[2024-01-24 14:19:46,080] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:46,082] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:46,082] [INFO] DQC Reference Directory: /var/lib/cwl/stged0186ba-5011-4f1b-8c46-db69ee21a0bf/dqc_reference
[2024-01-24 14:19:47,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,681] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,681] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8395242-c782-4cac-a218-f49b61ed66be/GCF_002019225.1_ASM201922v1_genomic.fna.gz | prodigal -d GCF_002019225.1_ASM201922v1_genomic.fna/cds.fna -a GCF_002019225.1_ASM201922v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:06,824] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:06,824] [INFO] Task started: HMMsearch
[2024-01-24 14:20:06,824] [INFO] Running command: hmmsearch --tblout GCF_002019225.1_ASM201922v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged0186ba-5011-4f1b-8c46-db69ee21a0bf/dqc_reference/reference_markers.hmm GCF_002019225.1_ASM201922v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:07,120] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:07,121] [INFO] Found 6/6 markers.
[2024-01-24 14:20:07,167] [INFO] Query marker FASTA was written to GCF_002019225.1_ASM201922v1_genomic.fna/markers.fasta
[2024-01-24 14:20:07,168] [INFO] Task started: Blastn
[2024-01-24 14:20:07,168] [INFO] Running command: blastn -query GCF_002019225.1_ASM201922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged0186ba-5011-4f1b-8c46-db69ee21a0bf/dqc_reference/reference_markers.fasta -out GCF_002019225.1_ASM201922v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:08,113] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:08,116] [INFO] Selected 20 target genomes.
[2024-01-24 14:20:08,117] [INFO] Target genome list was writen to GCF_002019225.1_ASM201922v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:08,138] [INFO] Task started: fastANI
[2024-01-24 14:20:08,138] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8395242-c782-4cac-a218-f49b61ed66be/GCF_002019225.1_ASM201922v1_genomic.fna.gz --refList GCF_002019225.1_ASM201922v1_genomic.fna/target_genomes.txt --output GCF_002019225.1_ASM201922v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:30,324] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:30,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged0186ba-5011-4f1b-8c46-db69ee21a0bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:30,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged0186ba-5011-4f1b-8c46-db69ee21a0bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:30,342] [INFO] Found 20 fastANI hits (11 hits with ANI > threshold)
[2024-01-24 14:20:30,342] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:20:30,343] [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 cissicola	strain=LMG21719	GCA_002019225.1	86186	86186	suspected-type	True	100.0	1596	1605	95	inconclusive
Xanthomonas cissicola	strain=CCUG 18839	GCA_008801575.1	86186	86186	suspected-type	True	99.989	1585	1605	95	inconclusive
Xanthomonas citri	strain=LMG 965	GCA_000723725.1	346	346	pathovar	True	98.6709	1471	1605	95	inconclusive
Xanthomonas citri	strain=LMG 859	GCA_000285775.1	346	346	pathovar	True	98.4687	1377	1605	95	inconclusive
Xanthomonas citri	strain=CFBP 2526	GCA_000495275.1	346	346	pathovar	True	98.4534	1468	1605	95	inconclusive
Xanthomonas citri	strain=LMG 941	GCA_000263335.1	346	346	pathovar	True	98.4442	1401	1605	95	inconclusive
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	98.4278	1475	1605	95	inconclusive
Xanthomonas citri	strain=LMG712	GCA_002019125.1	346	346	pathovar	True	98.4185	1441	1605	95	inconclusive
Xanthomonas citri	strain=LMG9322	GCA_002018575.1	346	346	suspected-type	True	98.4037	1412	1605	95	inconclusive
Xanthomonas citri	strain=WHRI 5232	GCA_003064125.1	346	346	pathovar	True	98.3032	1456	1605	95	inconclusive
Xanthomonas citri	strain=LMG 9322	GCA_001401655.1	346	346	suspected-type	True	98.0911	1153	1605	95	inconclusive
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	94.5121	1382	1605	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	86.966	1313	1605	95	below_threshold
Xanthomonas fragariae	strain=PD 885	GCA_900380235.1	48664	48664	type	True	85.8139	948	1605	95	below_threshold
Xanthomonas fragariae	strain=PD885	GCA_900183975.1	48664	48664	type	True	85.4887	1047	1605	95	below_threshold
Pseudoxanthomonas spadix	strain=DSM 18855	GCA_003703395.1	415229	415229	type	True	79.804	568	1605	95	below_threshold
Luteimonas chenhongjianii	strain=100111	GCA_002327105.1	2006110	2006110	type	True	78.6672	444	1605	95	below_threshold
