[2024-01-25 19:50:50,479] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:50,480] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:50,480] [INFO] DQC Reference Directory: /var/lib/cwl/stgafd40e30-c2a0-4e0f-86a9-8f2cb5bb3677/dqc_reference
[2024-01-25 19:50:51,610] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:51,611] [INFO] Task started: Prodigal
[2024-01-25 19:50:51,611] [INFO] Running command: gunzip -c /var/lib/cwl/stgea0697bf-5045-4657-82c7-0477eea44ed6/GCF_027924565.1_ASM2792456v1_genomic.fna.gz | prodigal -d GCF_027924565.1_ASM2792456v1_genomic.fna/cds.fna -a GCF_027924565.1_ASM2792456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:51:03,210] [INFO] Task succeeded: Prodigal
[2024-01-25 19:51:03,210] [INFO] Task started: HMMsearch
[2024-01-25 19:51:03,210] [INFO] Running command: hmmsearch --tblout GCF_027924565.1_ASM2792456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafd40e30-c2a0-4e0f-86a9-8f2cb5bb3677/dqc_reference/reference_markers.hmm GCF_027924565.1_ASM2792456v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:51:03,465] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:51:03,468] [INFO] Found 6/6 markers.
[2024-01-25 19:51:03,506] [INFO] Query marker FASTA was written to GCF_027924565.1_ASM2792456v1_genomic.fna/markers.fasta
[2024-01-25 19:51:03,507] [INFO] Task started: Blastn
[2024-01-25 19:51:03,507] [INFO] Running command: blastn -query GCF_027924565.1_ASM2792456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafd40e30-c2a0-4e0f-86a9-8f2cb5bb3677/dqc_reference/reference_markers.fasta -out GCF_027924565.1_ASM2792456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:04,405] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:04,407] [INFO] Selected 14 target genomes.
[2024-01-25 19:51:04,408] [INFO] Target genome list was writen to GCF_027924565.1_ASM2792456v1_genomic.fna/target_genomes.txt
[2024-01-25 19:51:04,416] [INFO] Task started: fastANI
[2024-01-25 19:51:04,416] [INFO] Running command: fastANI --query /var/lib/cwl/stgea0697bf-5045-4657-82c7-0477eea44ed6/GCF_027924565.1_ASM2792456v1_genomic.fna.gz --refList GCF_027924565.1_ASM2792456v1_genomic.fna/target_genomes.txt --output GCF_027924565.1_ASM2792456v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:17,786] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:17,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafd40e30-c2a0-4e0f-86a9-8f2cb5bb3677/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:17,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafd40e30-c2a0-4e0f-86a9-8f2cb5bb3677/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:17,796] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:51:17,796] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:51:17,796] [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
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	90.3067	1143	1385	95	below_threshold
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	85.9755	1033	1385	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	84.0561	912	1385	95	below_threshold
Lysobacter niastensis	strain=DSM 18481	GCA_015453285.1	380629	380629	type	True	83.6042	855	1385	95	below_threshold
Lysobacter prati	strain=SYSU H10001	GCA_009765215.1	2596704	2596704	type	True	83.5695	929	1385	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	83.4018	827	1385	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	83.3557	801	1385	95	below_threshold
Lysobacter terrestris	strain=II4	GCA_014489475.1	2865112	2865112	type	True	82.6634	750	1385	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	82.2674	827	1385	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	81.977	831	1385	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	81.9121	632	1385	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	81.6696	817	1385	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	80.9512	738	1385	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	80.843	626	1385	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:51:17,797] [INFO] DFAST Taxonomy check result was written to GCF_027924565.1_ASM2792456v1_genomic.fna/tc_result.tsv
[2024-01-25 19:51:17,798] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:17,798] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:17,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafd40e30-c2a0-4e0f-86a9-8f2cb5bb3677/dqc_reference/checkm_data
[2024-01-25 19:51:17,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:17,839] [INFO] Task started: CheckM
[2024-01-25 19:51:17,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027924565.1_ASM2792456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027924565.1_ASM2792456v1_genomic.fna/checkm_input GCF_027924565.1_ASM2792456v1_genomic.fna/checkm_result
[2024-01-25 19:52:11,435] [INFO] Task succeeded: CheckM
[2024-01-25 19:52:11,436] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:52:11,452] [INFO] ===== Completeness check finished =====
[2024-01-25 19:52:11,452] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:52:11,453] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027924565.1_ASM2792456v1_genomic.fna/markers.fasta)
[2024-01-25 19:52:11,453] [INFO] Task started: Blastn
[2024-01-25 19:52:11,453] [INFO] Running command: blastn -query GCF_027924565.1_ASM2792456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafd40e30-c2a0-4e0f-86a9-8f2cb5bb3677/dqc_reference/reference_markers_gtdb.fasta -out GCF_027924565.1_ASM2792456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:13,118] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:13,121] [INFO] Selected 8 target genomes.
[2024-01-25 19:52:13,121] [INFO] Target genome list was writen to GCF_027924565.1_ASM2792456v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:52:13,132] [INFO] Task started: fastANI
[2024-01-25 19:52:13,132] [INFO] Running command: fastANI --query /var/lib/cwl/stgea0697bf-5045-4657-82c7-0477eea44ed6/GCF_027924565.1_ASM2792456v1_genomic.fna.gz --refList GCF_027924565.1_ASM2792456v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027924565.1_ASM2792456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:52:21,610] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:21,615] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:52:21,616] [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_003382285.1	s__Lysobacter soli	90.2853	1145	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.84	96.81	0.94	0.93	3	-
GCF_017308985.1	s__Lysobacter sp017308985	89.8512	1132	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735495.2	s__Lysobacter sp016735495	87.2485	1088	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503055.1	s__Lysobacter sp005503055	86.3879	1067	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765165.1	s__Lysobacter panacisoli	85.981	1030	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884235.1	s__CAIYLH01 sp903884235	76.1231	199	1385	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CAIYLH01	95.0	99.42	99.08	0.95	0.88	22	-
GCA_003140315.1	s__PALSA-894 sp003140315	74.9895	130	1385	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__PALSA-894	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:52:21,617] [INFO] GTDB search result was written to GCF_027924565.1_ASM2792456v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:52:21,618] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:52:21,620] [INFO] DFAST_QC result json was written to GCF_027924565.1_ASM2792456v1_genomic.fna/dqc_result.json
[2024-01-25 19:52:21,620] [INFO] DFAST_QC completed!
[2024-01-25 19:52:21,621] [INFO] Total running time: 0h1m31s