[2024-01-24 15:27:20,822] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:20,825] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:20,825] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ca7d3e3-def4-43dc-9a12-1b7f6d51a8db/dqc_reference
[2024-01-24 15:27:23,295] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:23,296] [INFO] Task started: Prodigal
[2024-01-24 15:27:23,297] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d1237c8-a1ea-4712-9340-59f6b8c4476a/GCF_004136375.1_ASM413637v1_genomic.fna.gz | prodigal -d GCF_004136375.1_ASM413637v1_genomic.fna/cds.fna -a GCF_004136375.1_ASM413637v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:41,841] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:41,842] [INFO] Task started: HMMsearch
[2024-01-24 15:27:41,842] [INFO] Running command: hmmsearch --tblout GCF_004136375.1_ASM413637v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ca7d3e3-def4-43dc-9a12-1b7f6d51a8db/dqc_reference/reference_markers.hmm GCF_004136375.1_ASM413637v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:42,133] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:42,135] [INFO] Found 6/6 markers.
[2024-01-24 15:27:42,179] [INFO] Query marker FASTA was written to GCF_004136375.1_ASM413637v1_genomic.fna/markers.fasta
[2024-01-24 15:27:42,180] [INFO] Task started: Blastn
[2024-01-24 15:27:42,180] [INFO] Running command: blastn -query GCF_004136375.1_ASM413637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ca7d3e3-def4-43dc-9a12-1b7f6d51a8db/dqc_reference/reference_markers.fasta -out GCF_004136375.1_ASM413637v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:43,107] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:43,112] [INFO] Selected 18 target genomes.
[2024-01-24 15:27:43,112] [INFO] Target genome list was writen to GCF_004136375.1_ASM413637v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:43,120] [INFO] Task started: fastANI
[2024-01-24 15:27:43,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d1237c8-a1ea-4712-9340-59f6b8c4476a/GCF_004136375.1_ASM413637v1_genomic.fna.gz --refList GCF_004136375.1_ASM413637v1_genomic.fna/target_genomes.txt --output GCF_004136375.1_ASM413637v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:22,477] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:22,478] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ca7d3e3-def4-43dc-9a12-1b7f6d51a8db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:22,478] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ca7d3e3-def4-43dc-9a12-1b7f6d51a8db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:22,493] [INFO] Found 18 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:28:22,493] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:22,493] [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
Xanthomonas oryzae	strain=ICMP3125	GCA_004136375.1	347	347	type	True	100.0	1662	1663	95	conclusive
Xanthomonas oryzae	strain=ATCC 35933	GCA_000482445.1	347	347	type	True	99.7545	1282	1663	95	conclusive
Xanthomonas oryzae	strain=WHRI 5234	GCA_003064145.1	347	347	pathovar	True	97.4364	1289	1663	95	conclusive
Xanthomonas vasicola	strain=SAM119	GCA_003015715.1	56459	56459	pathovar	True	90.9554	1279	1663	95	below_threshold
Xanthomonas vasicola	strain=SAM119	GCA_002191955.1	56459	56459	pathovar	True	90.927	1260	1663	95	below_threshold
Xanthomonas vasicola	strain=CFBP2543	GCA_002939925.1	56459	56459	type	True	90.9014	1253	1663	95	below_threshold
Xanthomonas vasicola	strain=NCPPB 2649	GCA_000770355.2	56459	56459	pathovar	True	90.8898	1274	1663	95	below_threshold
Xanthomonas vasicola	strain=NCPPB 2417	GCA_000772705.2	56459	56459	type	True	90.8397	1258	1663	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	89.708	1216	1663	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	89.6863	1239	1663	95	below_threshold
Xanthomonas cissicola	strain=LMG21719	GCA_002019225.1	86186	86186	suspected-type	True	89.6819	1179	1663	95	below_threshold
Xanthomonas citri	strain=CFBP7112	GCA_002218265.1	346	346	pathovar	True	89.6019	1258	1663	95	below_threshold
Xanthomonas citri	strain=LMG9322	GCA_002018575.1	346	346	suspected-type	True	89.5949	1178	1663	95	below_threshold
Xanthomonas cassavae	strain=NCPPB 101	GCA_020783895.1	56450	56450	type	True	86.577	1076	1663	95	below_threshold
Xanthomonas cassavae	strain=CFBP 4642	GCA_000454545.1	56450	56450	type	True	86.5147	1137	1663	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	86.2424	1198	1663	95	below_threshold
Xanthomonas fragariae	strain=PD 885	GCA_900380235.1	48664	48664	type	True	85.5362	923	1663	95	below_threshold
