[2024-01-24 11:09:50,715] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:09:50,716] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:09:50,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ab0b35e-f61f-4353-a41b-d55d354defd3/dqc_reference
[2024-01-24 11:09:53,304] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:09:53,305] [INFO] Task started: Prodigal
[2024-01-24 11:09:53,305] [INFO] Running command: gunzip -c /var/lib/cwl/stg670c7902-10ff-4878-8089-9301863d53b7/GCF_002209535.1_ASM220953v1_genomic.fna.gz | prodigal -d GCF_002209535.1_ASM220953v1_genomic.fna/cds.fna -a GCF_002209535.1_ASM220953v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:10:16,456] [INFO] Task succeeded: Prodigal
[2024-01-24 11:10:16,457] [INFO] Task started: HMMsearch
[2024-01-24 11:10:16,457] [INFO] Running command: hmmsearch --tblout GCF_002209535.1_ASM220953v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ab0b35e-f61f-4353-a41b-d55d354defd3/dqc_reference/reference_markers.hmm GCF_002209535.1_ASM220953v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:10:16,790] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:10:16,792] [INFO] Found 6/6 markers.
[2024-01-24 11:10:16,849] [INFO] Query marker FASTA was written to GCF_002209535.1_ASM220953v1_genomic.fna/markers.fasta
[2024-01-24 11:10:16,850] [INFO] Task started: Blastn
[2024-01-24 11:10:16,850] [INFO] Running command: blastn -query GCF_002209535.1_ASM220953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ab0b35e-f61f-4353-a41b-d55d354defd3/dqc_reference/reference_markers.fasta -out GCF_002209535.1_ASM220953v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:17,834] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:17,839] [INFO] Selected 19 target genomes.
[2024-01-24 11:10:17,840] [INFO] Target genome list was writen to GCF_002209535.1_ASM220953v1_genomic.fna/target_genomes.txt
[2024-01-24 11:10:17,848] [INFO] Task started: fastANI
[2024-01-24 11:10:17,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg670c7902-10ff-4878-8089-9301863d53b7/GCF_002209535.1_ASM220953v1_genomic.fna.gz --refList GCF_002209535.1_ASM220953v1_genomic.fna/target_genomes.txt --output GCF_002209535.1_ASM220953v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:10:42,880] [INFO] Task succeeded: fastANI
[2024-01-24 11:10:42,881] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ab0b35e-f61f-4353-a41b-d55d354defd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:10:42,881] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ab0b35e-f61f-4353-a41b-d55d354defd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:10:42,906] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:10:42,906] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:10:42,906] [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
Achromobacter marplatensis	strain=B2	GCA_002209535.1	470868	470868	type	True	100.0	2263	2268	95	conclusive
Achromobacter marplatensis	strain=CECT 7342	GCA_003315095.1	470868	470868	type	True	99.9977	2255	2268	95	conclusive
Achromobacter marplatensis	strain=LMG 26219	GCA_902859635.1	470868	470868	type	True	99.9932	2254	2268	95	conclusive
Achromobacter pestifer	strain=LMG 3431	GCA_902859625.1	1353889	1353889	type	True	88.5898	1781	2268	95	below_threshold
Achromobacter kerstersii	strain=LMG 3441	GCA_902859595.1	1353890	1353890	type	True	87.7722	1731	2268	95	below_threshold
Achromobacter spanius	strain=LMG 5911	GCA_902859605.1	217203	217203	suspected-type	True	87.1472	1596	2268	95	below_threshold
Achromobacter piechaudii	strain=LMG 1873	GCA_902859685.1	72556	72556	type	True	86.8941	1619	2268	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	86.619	1468	2268	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	85.9437	1599	2268	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	85.6313	1587	2268	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	85.299	1557	2268	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	81.7985	856	2268	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.6791	344	2268	95	below_threshold
Ralstonia solanacearum	strain=K60	GCA_002251695.1	305	305	type	True	77.6027	380	2268	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	77.2796	295	2268	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	77.245	433	2268	95	below_threshold
