[2024-01-24 12:23:03,363] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,365] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,365] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c1edcd2-c5d0-4e7e-a0a3-d53a8e46d174/dqc_reference
[2024-01-24 12:23:04,538] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:04,539] [INFO] Task started: Prodigal
[2024-01-24 12:23:04,539] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a95de27-671f-4bf4-b8b1-675ffdd59b25/GCF_003382285.1_ASM338228v1_genomic.fna.gz | prodigal -d GCF_003382285.1_ASM338228v1_genomic.fna/cds.fna -a GCF_003382285.1_ASM338228v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:15,260] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:15,260] [INFO] Task started: HMMsearch
[2024-01-24 12:23:15,260] [INFO] Running command: hmmsearch --tblout GCF_003382285.1_ASM338228v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c1edcd2-c5d0-4e7e-a0a3-d53a8e46d174/dqc_reference/reference_markers.hmm GCF_003382285.1_ASM338228v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:15,481] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:15,482] [INFO] Found 6/6 markers.
[2024-01-24 12:23:15,511] [INFO] Query marker FASTA was written to GCF_003382285.1_ASM338228v1_genomic.fna/markers.fasta
[2024-01-24 12:23:15,511] [INFO] Task started: Blastn
[2024-01-24 12:23:15,511] [INFO] Running command: blastn -query GCF_003382285.1_ASM338228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c1edcd2-c5d0-4e7e-a0a3-d53a8e46d174/dqc_reference/reference_markers.fasta -out GCF_003382285.1_ASM338228v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:16,479] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:16,481] [INFO] Selected 12 target genomes.
[2024-01-24 12:23:16,481] [INFO] Target genome list was writen to GCF_003382285.1_ASM338228v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:16,486] [INFO] Task started: fastANI
[2024-01-24 12:23:16,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a95de27-671f-4bf4-b8b1-675ffdd59b25/GCF_003382285.1_ASM338228v1_genomic.fna.gz --refList GCF_003382285.1_ASM338228v1_genomic.fna/target_genomes.txt --output GCF_003382285.1_ASM338228v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:28,174] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:28,175] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c1edcd2-c5d0-4e7e-a0a3-d53a8e46d174/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:28,175] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c1edcd2-c5d0-4e7e-a0a3-d53a8e46d174/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:28,183] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:28,183] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:28,183] [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	100.0	1305	1305	95	conclusive
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	85.9547	1010	1305	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	84.2126	902	1305	95	below_threshold
Lysobacter prati	strain=SYSU H10001	GCA_009765215.1	2596704	2596704	type	True	83.7579	920	1305	95	below_threshold
Lysobacter niastensis	strain=DSM 18481	GCA_015453285.1	380629	380629	type	True	83.616	819	1305	95	below_threshold
Lysobacter terrestris	strain=II4	GCA_014489475.1	2865112	2865112	type	True	82.7058	731	1305	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	82.4754	795	1305	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	82.0428	802	1305	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	81.9038	624	1305	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	81.6574	798	1305	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	81.1322	590	1305	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	81.0917	702	1305	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:28,185] [INFO] DFAST Taxonomy check result was written to GCF_003382285.1_ASM338228v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:28,185] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:28,185] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:28,185] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c1edcd2-c5d0-4e7e-a0a3-d53a8e46d174/dqc_reference/checkm_data
[2024-01-24 12:23:28,186] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:28,225] [INFO] Task started: CheckM
[2024-01-24 12:23:28,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003382285.1_ASM338228v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003382285.1_ASM338228v1_genomic.fna/checkm_input GCF_003382285.1_ASM338228v1_genomic.fna/checkm_result
[2024-01-24 12:24:08,041] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:08,042] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:08,062] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:08,062] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:08,062] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003382285.1_ASM338228v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:08,063] [INFO] Task started: Blastn
[2024-01-24 12:24:08,063] [INFO] Running command: blastn -query GCF_003382285.1_ASM338228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c1edcd2-c5d0-4e7e-a0a3-d53a8e46d174/dqc_reference/reference_markers_gtdb.fasta -out GCF_003382285.1_ASM338228v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:10,032] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:10,034] [INFO] Selected 6 target genomes.
[2024-01-24 12:24:10,035] [INFO] Target genome list was writen to GCF_003382285.1_ASM338228v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:10,039] [INFO] Task started: fastANI
[2024-01-24 12:24:10,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a95de27-671f-4bf4-b8b1-675ffdd59b25/GCF_003382285.1_ASM338228v1_genomic.fna.gz --refList GCF_003382285.1_ASM338228v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003382285.1_ASM338228v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:17,085] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:17,090] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:17,091] [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	100.0	1305	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.84	96.81	0.94	0.93	3	conclusive
GCF_017308985.1	s__Lysobacter sp017308985	89.5371	1119	1305	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	87.3326	1080	1305	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	86.4301	1078	1305	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	85.93	1013	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442515.1	s__Lysobacter enzymogenes_B	82.013	837	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:17,092] [INFO] GTDB search result was written to GCF_003382285.1_ASM338228v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:17,092] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:17,096] [INFO] DFAST_QC result json was written to GCF_003382285.1_ASM338228v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:17,096] [INFO] DFAST_QC completed!
[2024-01-24 12:24:17,096] [INFO] Total running time: 0h1m14s