Xanthomonas fragariae	strain=PD885	GCA_900183975.1	48664	48664	type	True	85.3281	1043	1663	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:22,495] [INFO] DFAST Taxonomy check result was written to GCF_004136375.1_ASM413637v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:22,496] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:22,496] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:22,496] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ca7d3e3-def4-43dc-9a12-1b7f6d51a8db/dqc_reference/checkm_data
[2024-01-24 15:28:22,498] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:22,555] [INFO] Task started: CheckM
[2024-01-24 15:28:22,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004136375.1_ASM413637v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004136375.1_ASM413637v1_genomic.fna/checkm_input GCF_004136375.1_ASM413637v1_genomic.fna/checkm_result
[2024-01-24 15:29:20,781] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:20,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:20,806] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:20,806] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:20,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004136375.1_ASM413637v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:20,808] [INFO] Task started: Blastn
[2024-01-24 15:29:20,808] [INFO] Running command: blastn -query GCF_004136375.1_ASM413637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ca7d3e3-def4-43dc-9a12-1b7f6d51a8db/dqc_reference/reference_markers_gtdb.fasta -out GCF_004136375.1_ASM413637v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:22,430] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:22,436] [INFO] Selected 14 target genomes.
[2024-01-24 15:29:22,436] [INFO] Target genome list was writen to GCF_004136375.1_ASM413637v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:22,452] [INFO] Task started: fastANI
[2024-01-24 15:29:22,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d1237c8-a1ea-4712-9340-59f6b8c4476a/GCF_004136375.1_ASM413637v1_genomic.fna.gz --refList GCF_004136375.1_ASM413637v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004136375.1_ASM413637v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:50,351] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:50,365] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:50,365] [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_004136375.1	s__Xanthomonas oryzae	100.0	1662	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.14	96.34	0.95	0.82	364	conclusive
GCF_000772705.2	s__Xanthomonas vasicola	90.8666	1255	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.75	98.20	0.95	0.92	113	-
GCF_002846205.1	s__Xanthomonas prunicola	90.8603	1240	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_013112235.1	s__Xanthomonas perforans	89.7617	1251	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.28	96.72	0.95	0.89	246	-
GCF_008801575.1	s__Xanthomonas cissicola	89.6141	1230	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	97.71	95.83	0.91	0.86	247	-
GCF_001304695.1	s__Xanthomonas axonopodis	89.4256	1131	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.43	97.90	0.94	0.92	5	-
GCF_900092025.1	s__Xanthomonas bromi	89.3096	1212	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003999565.1	s__Xanthomonas phaseoli	89.2538	1256	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.19	96.38	0.95	0.90	158	-
GCF_001660815.1	s__Xanthomonas nasturtii	88.4833	1168	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.97	98.97	0.95	0.95	2	-
GCF_000802365.1	s__Xanthomonas cannabis	86.7186	1047	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.66	96.40	0.92	0.89	21	-
GCF_900476395.1	s__Xanthomonas euroxanthea	86.5659	1137	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.09	97.74	0.93	0.92	25	-
GCF_000454545.1	s__Xanthomonas cassavae	86.5105	1140	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012848175.1	s__Xanthomonas campestris_C	86.3715	1159	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642575.1	s__Xanthomonas floridensis	86.0797	1138	1663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:50,367] [INFO] GTDB search result was written to GCF_004136375.1_ASM413637v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:50,368] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:50,372] [INFO] DFAST_QC result json was written to GCF_004136375.1_ASM413637v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:50,372] [INFO] DFAST_QC completed!
[2024-01-24 15:29:50,372] [INFO] Total running time: 0h2m30s