[2024-01-24 11:51:37,442] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:37,444] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:37,444] [INFO] DQC Reference Directory: /var/lib/cwl/stgf870f395-6f81-4908-a255-a5aa679852fd/dqc_reference
[2024-01-24 11:51:38,694] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:38,695] [INFO] Task started: Prodigal
[2024-01-24 11:51:38,695] [INFO] Running command: gunzip -c /var/lib/cwl/stg375f34f3-6b50-47dd-a350-c46c26b6ee5c/GCF_902859635.1_LMG_26219_genomic.fna.gz | prodigal -d GCF_902859635.1_LMG_26219_genomic.fna/cds.fna -a GCF_902859635.1_LMG_26219_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:01,999] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:02,000] [INFO] Task started: HMMsearch
[2024-01-24 11:52:02,000] [INFO] Running command: hmmsearch --tblout GCF_902859635.1_LMG_26219_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf870f395-6f81-4908-a255-a5aa679852fd/dqc_reference/reference_markers.hmm GCF_902859635.1_LMG_26219_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:02,377] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:02,379] [INFO] Found 6/6 markers.
[2024-01-24 11:52:02,435] [INFO] Query marker FASTA was written to GCF_902859635.1_LMG_26219_genomic.fna/markers.fasta
[2024-01-24 11:52:02,436] [INFO] Task started: Blastn
[2024-01-24 11:52:02,436] [INFO] Running command: blastn -query GCF_902859635.1_LMG_26219_genomic.fna/markers.fasta -db /var/lib/cwl/stgf870f395-6f81-4908-a255-a5aa679852fd/dqc_reference/reference_markers.fasta -out GCF_902859635.1_LMG_26219_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:03,405] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:03,410] [INFO] Selected 19 target genomes.
[2024-01-24 11:52:03,410] [INFO] Target genome list was writen to GCF_902859635.1_LMG_26219_genomic.fna/target_genomes.txt
[2024-01-24 11:52:03,418] [INFO] Task started: fastANI
[2024-01-24 11:52:03,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg375f34f3-6b50-47dd-a350-c46c26b6ee5c/GCF_902859635.1_LMG_26219_genomic.fna.gz --refList GCF_902859635.1_LMG_26219_genomic.fna/target_genomes.txt --output GCF_902859635.1_LMG_26219_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:29,159] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:29,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf870f395-6f81-4908-a255-a5aa679852fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:29,160] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf870f395-6f81-4908-a255-a5aa679852fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:29,175] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:52:29,175] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:29,176] [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=LMG 26219	GCA_902859635.1	470868	470868	type	True	100.0	2261	2268	95	conclusive
Achromobacter marplatensis	strain=CECT 7342	GCA_003315095.1	470868	470868	type	True	99.9982	2259	2268	95	conclusive
Achromobacter marplatensis	strain=B2	GCA_002209535.1	470868	470868	type	True	99.9962	2260	2268	95	conclusive
Achromobacter pestifer	strain=LMG 3431	GCA_902859625.1	1353889	1353889	type	True	88.6238	1789	2268	95	below_threshold
Achromobacter kerstersii	strain=LMG 3441	GCA_902859595.1	1353890	1353890	type	True	87.8387	1723	2268	95	below_threshold
Achromobacter spanius	strain=LMG 5911	GCA_902859605.1	217203	217203	suspected-type	True	87.1801	1606	2268	95	below_threshold
Achromobacter piechaudii	strain=LMG 1873	GCA_902859685.1	72556	72556	type	True	86.9055	1618	2268	95	below_threshold
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	86.6135	1472	2268	95	below_threshold
Achromobacter deleyi	strain=LMG 3458	GCA_902859705.1	1353891	1353891	type	True	86.059	1578	2268	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	85.6253	1580	2268	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	85.2933	1558	2268	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	81.8782	852	2268	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.9468	322	2268	95	below_threshold
Ralstonia solanacearum	strain=K60	GCA_002251695.1	305	305	type	True	77.716	385	2268	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	77.3367	303	2268	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	77.1767	448	2268	95	below_threshold
Pseudoxanthomonas yeongjuensis	strain=DSM 18204	GCA_010093345.1	377616	377616	type	True	75.7937	154	2268	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:29,178] [INFO] DFAST Taxonomy check result was written to GCF_902859635.1_LMG_26219_genomic.fna/tc_result.tsv
[2024-01-24 11:52:29,179] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:29,179] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:29,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf870f395-6f81-4908-a255-a5aa679852fd/dqc_reference/checkm_data
[2024-01-24 11:52:29,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:29,243] [INFO] Task started: CheckM
[2024-01-24 11:52:29,243] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902859635.1_LMG_26219_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902859635.1_LMG_26219_genomic.fna/checkm_input GCF_902859635.1_LMG_26219_genomic.fna/checkm_result
[2024-01-24 11:53:33,852] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:33,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:33,878] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:33,879] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:33,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902859635.1_LMG_26219_genomic.fna/markers.fasta)
[2024-01-24 11:53:33,880] [INFO] Task started: Blastn
[2024-01-24 11:53:33,880] [INFO] Running command: blastn -query GCF_902859635.1_LMG_26219_genomic.fna/markers.fasta -db /var/lib/cwl/stgf870f395-6f81-4908-a255-a5aa679852fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_902859635.1_LMG_26219_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:35,594] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:35,598] [INFO] Selected 13 target genomes.
[2024-01-24 11:53:35,599] [INFO] Target genome list was writen to GCF_902859635.1_LMG_26219_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:35,612] [INFO] Task started: fastANI
[2024-01-24 11:53:35,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg375f34f3-6b50-47dd-a350-c46c26b6ee5c/GCF_902859635.1_LMG_26219_genomic.fna.gz --refList GCF_902859635.1_LMG_26219_genomic.fna/target_genomes_gtdb.txt --output GCF_902859635.1_LMG_26219_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:54,992] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:55,009] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:55,009] [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	99.9962	2260	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	91.7483	1815	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	91.1649	1827	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	89.9216	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	88.6198	1790	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	87.8167	1726	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	86.9376	1599	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	86.8613	1574	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	86.7107	1581	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	86.1149	1487	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	86.0272	1422	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	75.9954	76	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	75.7705	155	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 11:53:55,011] [INFO] GTDB search result was written to GCF_902859635.1_LMG_26219_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:55,011] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:55,016] [INFO] DFAST_QC result json was written to GCF_902859635.1_LMG_26219_genomic.fna/dqc_result.json
[2024-01-24 11:53:55,017] [INFO] DFAST_QC completed!
[2024-01-24 11:53:55,017] [INFO] Total running time: 0h2m18s