[2024-01-25 19:47:35,775] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:35,776] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:35,776] [INFO] DQC Reference Directory: /var/lib/cwl/stg2839f332-80d6-474f-9529-0302e5194f19/dqc_reference
[2024-01-25 19:47:36,947] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:36,947] [INFO] Task started: Prodigal
[2024-01-25 19:47:36,948] [INFO] Running command: gunzip -c /var/lib/cwl/stg16e61d01-5cbe-4afc-a178-418c171e9536/GCF_021129175.1_ASM2112917v1_genomic.fna.gz | prodigal -d GCF_021129175.1_ASM2112917v1_genomic.fna/cds.fna -a GCF_021129175.1_ASM2112917v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:49,753] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:49,754] [INFO] Task started: HMMsearch
[2024-01-25 19:47:49,754] [INFO] Running command: hmmsearch --tblout GCF_021129175.1_ASM2112917v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2839f332-80d6-474f-9529-0302e5194f19/dqc_reference/reference_markers.hmm GCF_021129175.1_ASM2112917v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:50,049] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:50,050] [INFO] Found 6/6 markers.
[2024-01-25 19:47:50,093] [INFO] Query marker FASTA was written to GCF_021129175.1_ASM2112917v1_genomic.fna/markers.fasta
[2024-01-25 19:47:50,093] [INFO] Task started: Blastn
[2024-01-25 19:47:50,094] [INFO] Running command: blastn -query GCF_021129175.1_ASM2112917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2839f332-80d6-474f-9529-0302e5194f19/dqc_reference/reference_markers.fasta -out GCF_021129175.1_ASM2112917v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:51,057] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:51,060] [INFO] Selected 16 target genomes.
[2024-01-25 19:47:51,061] [INFO] Target genome list was writen to GCF_021129175.1_ASM2112917v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:51,067] [INFO] Task started: fastANI
[2024-01-25 19:47:51,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg16e61d01-5cbe-4afc-a178-418c171e9536/GCF_021129175.1_ASM2112917v1_genomic.fna.gz --refList GCF_021129175.1_ASM2112917v1_genomic.fna/target_genomes.txt --output GCF_021129175.1_ASM2112917v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:48:07,282] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:07,282] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2839f332-80d6-474f-9529-0302e5194f19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:48:07,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2839f332-80d6-474f-9529-0302e5194f19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:48:07,292] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:48:07,292] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:48:07,292] [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
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	100.0	1571	1578	95	conclusive
Chromobacterium vaccinii	strain=MWU205	GCA_000971335.1	1108595	1108595	type	True	94.7019	1302	1578	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	91.0257	1267	1578	95	below_threshold
Chromobacterium violaceum	strain=NCTC9757	GCA_900446805.1	536	536	type	True	90.9609	1283	1578	95	below_threshold
Chromobacterium phragmitis	strain=IIBBL 112-1	GCA_003325475.1	2202141	2202141	type	True	89.0415	1215	1578	95	below_threshold
Chromobacterium subtsugae	strain=PRAA4-1	GCA_001676875.1	251747	251747	type	True	87.5147	1127	1578	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	86.4392	1044	1578	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	86.328	1028	1578	95	below_threshold
Chromobacterium sphagni	strain=IIBBL 14B-1	GCA_001855555.1	1903179	1903179	type	True	86.0462	1037	1578	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	83.3479	886	1578	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.4221	311	1578	95	below_threshold
Chitinilyticum aquatile	strain=DSM 21506	GCA_000430805.1	362520	362520	type	True	77.1775	243	1578	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	76.6885	257	1578	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.2888	126	1578	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:48:07,293] [INFO] DFAST Taxonomy check result was written to GCF_021129175.1_ASM2112917v1_genomic.fna/tc_result.tsv
[2024-01-25 19:48:07,294] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:48:07,294] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:48:07,294] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2839f332-80d6-474f-9529-0302e5194f19/dqc_reference/checkm_data
[2024-01-25 19:48:07,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:48:07,342] [INFO] Task started: CheckM
[2024-01-25 19:48:07,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021129175.1_ASM2112917v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021129175.1_ASM2112917v1_genomic.fna/checkm_input GCF_021129175.1_ASM2112917v1_genomic.fna/checkm_result
[2024-01-25 19:48:44,167] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:44,168] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:44,185] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:44,185] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:44,185] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021129175.1_ASM2112917v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:44,186] [INFO] Task started: Blastn
[2024-01-25 19:48:44,186] [INFO] Running command: blastn -query GCF_021129175.1_ASM2112917v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2839f332-80d6-474f-9529-0302e5194f19/dqc_reference/reference_markers_gtdb.fasta -out GCF_021129175.1_ASM2112917v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:45,835] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:45,839] [INFO] Selected 19 target genomes.
[2024-01-25 19:48:45,839] [INFO] Target genome list was writen to GCF_021129175.1_ASM2112917v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:45,857] [INFO] Task started: fastANI
[2024-01-25 19:48:45,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg16e61d01-5cbe-4afc-a178-418c171e9536/GCF_021129175.1_ASM2112917v1_genomic.fna.gz --refList GCF_021129175.1_ASM2112917v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021129175.1_ASM2112917v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:49:04,061] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:04,071] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:49:04,071] [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_011601295.1	s__Chromobacterium vaccinii_A	98.8232	1451	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	95.84	95.77	0.89	0.88	3	conclusive
GCF_000971335.1	s__Chromobacterium vaccinii	94.7175	1301	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.63	98.56	0.92	0.92	4	-
GCF_000007705.1	s__Chromobacterium violaceum	91.0353	1266	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.58	98.16	0.94	0.91	26	-
GCF_003325475.1	s__Chromobacterium phragmitis	89.0316	1216	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.00	99.00	0.92	0.92	2	-
GCF_002848345.1	s__Chromobacterium sp002848345	87.7267	1168	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001676875.1	s__Chromobacterium subtsugae	87.5085	1128	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	99.12	98.52	0.94	0.91	9	-
GCF_001855565.1	s__Chromobacterium amazonense	86.4854	1006	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.81	97.67	0.91	0.90	4	-
GCF_008275125.1	s__Chromobacterium paludis	86.4758	1019	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002924365.1	s__Chromobacterium sp002924365	86.4556	1042	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428945.1	s__Chromobacterium sp016428945	86.262	1017	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	97.99	97.99	0.89	0.89	2	-
GCF_900177275.1	s__Pseudogulbenkiania subflava	80.8683	620	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Pseudogulbenkiania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428465.1	s__Chitinimonas koreensis	78.1604	538	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013363835.1	s__Azonexus sp013363835	76.7917	170	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278265.1	s__Guyparkeria sp016278265	75.8077	83	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__Halothiobacillaceae;g__Guyparkeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001648175.1	s__Halotalea alkalilenta_A	75.5957	101	1578	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halotalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:49:04,072] [INFO] GTDB search result was written to GCF_021129175.1_ASM2112917v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:49:04,073] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:49:04,075] [INFO] DFAST_QC result json was written to GCF_021129175.1_ASM2112917v1_genomic.fna/dqc_result.json
[2024-01-25 19:49:04,075] [INFO] DFAST_QC completed!
[2024-01-25 19:49:04,076] [INFO] Total running time: 0h1m28s