Pseudoxanthomonas yeongjuensis	strain=DSM 18204	GCA_010093345.1	377616	377616	type	True	75.7719	155	2268	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:10:42,908] [INFO] DFAST Taxonomy check result was written to GCF_002209535.1_ASM220953v1_genomic.fna/tc_result.tsv
[2024-01-24 11:10:42,909] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:10:42,909] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:10:42,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ab0b35e-f61f-4353-a41b-d55d354defd3/dqc_reference/checkm_data
[2024-01-24 11:10:42,910] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:10:42,969] [INFO] Task started: CheckM
[2024-01-24 11:10:42,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002209535.1_ASM220953v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002209535.1_ASM220953v1_genomic.fna/checkm_input GCF_002209535.1_ASM220953v1_genomic.fna/checkm_result
[2024-01-24 11:11:48,919] [INFO] Task succeeded: CheckM
[2024-01-24 11:11:48,920] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:11:48,950] [INFO] ===== Completeness check finished =====
[2024-01-24 11:11:48,951] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:11:48,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002209535.1_ASM220953v1_genomic.fna/markers.fasta)
[2024-01-24 11:11:48,953] [INFO] Task started: Blastn
[2024-01-24 11:11:48,953] [INFO] Running command: blastn -query GCF_002209535.1_ASM220953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ab0b35e-f61f-4353-a41b-d55d354defd3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002209535.1_ASM220953v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:11:50,710] [INFO] Task succeeded: Blastn
[2024-01-24 11:11:50,725] [INFO] Selected 13 target genomes.
[2024-01-24 11:11:50,726] [INFO] Target genome list was writen to GCF_002209535.1_ASM220953v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:11:50,737] [INFO] Task started: fastANI
[2024-01-24 11:11:50,737] [INFO] Running command: fastANI --query /var/lib/cwl/stg670c7902-10ff-4878-8089-9301863d53b7/GCF_002209535.1_ASM220953v1_genomic.fna.gz --refList GCF_002209535.1_ASM220953v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002209535.1_ASM220953v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:12:10,358] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:10,370] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:12:10,370] [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_002209535.1	s__Achromobacter marplatensis	100.0	2263	2268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.15	97.44	0.96	0.90	4	conclusive
GCF_012928505.1	s__Achromobacter sp012928505	91.7163	1816	2268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014170335.1	s__Achromobacter sp014170335	91.1348	1819	2268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002975275.1	s__Achromobacter sp002975275	89.9459	1757	2268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859625.1	s__Achromobacter pestifer	88.6041	1779	2268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859595.1	s__Achromobacter kerstersii	87.7811	1729	2268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.61	98.61	0.95	0.95	2	-
GCF_013116765.2	s__Achromobacter deleyi_A	86.9286	1591	2268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003600685.1	s__Achromobacter spanius_B	86.8944	1565	2268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.56	98.20	0.94	0.92	5	-
GCF_003994415.1	s__Achromobacter spanius_C	86.7514	1568	2268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.60	98.60	0.94	0.94	2	-
GCF_000236785.1	s__Achromobacter arsenitoxydans	86.0873	1497	2268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002885955.2	s__Achromobacter pulmonis_A	86.0429	1415	2268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCA_002068855.1	s__UBA1934 sp002068855	76.02	80	2268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA1934	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093345.1	s__Pseudoxanthomonas_A yeongjuensis	75.743	157	2268	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:12:10,372] [INFO] GTDB search result was written to GCF_002209535.1_ASM220953v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:12:10,372] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:12:10,376] [INFO] DFAST_QC result json was written to GCF_002209535.1_ASM220953v1_genomic.fna/dqc_result.json
[2024-01-24 11:12:10,377] [INFO] DFAST_QC completed!
[2024-01-24 11:12:10,377] [INFO] Total running time: 0h2m20s