24 11:35:38,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:38,379] [INFO] Task started: CheckM
[2024-01-24 11:35:38,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019132845.1_ASM1913284v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019132845.1_ASM1913284v1_genomic.fna/checkm_input GCF_019132845.1_ASM1913284v1_genomic.fna/checkm_result
[2024-01-24 11:36:10,644] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:10,646] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:10,671] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:10,671] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:10,672] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019132845.1_ASM1913284v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:10,672] [INFO] Task started: Blastn
[2024-01-24 11:36:10,672] [INFO] Running command: blastn -query GCF_019132845.1_ASM1913284v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2f44a54-4b7e-4b46-ad2e-da2000223ffb/dqc_reference/reference_markers_gtdb.fasta -out GCF_019132845.1_ASM1913284v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:11,749] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:11,753] [INFO] Selected 13 target genomes.
[2024-01-24 11:36:11,753] [INFO] Target genome list was writen to GCF_019132845.1_ASM1913284v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:11,766] [INFO] Task started: fastANI
[2024-01-24 11:36:11,766] [INFO] Running command: fastANI --query /var/lib/cwl/stgd959245a-f05a-48bd-a97a-09e1c638b7b3/GCF_019132845.1_ASM1913284v1_genomic.fna.gz --refList GCF_019132845.1_ASM1913284v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019132845.1_ASM1913284v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:20,614] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:20,628] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:20,628] [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_019132845.1	s__Advenella alkanexedens	100.0	985	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	98.89	98.76	0.91	0.89	3	conclusive
GCF_014652395.1	s__Advenella faeciporci	90.267	825	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	97.16	97.10	0.89	0.86	3	-
GCF_016595155.1	s__Advenella sp016595155	87.22	819	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012735395.1	s__Advenella sp012735395	80.4576	444	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521505.1	s__Advenella mimigardefordensis	77.4085	171	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000506985.1	s__Advenella kashmirensis_A	77.2348	155	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002810445.1	s__Advenella sp002810445	77.1954	124	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Advenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857885.1	s__Pusillimonas_B sp009857885	76.7746	70	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012744285.1	s__Pusillimonas_A sp012744285	76.5259	77	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076515.1	s__Alcaligenes aquatilis	76.4227	72	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	98.23	96.52	0.93	0.89	8	-
GCF_002119685.1	s__Bordetella_C sp002119685	76.2431	55	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:20,630] [INFO] GTDB search result was written to GCF_019132845.1_ASM1913284v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:20,631] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:20,635] [INFO] DFAST_QC result json was written to GCF_019132845.1_ASM1913284v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:20,636] [INFO] DFAST_QC completed!
[2024-01-24 11:36:20,636] [INFO] Total running time: 0h1m9s