Lysobacter ciconiae	strain=H21R20	GCA_015209725.1	2781022	2781022	type	True	78.4194	357	1605	95	below_threshold
Halomonas taeanensis	strain=BH539	GCA_900100755.1	284577	284577	type	True	75.9473	85	1605	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	75.9067	109	1605	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:30,346] [INFO] DFAST Taxonomy check result was written to GCF_002019225.1_ASM201922v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:30,347] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:30,347] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:30,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged0186ba-5011-4f1b-8c46-db69ee21a0bf/dqc_reference/checkm_data
[2024-01-24 14:20:30,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:30,403] [INFO] Task started: CheckM
[2024-01-24 14:20:30,403] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002019225.1_ASM201922v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002019225.1_ASM201922v1_genomic.fna/checkm_input GCF_002019225.1_ASM201922v1_genomic.fna/checkm_result
[2024-01-24 14:21:26,982] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:26,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:26,999] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:26,999] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:27,000] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002019225.1_ASM201922v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:27,000] [INFO] Task started: Blastn
[2024-01-24 14:21:27,000] [INFO] Running command: blastn -query GCF_002019225.1_ASM201922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged0186ba-5011-4f1b-8c46-db69ee21a0bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_002019225.1_ASM201922v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:28,339] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:28,342] [INFO] Selected 12 target genomes.
[2024-01-24 14:21:28,342] [INFO] Target genome list was writen to GCF_002019225.1_ASM201922v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:28,366] [INFO] Task started: fastANI
[2024-01-24 14:21:28,367] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8395242-c782-4cac-a218-f49b61ed66be/GCF_002019225.1_ASM201922v1_genomic.fna.gz --refList GCF_002019225.1_ASM201922v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002019225.1_ASM201922v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:41,312] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:41,322] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:41,323] [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_008801575.1	s__Xanthomonas cissicola	99.989	1585	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	97.71	95.83	0.91	0.86	247	conclusive
GCF_013112235.1	s__Xanthomonas perforans	94.5536	1396	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.28	96.72	0.95	0.89	246	-
GCF_003999565.1	s__Xanthomonas phaseoli	93.7305	1390	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.19	96.38	0.95	0.90	158	-
GCF_001304695.1	s__Xanthomonas axonopodis	93.1571	1163	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.43	97.90	0.94	0.92	5	-
GCF_002846205.1	s__Xanthomonas prunicola	90.1376	1348	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_004136375.1	s__Xanthomonas oryzae	89.5534	1199	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.14	96.34	0.95	0.82	364	-
GCF_001660815.1	s__Xanthomonas nasturtii	89.1811	1256	1605	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	87.285	1191	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.66	96.40	0.92	0.89	21	-
GCF_003703395.1	s__Pseudoxanthomonas_A spadix	79.7761	571	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.25	98.51	0.95	0.90	3	-
GCF_002327105.1	s__Luteimonas chenhongjianii	78.6779	442	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	98.75	98.75	0.95	0.95	2	-
GCF_015209725.1	s__Lysobacter sp015209725	78.4194	357	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.91	96.91	0.94	0.94	2	-
GCF_000953855.2	s__Mizugakiibacter sediminis	77.4477	297	1605	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:41,324] [INFO] GTDB search result was written to GCF_002019225.1_ASM201922v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:41,325] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:41,329] [INFO] DFAST_QC result json was written to GCF_002019225.1_ASM201922v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:41,329] [INFO] DFAST_QC completed!
[2024-01-24 14:21:41,329] [INFO] Total running time: 0h1m55s