[2024-01-25 20:02:35,564] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:02:35,565] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:02:35,566] [INFO] DQC Reference Directory: /var/lib/cwl/stg6747b986-782d-441d-aa2a-3fb968befac3/dqc_reference
[2024-01-25 20:02:36,688] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:02:36,689] [INFO] Task started: Prodigal
[2024-01-25 20:02:36,689] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c765f56-ccbd-4f13-8371-dfcde62ebb8c/GCF_014779555.2_ASM1477955v2_genomic.fna.gz | prodigal -d GCF_014779555.2_ASM1477955v2_genomic.fna/cds.fna -a GCF_014779555.2_ASM1477955v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:02:57,219] [INFO] Task succeeded: Prodigal
[2024-01-25 20:02:57,220] [INFO] Task started: HMMsearch
[2024-01-25 20:02:57,220] [INFO] Running command: hmmsearch --tblout GCF_014779555.2_ASM1477955v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6747b986-782d-441d-aa2a-3fb968befac3/dqc_reference/reference_markers.hmm GCF_014779555.2_ASM1477955v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:02:57,483] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:02:57,484] [INFO] Found 6/6 markers.
[2024-01-25 20:02:57,527] [INFO] Query marker FASTA was written to GCF_014779555.2_ASM1477955v2_genomic.fna/markers.fasta
[2024-01-25 20:02:57,527] [INFO] Task started: Blastn
[2024-01-25 20:02:57,527] [INFO] Running command: blastn -query GCF_014779555.2_ASM1477955v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6747b986-782d-441d-aa2a-3fb968befac3/dqc_reference/reference_markers.fasta -out GCF_014779555.2_ASM1477955v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:58,491] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:58,494] [INFO] Selected 12 target genomes.
[2024-01-25 20:02:58,494] [INFO] Target genome list was writen to GCF_014779555.2_ASM1477955v2_genomic.fna/target_genomes.txt
[2024-01-25 20:02:58,509] [INFO] Task started: fastANI
[2024-01-25 20:02:58,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c765f56-ccbd-4f13-8371-dfcde62ebb8c/GCF_014779555.2_ASM1477955v2_genomic.fna.gz --refList GCF_014779555.2_ASM1477955v2_genomic.fna/target_genomes.txt --output GCF_014779555.2_ASM1477955v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:14,290] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:14,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6747b986-782d-441d-aa2a-3fb968befac3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:14,291] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6747b986-782d-441d-aa2a-3fb968befac3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:14,299] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:03:14,299] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:14,299] [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 capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	100.0	2078	2079	95	conclusive
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	86.0521	1485	2079	95	below_threshold
Lysobacter antibioticus	strain=ATCC 29479	GCA_001442535.1	84531	84531	type	True	85.8229	1385	2079	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	83.8106	1052	2079	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	82.4156	866	2079	95	below_threshold
Lysobacter terrestris	strain=II4	GCA_014489475.1	2865112	2865112	type	True	81.8323	765	2079	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	81.8107	656	2079	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	81.4686	809	2079	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	81.0648	599	2079	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	80.7876	800	2079	95	below_threshold
Lysobacter penaei	strain=SG-8	GCA_014145395.1	2759900	2759900	type	True	80.3144	591	2079	95	below_threshold
Stenotrophomonas bentonitica	strain=DSM 103927	GCA_013185915.1	1450134	1450134	type	True	79.7976	651	2079	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:14,301] [INFO] DFAST Taxonomy check result was written to GCF_014779555.2_ASM1477955v2_genomic.fna/tc_result.tsv
[2024-01-25 20:03:14,301] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:14,301] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:14,301] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6747b986-782d-441d-aa2a-3fb968befac3/dqc_reference/checkm_data
[2024-01-25 20:03:14,302] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:14,361] [INFO] Task started: CheckM
[2024-01-25 20:03:14,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014779555.2_ASM1477955v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014779555.2_ASM1477955v2_genomic.fna/checkm_input GCF_014779555.2_ASM1477955v2_genomic.fna/checkm_result
[2024-01-25 20:04:28,982] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:28,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:29,003] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:29,003] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:29,004] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014779555.2_ASM1477955v2_genomic.fna/markers.fasta)
[2024-01-25 20:04:29,004] [INFO] Task started: Blastn
[2024-01-25 20:04:29,004] [INFO] Running command: blastn -query GCF_014779555.2_ASM1477955v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6747b986-782d-441d-aa2a-3fb968befac3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014779555.2_ASM1477955v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:30,947] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:31,101] [INFO] Selected 7 target genomes.
[2024-01-25 20:04:31,101] [INFO] Target genome list was writen to GCF_014779555.2_ASM1477955v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:31,110] [INFO] Task started: fastANI
[2024-01-25 20:04:31,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c765f56-ccbd-4f13-8371-dfcde62ebb8c/GCF_014779555.2_ASM1477955v2_genomic.fna.gz --refList GCF_014779555.2_ASM1477955v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014779555.2_ASM1477955v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:49,515] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:49,520] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:04:49,521] [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_014779555.1	s__Lysobacter capsici	99.9579	1996	2079	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.59	97.48	0.93	0.93	5	conclusive
GCF_001427785.1	s__Lysobacter sp001427785	93.9701	1876	2079	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018732085.1	s__Lysobacter capsici_A	93.838	1871	2079	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018612875.1	s__Lysobacter sp018612875	87.3489	1403	2079	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.97	0.96	0.96	4	-
GCF_001442805.1	s__Lysobacter gummosus	87.3303	1510	2079	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107375.1	s__Lysobacter sp900107375	86.2432	1452	2079	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336385.2	s__Lysobacter antibioticus_A	85.5129	1247	2079	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:04:49,522] [INFO] GTDB search result was written to GCF_014779555.2_ASM1477955v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:49,522] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:49,525] [INFO] DFAST_QC result json was written to GCF_014779555.2_ASM1477955v2_genomic.fna/dqc_result.json
[2024-01-25 20:04:49,525] [INFO] DFAST_QC completed!
[2024-01-25 20:04:49,525] [INFO] Total running time: 0h2m14s