[2024-01-25 19:12:05,641] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:12:05,642] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:12:05,642] [INFO] DQC Reference Directory: /var/lib/cwl/stgb093e2e4-213a-47aa-9e57-c2b16321b614/dqc_reference
[2024-01-25 19:12:06,774] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:12:06,779] [INFO] Task started: Prodigal
[2024-01-25 19:12:06,779] [INFO] Running command: gunzip -c /var/lib/cwl/stg27cd6405-59b3-44c2-9477-e598ad9f9be6/GCF_001310775.1_ASM131077v1_genomic.fna.gz | prodigal -d GCF_001310775.1_ASM131077v1_genomic.fna/cds.fna -a GCF_001310775.1_ASM131077v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:12:14,760] [INFO] Task succeeded: Prodigal
[2024-01-25 19:12:14,760] [INFO] Task started: HMMsearch
[2024-01-25 19:12:14,760] [INFO] Running command: hmmsearch --tblout GCF_001310775.1_ASM131077v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb093e2e4-213a-47aa-9e57-c2b16321b614/dqc_reference/reference_markers.hmm GCF_001310775.1_ASM131077v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:12:14,960] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:12:14,962] [INFO] Found 6/6 markers.
[2024-01-25 19:12:14,991] [INFO] Query marker FASTA was written to GCF_001310775.1_ASM131077v1_genomic.fna/markers.fasta
[2024-01-25 19:12:14,991] [INFO] Task started: Blastn
[2024-01-25 19:12:14,991] [INFO] Running command: blastn -query GCF_001310775.1_ASM131077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb093e2e4-213a-47aa-9e57-c2b16321b614/dqc_reference/reference_markers.fasta -out GCF_001310775.1_ASM131077v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:15,768] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:15,771] [INFO] Selected 25 target genomes.
[2024-01-25 19:12:15,772] [INFO] Target genome list was writen to GCF_001310775.1_ASM131077v1_genomic.fna/target_genomes.txt
[2024-01-25 19:12:15,790] [INFO] Task started: fastANI
[2024-01-25 19:12:15,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg27cd6405-59b3-44c2-9477-e598ad9f9be6/GCF_001310775.1_ASM131077v1_genomic.fna.gz --refList GCF_001310775.1_ASM131077v1_genomic.fna/target_genomes.txt --output GCF_001310775.1_ASM131077v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:12:33,976] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:33,977] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb093e2e4-213a-47aa-9e57-c2b16321b614/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:12:33,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb093e2e4-213a-47aa-9e57-c2b16321b614/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:12:33,990] [INFO] Found 24 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:12:33,991] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:12:33,991] [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
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001310775.1	86184	86184	type	True	100.0	707	728	95	conclusive
Stenotrophomonas pictorum	strain=JCM 9942	GCA_001431585.1	86184	86184	type	True	99.9385	719	728	95	conclusive
Stenotrophomonas nitritireducens	strain=DSM 12575	GCA_001431425.1	83617	83617	type	True	86.0498	539	728	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	85.6237	572	728	95	below_threshold
Stenotrophomonas acidaminiphila	strain=JCM 13310	GCA_001431595.1	128780	128780	type	True	85.5333	561	728	95	below_threshold
Stenotrophomonas terrae	strain=DSM 18941	GCA_001431465.1	405446	405446	type	True	85.5303	545	728	95	below_threshold
Stenotrophomonas daejeonensis	strain=JCM 16244	GCA_001431505.1	659018	659018	type	True	85.2384	521	728	95	below_threshold
Stenotrophomonas humi	strain=DSM 18929	GCA_001431415.1	405444	405444	type	True	84.9575	563	728	95	below_threshold
Stenotrophomonas nematodicola	strain=CPCC 101271	GCA_009467805.1	2656746	2656746	type	True	83.6059	511	728	95	below_threshold
Stenotrophomonas bentonitica	strain=DSM 103927	GCA_013185915.1	1450134	1450134	type	True	83.5349	499	728	95	below_threshold
Stenotrophomonas indicatrix	strain=WS40	GCA_002750975.1	2045451	2045451	type	True	83.3765	496	728	95	below_threshold
Stenotrophomonas pennii	strain=Sa5BUN4	GCA_014836545.1	2762239	2762239	type	True	82.7668	464	728	95	below_threshold
Xanthomonas melonis	strain=NCPPB 3434	GCA_020783655.1	56456	56456	type	True	81.8848	434	728	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	81.7816	438	728	95	below_threshold
Xanthomonas cucurbitae	strain=CFBP2542	GCA_002939885.1	56453	56453	type	True	81.5161	431	728	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	81.4627	448	728	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	81.4602	451	728	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	81.4468	445	728	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	81.3094	447	728	95	below_threshold
Xanthomonas populi	strain=CFBP1817	GCA_002940065.1	53414	53414	type	True	80.9359	391	728	95	below_threshold
Halomonas fontilapidosi	strain=CECT 7341	GCA_014192285.1	616675	616675	type	True	76.603	80	728	95	below_threshold
Salinicola socius	strain=DSM 19940	GCA_003206115.1	404433	404433	type	True	76.5929	73	728	95	below_threshold
Salinicola socius	strain=SMB35	GCA_001937195.1	404433	404433	type	True	76.591	75	728	95	below_threshold
Lampropedia hyalina	strain=DSM 16112	GCA_900129055.1	198706	198706	type	True	76.2696	52	728	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:12:33,999] [INFO] DFAST Taxonomy check result was written to GCF_001310775.1_ASM131077v1_genomic.fna/tc_result.tsv
[2024-01-25 19:12:34,001] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:12:34,002] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:12:34,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb093e2e4-213a-47aa-9e57-c2b16321b614/dqc_reference/checkm_data
[2024-01-25 19:12:34,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:12:34,048] [INFO] Task started: CheckM
[2024-01-25 19:12:34,049] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001310775.1_ASM131077v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001310775.1_ASM131077v1_genomic.fna/checkm_input GCF_001310775.1_ASM131077v1_genomic.fna/checkm_result
[2024-01-25 19:13:00,903] [INFO] Task succeeded: CheckM
[2024-01-25 19:13:00,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:13:00,926] [INFO] ===== Completeness check finished =====
[2024-01-25 19:13:00,926] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:13:00,926] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001310775.1_ASM131077v1_genomic.fna/markers.fasta)
[2024-01-25 19:13:00,926] [INFO] Task started: Blastn
[2024-01-25 19:13:00,927] [INFO] Running command: blastn -query GCF_001310775.1_ASM131077v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb093e2e4-213a-47aa-9e57-c2b16321b614/dqc_reference/reference_markers_gtdb.fasta -out GCF_001310775.1_ASM131077v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:02,334] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:02,337] [INFO] Selected 27 target genomes.
