[2024-01-24 11:43:34,975] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:34,977] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:34,977] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbd3b4f9-94c3-4179-8a48-7faeda7534c0/dqc_reference
[2024-01-24 11:43:36,175] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:36,176] [INFO] Task started: Prodigal
[2024-01-24 11:43:36,176] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f5a46f6-cef2-473c-bb53-fec50d5b3f21/GCF_008801575.1_ASM880157v1_genomic.fna.gz | prodigal -d GCF_008801575.1_ASM880157v1_genomic.fna/cds.fna -a GCF_008801575.1_ASM880157v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:54,088] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:54,088] [INFO] Task started: HMMsearch
[2024-01-24 11:43:54,089] [INFO] Running command: hmmsearch --tblout GCF_008801575.1_ASM880157v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbd3b4f9-94c3-4179-8a48-7faeda7534c0/dqc_reference/reference_markers.hmm GCF_008801575.1_ASM880157v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:54,379] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:54,381] [INFO] Found 6/6 markers.
[2024-01-24 11:43:54,426] [INFO] Query marker FASTA was written to GCF_008801575.1_ASM880157v1_genomic.fna/markers.fasta
[2024-01-24 11:43:54,426] [INFO] Task started: Blastn
[2024-01-24 11:43:54,426] [INFO] Running command: blastn -query GCF_008801575.1_ASM880157v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbd3b4f9-94c3-4179-8a48-7faeda7534c0/dqc_reference/reference_markers.fasta -out GCF_008801575.1_ASM880157v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:55,237] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:55,241] [INFO] Selected 20 target genomes.
[2024-01-24 11:43:55,242] [INFO] Target genome list was writen to GCF_008801575.1_ASM880157v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:55,325] [INFO] Task started: fastANI
[2024-01-24 11:43:55,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f5a46f6-cef2-473c-bb53-fec50d5b3f21/GCF_008801575.1_ASM880157v1_genomic.fna.gz --refList GCF_008801575.1_ASM880157v1_genomic.fna/target_genomes.txt --output GCF_008801575.1_ASM880157v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:16,678] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:16,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbd3b4f9-94c3-4179-8a48-7faeda7534c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:16,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbd3b4f9-94c3-4179-8a48-7faeda7534c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:16,694] [INFO] Found 20 fastANI hits (11 hits with ANI > threshold)
[2024-01-24 11:44:16,694] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:44:16,694] [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=CCUG 18839	GCA_008801575.1	86186	86186	suspected-type	True	100.0	1659	1664	95	inconclusive
Xanthomonas cissicola	strain=LMG21719	GCA_002019225.1	86186	86186	suspected-type	True	99.9591	1554	1664	95	inconclusive
Xanthomonas citri	strain=LMG 965	GCA_000723725.1	346	346	pathovar	True	98.6711	1503	1664	95	inconclusive
Xanthomonas citri	strain=LMG 859	GCA_000285775.1	346	346	pathovar	True	98.5005	1416	1664	95	inconclusive
Xanthomonas citri	strain=LMG 941	GCA_000263335.1	346	346	pathovar	True	98.4482	1439	1664	95	inconclusive
Xanthomonas citri	strain=LMG712	GCA_002019125.1	346	346	pathovar	True	98.4001	1475	1664	95	inconclusive
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	98.3503	1526	1664	95	inconclusive
Xanthomonas citri	strain=CFBP 2526	GCA_000495275.1	346	346	pathovar	True	98.3378	1526	1664	95	inconclusive
Xanthomonas citri	strain=LMG9322	GCA_002018575.1	346	346	suspected-type	True	98.2846	1457	1664	95	inconclusive
Xanthomonas citri	strain=WHRI 5232	GCA_003064125.1	346	346	pathovar	True	98.251	1492	1664	95	inconclusive
Xanthomonas citri	strain=LMG 9322	GCA_001401655.1	346	346	suspected-type	True	98.0749	1168	1664	95	inconclusive
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	94.5065	1420	1664	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	87.0096	1349	1664	95	below_threshold
Xanthomonas fragariae	strain=PD 885	GCA_900380235.1	48664	48664	type	True	85.9261	973	1664	95	below_threshold
Xanthomonas fragariae	strain=PD885	GCA_900183975.1	48664	48664	type	True	85.6027	1073	1664	95	below_threshold
Pseudoxanthomonas spadix	strain=DSM 18855	GCA_003703395.1	415229	415229	type	True	79.9692	580	1664	95	below_threshold
Luteimonas chenhongjianii	strain=100111	GCA_002327105.1	2006110	2006110	type	True	78.8769	448	1664	95	below_threshold
Lysobacter ciconiae	strain=H21R20	GCA_015209725.1	2781022	2781022	type	True	78.5536	362	1664	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	76.0088	113	1664	95	below_threshold
Halomonas taeanensis	strain=BH539	GCA_900100755.1	284577	284577	type	True	75.963	88	1664	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:16,696] [INFO] DFAST Taxonomy check result was written to GCF_008801575.1_ASM880157v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:16,697] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:16,697] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:16,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbd3b4f9-94c3-4179-8a48-7faeda7534c0/dqc_reference/checkm_data
[2024-01-24 11:44:16,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:16,752] [INFO] Task started: CheckM
[2024-01-24 11:44:16,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008801575.1_ASM880157v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008801575.1_ASM880157v1_genomic.fna/checkm_input GCF_008801575.1_ASM880157v1_genomic.fna/checkm_result
[2024-01-24 11:45:13,354] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:13,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:13,378] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:13,379] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:13,379] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008801575.1_ASM880157v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:13,379] [INFO] Task started: Blastn
[2024-01-24 11:45:13,380] [INFO] Running command: blastn -query GCF_008801575.1_ASM880157v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbd3b4f9-94c3-4179-8a48-7faeda7534c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_008801575.1_ASM880157v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:14,752] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:14,756] [INFO] Selected 12 target genomes.
[2024-01-24 11:45:14,756] [INFO] Target genome list was writen to GCF_008801575.1_ASM880157v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:14,766] [INFO] Task started: fastANI
[2024-01-24 11:45:14,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f5a46f6-cef2-473c-bb53-fec50d5b3f21/GCF_008801575.1_ASM880157v1_genomic.fna.gz --refList GCF_008801575.1_ASM880157v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008801575.1_ASM880157v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:28,280] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:28,293] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:28,293] [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	100.0	1659	1664	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	94.4974	1451	1664	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	93.695	1452	1664	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	93.2031	1197	1664	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	90.1365	1389	1664	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	89.6347	1222	1664	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	89.1776	1295	1664	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	87.4069	1213	1664	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	79.9691	580	1664	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	78.8769	448	1664	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	78.5878	359	1664	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	77.4758	313	1664	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 11:45:28,295] [INFO] GTDB search result was written to GCF_008801575.1_ASM880157v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:28,295] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:28,300] [INFO] DFAST_QC result json was written to GCF_008801575.1_ASM880157v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:28,300] [INFO] DFAST_QC completed!
[2024-01-24 11:45:28,300] [INFO] Total running time: 0h1m53s