[2024-01-25 19:43:20,413] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:20,414] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:20,414] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfa7281b-e00b-49c9-8c48-3e9cc9d9f775/dqc_reference
[2024-01-25 19:43:21,551] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:21,552] [INFO] Task started: Prodigal
[2024-01-25 19:43:21,552] [INFO] Running command: gunzip -c /var/lib/cwl/stgbedb0a05-5c8e-4c63-bacf-d2c0721733ce/GCF_002018575.1_ASM201857v1_genomic.fna.gz | prodigal -d GCF_002018575.1_ASM201857v1_genomic.fna/cds.fna -a GCF_002018575.1_ASM201857v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:43:37,786] [INFO] Task succeeded: Prodigal
[2024-01-25 19:43:37,787] [INFO] Task started: HMMsearch
[2024-01-25 19:43:37,787] [INFO] Running command: hmmsearch --tblout GCF_002018575.1_ASM201857v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfa7281b-e00b-49c9-8c48-3e9cc9d9f775/dqc_reference/reference_markers.hmm GCF_002018575.1_ASM201857v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:43:38,047] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:43:38,048] [INFO] Found 6/6 markers.
[2024-01-25 19:43:38,087] [INFO] Query marker FASTA was written to GCF_002018575.1_ASM201857v1_genomic.fna/markers.fasta
[2024-01-25 19:43:38,088] [INFO] Task started: Blastn
[2024-01-25 19:43:38,088] [INFO] Running command: blastn -query GCF_002018575.1_ASM201857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfa7281b-e00b-49c9-8c48-3e9cc9d9f775/dqc_reference/reference_markers.fasta -out GCF_002018575.1_ASM201857v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:38,975] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:38,979] [INFO] Selected 15 target genomes.
[2024-01-25 19:43:38,980] [INFO] Target genome list was writen to GCF_002018575.1_ASM201857v1_genomic.fna/target_genomes.txt
[2024-01-25 19:43:39,007] [INFO] Task started: fastANI
[2024-01-25 19:43:39,007] [INFO] Running command: fastANI --query /var/lib/cwl/stgbedb0a05-5c8e-4c63-bacf-d2c0721733ce/GCF_002018575.1_ASM201857v1_genomic.fna.gz --refList GCF_002018575.1_ASM201857v1_genomic.fna/target_genomes.txt --output GCF_002018575.1_ASM201857v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:43:57,496] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:57,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfa7281b-e00b-49c9-8c48-3e9cc9d9f775/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:43:57,497] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfa7281b-e00b-49c9-8c48-3e9cc9d9f775/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:43:57,507] [INFO] Found 15 fastANI hits (11 hits with ANI > threshold)
[2024-01-25 19:43:57,507] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:43:57,507] [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 citri	strain=LMG9322	GCA_002018575.1	346	346	suspected-type	True	100.0	1622	1629	95	inconclusive
Xanthomonas citri	strain=LMG 9322	GCA_001401655.1	346	346	suspected-type	True	99.679	1260	1629	95	inconclusive
Xanthomonas citri	strain=CFBP 2526	GCA_000495275.1	346	346	pathovar	True	98.8122	1499	1629	95	inconclusive
Xanthomonas citri	strain=LMG 941	GCA_000263335.1	346	346	pathovar	True	98.7988	1426	1629	95	inconclusive
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	98.7842	1506	1629	95	inconclusive
Xanthomonas citri	strain=LMG712	GCA_002019125.1	346	346	pathovar	True	98.7769	1464	1629	95	inconclusive
Xanthomonas citri	strain=LMG 859	GCA_000285775.1	346	346	pathovar	True	98.7134	1405	1629	95	inconclusive
Xanthomonas citri	strain=LMG 965	GCA_000723725.1	346	346	pathovar	True	98.6814	1489	1629	95	inconclusive
Xanthomonas citri	strain=WHRI 5232	GCA_003064125.1	346	346	pathovar	True	98.462	1475	1629	95	inconclusive
Xanthomonas cissicola	strain=CCUG 18839	GCA_008801575.1	86186	86186	suspected-type	True	98.3606	1450	1629	95	inconclusive
Xanthomonas cissicola	strain=LMG21719	GCA_002019225.1	86186	86186	suspected-type	True	98.3318	1420	1629	95	inconclusive
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	94.3401	1398	1629	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	86.8351	1300	1629	95	below_threshold
Xanthomonas fragariae	strain=PD 885	GCA_900380235.1	48664	48664	type	True	85.5982	947	1629	95	below_threshold
Xanthomonas fragariae	strain=PD885	GCA_900183975.1	48664	48664	type	True	85.2549	1035	1629	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:43:57,508] [INFO] DFAST Taxonomy check result was written to GCF_002018575.1_ASM201857v1_genomic.fna/tc_result.tsv
[2024-01-25 19:43:57,509] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:43:57,509] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:43:57,509] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfa7281b-e00b-49c9-8c48-3e9cc9d9f775/dqc_reference/checkm_data
[2024-01-25 19:43:57,510] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:43:57,560] [INFO] Task started: CheckM
[2024-01-25 19:43:57,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002018575.1_ASM201857v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002018575.1_ASM201857v1_genomic.fna/checkm_input GCF_002018575.1_ASM201857v1_genomic.fna/checkm_result
[2024-01-25 19:44:51,816] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:51,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:44:51,862] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:51,863] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:51,864] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002018575.1_ASM201857v1_genomic.fna/markers.fasta)
[2024-01-25 19:44:51,864] [INFO] Task started: Blastn
[2024-01-25 19:44:51,864] [INFO] Running command: blastn -query GCF_002018575.1_ASM201857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfa7281b-e00b-49c9-8c48-3e9cc9d9f775/dqc_reference/reference_markers_gtdb.fasta -out GCF_002018575.1_ASM201857v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:53,576] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:53,579] [INFO] Selected 8 target genomes.
[2024-01-25 19:44:53,579] [INFO] Target genome list was writen to GCF_002018575.1_ASM201857v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:44:53,590] [INFO] Task started: fastANI
[2024-01-25 19:44:53,590] [INFO] Running command: fastANI --query /var/lib/cwl/stgbedb0a05-5c8e-4c63-bacf-d2c0721733ce/GCF_002018575.1_ASM201857v1_genomic.fna.gz --refList GCF_002018575.1_ASM201857v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002018575.1_ASM201857v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:04,312] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:04,318] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:45:04,318] [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	98.3606	1450	1629	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	94.4086	1442	1629	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	93.702	1431	1629	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	93.2951	1167	1629	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	90.1062	1351	1629	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	89.5871	1180	1629	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	89.1657	1276	1629	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	87.3638	1209	1629	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.66	96.40	0.92	0.89	21	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:04,320] [INFO] GTDB search result was written to GCF_002018575.1_ASM201857v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:04,320] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:04,323] [INFO] DFAST_QC result json was written to GCF_002018575.1_ASM201857v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:04,323] [INFO] DFAST_QC completed!
[2024-01-25 19:45:04,323] [INFO] Total running time: 0h1m44s