[2024-01-25 19:13:02,337] [INFO] Target genome list was writen to GCF_001310775.1_ASM131077v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:13:02,363] [INFO] Task started: fastANI
[2024-01-25 19:13:02,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg27cd6405-59b3-44c2-9477-e598ad9f9be6/GCF_001310775.1_ASM131077v1_genomic.fna.gz --refList GCF_001310775.1_ASM131077v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001310775.1_ASM131077v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:13:23,994] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:24,009] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:13:24,010] [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_001310775.1	s__Stenotrophomonas pictorum	100.0	707	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.94	99.94	0.99	0.99	2	conclusive
GCA_002345545.1	s__Stenotrophomonas sp002345545	87.1058	572	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348115.1	s__Stenotrophomonas sp004348115	86.0551	584	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.00	98.00	0.94	0.94	2	-
GCF_001431425.1	s__Stenotrophomonas nitritireducens	86.0498	539	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.94	98.42	0.92	0.89	3	-
GCF_009496535.1	s__Stenotrophomonas sp003504055	85.8509	559	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	96.53	96.53	0.92	0.92	2	-
GCF_001700965.1	s__Stenotrophomonas nitritireducens_A	85.8496	575	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002471015.1	s__Stenotrophomonas sp002471015	85.5911	540	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	96.17	95.12	0.84	0.81	4	-
GCF_001431595.1	s__Stenotrophomonas acidaminiphila	85.5333	561	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.49	97.05	0.89	0.86	11	-
GCF_001431465.1	s__Stenotrophomonas terrae	85.5303	545	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002951995.1	s__Stenotrophomonas acidaminiphila_A	85.4982	570	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.50	98.36	0.92	0.88	13	-
GCF_001431505.1	s__Stenotrophomonas daejeonensis	85.2541	520	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002329155.1	s__Stenotrophomonas sp002329155	85.2495	535	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431415.1	s__Stenotrophomonas humi	84.9575	563	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248565.1	s__Stenotrophomonas sp003248565	84.637	459	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002359895.1	s__Stenotrophomonas sp002359895	84.3619	531	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011604605.1	s__Stenotrophomonas maltophilia_AO	83.7317	509	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.25	99.18	0.95	0.92	6	-
GCF_013185915.1	s__Stenotrophomonas bentonitica	83.5172	500	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002750975.1	s__Stenotrophomonas indicatrix	83.3983	494	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.78	96.47	0.93	0.89	30	-
GCA_002386405.1	s__Stenotrophomonas maltophilia_AD	83.3173	423	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684085.1	s__Stenotrophomonas maltophilia_AS	83.1745	484	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004920835.1	s__Stenotrophomonas maltophilia_AQ	83.1052	499	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.58	99.16	0.97	0.95	3	-
GCF_002939885.1	s__Xanthomonas cucurbitae	81.5161	431	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	99.30	0.96	0.96	2	-
GCF_000336385.2	s__Lysobacter antibioticus_A	80.3727	373	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001937195.1	s__Salinicola socius	76.6184	74	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.48	98.96	0.96	0.93	3	-
GCF_001447195.1	s__Aquabacterium parvum	76.431	99	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	97.32	96.21	0.91	0.89	4	-
GCF_900129055.1	s__Lampropedia hyalina	76.305	51	728	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:13:24,011] [INFO] GTDB search result was written to GCF_001310775.1_ASM131077v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:13:24,012] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:13:24,016] [INFO] DFAST_QC result json was written to GCF_001310775.1_ASM131077v1_genomic.fna/dqc_result.json
[2024-01-25 19:13:24,016] [INFO] DFAST_QC completed!
[2024-01-25 19:13:24,016] [INFO] Total running time: 0h1m18s