[2024-01-24 11:05:03,936] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,943] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,943] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7e2da94-996d-4c14-82b6-34312352bd92/dqc_reference
[2024-01-24 11:05:05,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,812] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,813] [INFO] Running command: gunzip -c /var/lib/cwl/stgd364910e-d064-4447-aa1b-b6440c4bae91/GCF_021725675.1_ASM2172567v1_genomic.fna.gz | prodigal -d GCF_021725675.1_ASM2172567v1_genomic.fna/cds.fna -a GCF_021725675.1_ASM2172567v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:17,167] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:17,167] [INFO] Task started: HMMsearch
[2024-01-24 11:05:17,168] [INFO] Running command: hmmsearch --tblout GCF_021725675.1_ASM2172567v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7e2da94-996d-4c14-82b6-34312352bd92/dqc_reference/reference_markers.hmm GCF_021725675.1_ASM2172567v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:17,427] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:17,428] [INFO] Found 6/6 markers.
[2024-01-24 11:05:17,464] [INFO] Query marker FASTA was written to GCF_021725675.1_ASM2172567v1_genomic.fna/markers.fasta
[2024-01-24 11:05:17,464] [INFO] Task started: Blastn
[2024-01-24 11:05:17,464] [INFO] Running command: blastn -query GCF_021725675.1_ASM2172567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7e2da94-996d-4c14-82b6-34312352bd92/dqc_reference/reference_markers.fasta -out GCF_021725675.1_ASM2172567v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:18,401] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:18,405] [INFO] Selected 15 target genomes.
[2024-01-24 11:05:18,405] [INFO] Target genome list was writen to GCF_021725675.1_ASM2172567v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:18,427] [INFO] Task started: fastANI
[2024-01-24 11:05:18,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgd364910e-d064-4447-aa1b-b6440c4bae91/GCF_021725675.1_ASM2172567v1_genomic.fna.gz --refList GCF_021725675.1_ASM2172567v1_genomic.fna/target_genomes.txt --output GCF_021725675.1_ASM2172567v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:41,061] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:41,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7e2da94-996d-4c14-82b6-34312352bd92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:41,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7e2da94-996d-4c14-82b6-34312352bd92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:41,072] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:41,072] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:41,072] [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 chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	100.0	1377	1417	95	conclusive
Lysobacter maris	strain=KCTC 42381	GCA_006546735.2	1605891	1605891	type	True	87.515	902	1417	95	below_threshold
Lysobacter alkalisoli	strain=SJ-36	GCA_006547045.1	2591633	2591633	type	True	84.4067	939	1417	95	below_threshold
Lysobacter spongiae	strain=119BY6-57	GCA_014145325.1	2025720	2025720	type	True	83.3278	832	1417	95	below_threshold
Lysobacter aestuarii	strain=JCM 31130	GCA_006546775.1	1706195	1706195	type	True	83.1946	774	1417	95	below_threshold
Lysobacter penaei	strain=SG-8	GCA_014145395.1	2759900	2759900	type	True	82.8821	726	1417	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	82.5862	642	1417	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	81.745	790	1417	95	below_threshold
Lysobacter niastensis	strain=DSM 18481	GCA_015453285.1	380629	380629	type	True	81.6488	677	1417	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	81.4422	612	1417	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	81.0487	791	1417	95	below_threshold
Luteimonas terricola	strain=BZ92r	GCA_004352845.1	645597	645597	type	True	80.5964	587	1417	95	below_threshold
Luteimonas granuli	strain=Gr-4	GCA_007795095.1	1176533	1176533	type	True	80.5669	558	1417	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	80.5357	646	1417	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP1156	GCA_002939895.1	56455	56455	type	True	80.494	649	1417	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:41,075] [INFO] DFAST Taxonomy check result was written to GCF_021725675.1_ASM2172567v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:41,076] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:41,076] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:41,076] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7e2da94-996d-4c14-82b6-34312352bd92/dqc_reference/checkm_data
[2024-01-24 11:05:41,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:41,122] [INFO] Task started: CheckM
[2024-01-24 11:05:41,122] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021725675.1_ASM2172567v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021725675.1_ASM2172567v1_genomic.fna/checkm_input GCF_021725675.1_ASM2172567v1_genomic.fna/checkm_result
[2024-01-24 11:06:28,360] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:28,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:28,378] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:28,378] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:28,378] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021725675.1_ASM2172567v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:28,378] [INFO] Task started: Blastn
[2024-01-24 11:06:28,379] [INFO] Running command: blastn -query GCF_021725675.1_ASM2172567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7e2da94-996d-4c14-82b6-34312352bd92/dqc_reference/reference_markers_gtdb.fasta -out GCF_021725675.1_ASM2172567v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:30,195] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:30,197] [INFO] Selected 14 target genomes.
[2024-01-24 11:06:30,197] [INFO] Target genome list was writen to GCF_021725675.1_ASM2172567v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:30,205] [INFO] Task started: fastANI
[2024-01-24 11:06:30,205] [INFO] Running command: fastANI --query /var/lib/cwl/stgd364910e-d064-4447-aa1b-b6440c4bae91/GCF_021725675.1_ASM2172567v1_genomic.fna.gz --refList GCF_021725675.1_ASM2172567v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021725675.1_ASM2172567v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:42,598] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:42,608] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:06:42,608] [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_006546735.2	s__Lysobacter maris	87.5047	904	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.39	98.39	0.88	0.88	2	-
GCF_006547045.1	s__Lysobacter alkalisoli	84.4065	939	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145325.1	s__Lysobacter spongiae	83.3382	831	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006546775.1	s__Lysobacter aestuarii	83.2191	773	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145395.1	s__Lysobacter penaei	82.8761	727	1417	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	81.8028	818	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	81.6438	603	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Vulcaniibacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015453285.1	s__Lysobacter niastensis	81.6245	680	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000731095.1	s__Lysobacter antibioticus_B	81.1996	753	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442535.1	s__Lysobacter antibioticus	81.0542	770	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.45	98.45	0.94	0.94	2	-
GCF_004352845.1	s__Luteimonas terricola	80.5961	587	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007795095.1	s__Luteimonas granuli	80.5559	559	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769165.1	s__Xanthomonas_A hyacinthi	80.5321	647	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004297225.1	s__Luteimonas_B sp004297225	80.5024	461	1417	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:42,609] [INFO] GTDB search result was written to GCF_021725675.1_ASM2172567v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:42,610] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:42,612] [INFO] DFAST_QC result json was written to GCF_021725675.1_ASM2172567v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:42,612] [INFO] DFAST_QC completed!
[2024-01-24 11:06:42,613] [INFO] Total running time: 0h1m39s