[2024-01-24 12:36:23,394] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:23,398] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:23,398] [INFO] DQC Reference Directory: /var/lib/cwl/stgf12b771a-ff46-48d7-abe5-6e50bf900138/dqc_reference
[2024-01-24 12:36:24,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:24,709] [INFO] Task started: Prodigal
[2024-01-24 12:36:24,710] [INFO] Running command: gunzip -c /var/lib/cwl/stg60d44f16-109e-4d0d-a64c-c3bb43609e90/GCF_007993815.1_ASM799381v1_genomic.fna.gz | prodigal -d GCF_007993815.1_ASM799381v1_genomic.fna/cds.fna -a GCF_007993815.1_ASM799381v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:43,329] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:43,330] [INFO] Task started: HMMsearch
[2024-01-24 12:36:43,331] [INFO] Running command: hmmsearch --tblout GCF_007993815.1_ASM799381v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf12b771a-ff46-48d7-abe5-6e50bf900138/dqc_reference/reference_markers.hmm GCF_007993815.1_ASM799381v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:43,630] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:43,632] [INFO] Found 6/6 markers.
[2024-01-24 12:36:43,672] [INFO] Query marker FASTA was written to GCF_007993815.1_ASM799381v1_genomic.fna/markers.fasta
[2024-01-24 12:36:43,673] [INFO] Task started: Blastn
[2024-01-24 12:36:43,673] [INFO] Running command: blastn -query GCF_007993815.1_ASM799381v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf12b771a-ff46-48d7-abe5-6e50bf900138/dqc_reference/reference_markers.fasta -out GCF_007993815.1_ASM799381v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:44,596] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:44,599] [INFO] Selected 13 target genomes.
[2024-01-24 12:36:44,600] [INFO] Target genome list was writen to GCF_007993815.1_ASM799381v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:44,606] [INFO] Task started: fastANI
[2024-01-24 12:36:44,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg60d44f16-109e-4d0d-a64c-c3bb43609e90/GCF_007993815.1_ASM799381v1_genomic.fna.gz --refList GCF_007993815.1_ASM799381v1_genomic.fna/target_genomes.txt --output GCF_007993815.1_ASM799381v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:59,904] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:59,905] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf12b771a-ff46-48d7-abe5-6e50bf900138/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:59,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf12b771a-ff46-48d7-abe5-6e50bf900138/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:59,919] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:36:59,919] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:36:59,919] [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
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	100.0	1663	1665	95	conclusive
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	88.5564	1326	1665	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	88.2524	1282	1665	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	86.9117	1299	1665	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	84.6414	844	1665	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	84.2657	913	1665	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	84.1822	976	1665	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	81.6404	878	1665	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	81.1734	809	1665	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.7652	646	1665	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.4559	554	1665	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.4525	646	1665	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.419	651	1665	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:59,921] [INFO] DFAST Taxonomy check result was written to GCF_007993815.1_ASM799381v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:59,922] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:59,922] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:59,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf12b771a-ff46-48d7-abe5-6e50bf900138/dqc_reference/checkm_data
[2024-01-24 12:36:59,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:59,970] [INFO] Task started: CheckM
[2024-01-24 12:36:59,971] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007993815.1_ASM799381v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007993815.1_ASM799381v1_genomic.fna/checkm_input GCF_007993815.1_ASM799381v1_genomic.fna/checkm_result
[2024-01-24 12:38:04,376] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:04,378] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:04,403] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:04,403] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:04,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007993815.1_ASM799381v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:04,404] [INFO] Task started: Blastn
[2024-01-24 12:38:04,404] [INFO] Running command: blastn -query GCF_007993815.1_ASM799381v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf12b771a-ff46-48d7-abe5-6e50bf900138/dqc_reference/reference_markers_gtdb.fasta -out GCF_007993815.1_ASM799381v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:06,262] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:06,265] [INFO] Selected 13 target genomes.
[2024-01-24 12:38:06,265] [INFO] Target genome list was writen to GCF_007993815.1_ASM799381v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:06,275] [INFO] Task started: fastANI
[2024-01-24 12:38:06,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg60d44f16-109e-4d0d-a64c-c3bb43609e90/GCF_007993815.1_ASM799381v1_genomic.fna.gz --refList GCF_007993815.1_ASM799381v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007993815.1_ASM799381v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:23,160] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:23,177] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:23,177] [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_007993815.1	s__Acidovorax delafieldii	100.0	1663	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.08	96.33	0.92	0.90	8	conclusive
GCA_016783915.1	s__Acidovorax sp016783915	92.9686	1283	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000302535.1	s__Acidovorax sp000302535	92.4493	1396	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	95.71	95.42	0.83	0.75	7	-
GCF_003058055.1	s__Acidovorax sp003058055	91.3797	1412	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.89	97.89	0.93	0.93	2	-
GCF_005405905.1	s__Acidovorax sp005405905	88.6003	1352	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001633105.1	s__Acidovorax sp001633105	88.5828	1336	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245625.1	s__Acidovorax kalamii	88.5671	1325	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376875.1	s__Acidovorax sp001411535	88.0528	1358	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	96.38	95.78	0.89	0.84	16	-
GCF_000238595.1	s__Acidovorax facilis	86.8887	1081	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.91	97.91	0.86	0.86	2	-
GCA_019218755.1	s__Acidovorax sp019218755	86.6913	1296	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.86	98.86	0.92	0.91	3	-
GCF_001714725.1	s__Acidovorax sp001714725	85.6377	1083	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003669015.1	s__Acidovorax sp002754495	84.7578	1100	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.04	96.96	0.91	0.90	3	-
GCF_000175235.1	s__Acidovorax delafieldii_B	84.1065	759	1665	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:23,179] [INFO] GTDB search result was written to GCF_007993815.1_ASM799381v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:23,179] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:23,183] [INFO] DFAST_QC result json was written to GCF_007993815.1_ASM799381v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:23,183] [INFO] DFAST_QC completed!
[2024-01-24 12:38:23,183] [INFO] Total running time: 0h1m60s