[2024-01-25 19:51:20,708] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:51:20,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:51:20,710] [INFO] DQC Reference Directory: /var/lib/cwl/stgc434f3e9-8415-47ca-8653-d150a9b91977/dqc_reference
[2024-01-25 19:51:21,903] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:51:21,903] [INFO] Task started: Prodigal
[2024-01-25 19:51:21,904] [INFO] Running command: gunzip -c /var/lib/cwl/stg56cc4abc-c4c7-418b-aa0e-846f964179f0/GCF_016613535.2_ASM1661353v2_genomic.fna.gz | prodigal -d GCF_016613535.2_ASM1661353v2_genomic.fna/cds.fna -a GCF_016613535.2_ASM1661353v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:51:33,237] [INFO] Task succeeded: Prodigal
[2024-01-25 19:51:33,238] [INFO] Task started: HMMsearch
[2024-01-25 19:51:33,238] [INFO] Running command: hmmsearch --tblout GCF_016613535.2_ASM1661353v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc434f3e9-8415-47ca-8653-d150a9b91977/dqc_reference/reference_markers.hmm GCF_016613535.2_ASM1661353v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:51:33,491] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:51:33,492] [INFO] Found 6/6 markers.
[2024-01-25 19:51:33,525] [INFO] Query marker FASTA was written to GCF_016613535.2_ASM1661353v2_genomic.fna/markers.fasta
[2024-01-25 19:51:33,525] [INFO] Task started: Blastn
[2024-01-25 19:51:33,525] [INFO] Running command: blastn -query GCF_016613535.2_ASM1661353v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc434f3e9-8415-47ca-8653-d150a9b91977/dqc_reference/reference_markers.fasta -out GCF_016613535.2_ASM1661353v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:34,543] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:34,545] [INFO] Selected 21 target genomes.
[2024-01-25 19:51:34,545] [INFO] Target genome list was writen to GCF_016613535.2_ASM1661353v2_genomic.fna/target_genomes.txt
[2024-01-25 19:51:34,575] [INFO] Task started: fastANI
[2024-01-25 19:51:34,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg56cc4abc-c4c7-418b-aa0e-846f964179f0/GCF_016613535.2_ASM1661353v2_genomic.fna.gz --refList GCF_016613535.2_ASM1661353v2_genomic.fna/target_genomes.txt --output GCF_016613535.2_ASM1661353v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:52,532] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:52,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc434f3e9-8415-47ca-8653-d150a9b91977/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:52,533] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc434f3e9-8415-47ca-8653-d150a9b91977/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:52,545] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:51:52,545] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:51:52,546] [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 solisilvae	strain=R19	GCA_016613535.2	2763317	2763317	type	True	100.0	1310	1311	95	conclusive
Lysobacter terrestris	strain=II4	GCA_014489475.1	2865112	2865112	type	True	83.5945	774	1311	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	82.2457	666	1311	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	82.2243	636	1311	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	82.1539	744	1311	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	81.9551	681	1311	95	below_threshold
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	81.8622	698	1311	95	below_threshold
Lysobacter ruishenii	strain=CGMCC 1.10136	GCA_007830115.1	686800	686800	type	True	81.5698	610	1311	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	81.5689	691	1311	95	below_threshold
Lysobacter prati	strain=SYSU H10001	GCA_009765215.1	2596704	2596704	type	True	81.5628	690	1311	95	below_threshold
Lysobacter daejeonensis	strain=GH1-9	GCA_000768355.1	346181	346181	type	True	81.4524	589	1311	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	81.4161	761	1311	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	81.2294	587	1311	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	81.1492	600	1311	95	below_threshold
Lysobacter maris	strain=KCTC 42381	GCA_006546735.2	1605891	1605891	type	True	81.0329	577	1311	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.015	650	1311	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	80.9977	581	1311	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	80.8825	730	1311	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	80.7206	627	1311	95	below_threshold
Lysobacter dokdonensis	strain=DS-58	GCA_000770795.1	414050	414050	type	True	80.524	548	1311	95	below_threshold
Thermomonas fusca	strain=DSM 15424	GCA_000423885.1	215690	215690	type	True	80.4539	555	1311	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:51:52,547] [INFO] DFAST Taxonomy check result was written to GCF_016613535.2_ASM1661353v2_genomic.fna/tc_result.tsv
[2024-01-25 19:51:52,548] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:52,548] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:52,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc434f3e9-8415-47ca-8653-d150a9b91977/dqc_reference/checkm_data
[2024-01-25 19:51:52,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:52,589] [INFO] Task started: CheckM
[2024-01-25 19:51:52,589] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016613535.2_ASM1661353v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016613535.2_ASM1661353v2_genomic.fna/checkm_input GCF_016613535.2_ASM1661353v2_genomic.fna/checkm_result
[2024-01-25 19:52:55,844] [INFO] Task succeeded: CheckM
[2024-01-25 19:52:55,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:52:55,862] [INFO] ===== Completeness check finished =====
[2024-01-25 19:52:55,862] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:52:55,863] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016613535.2_ASM1661353v2_genomic.fna/markers.fasta)
[2024-01-25 19:52:55,864] [INFO] Task started: Blastn
[2024-01-25 19:52:55,864] [INFO] Running command: blastn -query GCF_016613535.2_ASM1661353v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc434f3e9-8415-47ca-8653-d150a9b91977/dqc_reference/reference_markers_gtdb.fasta -out GCF_016613535.2_ASM1661353v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:57,764] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:57,767] [INFO] Selected 16 target genomes.
[2024-01-25 19:52:57,768] [INFO] Target genome list was writen to GCF_016613535.2_ASM1661353v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:52:57,782] [INFO] Task started: fastANI
[2024-01-25 19:52:57,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg56cc4abc-c4c7-418b-aa0e-846f964179f0/GCF_016613535.2_ASM1661353v2_genomic.fna.gz --refList GCF_016613535.2_ASM1661353v2_genomic.fna/target_genomes_gtdb.txt --output GCF_016613535.2_ASM1661353v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:53:12,685] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:12,695] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:53:12,695] [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_016613535.2	s__Lysobacter solisilvae_A	100.0	1310	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014489475.1	s__Lysobacter solisilvae	83.6161	772	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427225.1	s__Lysobacter sp001427225	82.0096	720	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016613475.2	s__Lysobacter arenosi	81.974	681	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003586305.1	s__Lysobacter tabacisoli	81.9311	696	1311	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	81.837	697	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428685.1	s__Lysobacter sp001428685	81.7605	745	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.42	98.61	0.98	0.96	4	-
GCF_900114355.1	s__Lysobacter sp900114355	81.6821	738	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429785.1	s__Lysobacter sp001429785	81.6514	746	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.47	98.45	0.97	0.97	3	-
GCF_009765215.1	s__Lysobacter prati	81.5899	686	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830115.1	s__Lysobacter ruishenii	81.558	611	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361435.1	s__Lysobacter sp013361435	81.5539	664	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006546735.2	s__Lysobacter maris	81.0398	575	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.39	98.39	0.88	0.88	2	-
GCA_016720345.1	s__Thermomonas sp016720345	80.818	553	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.48	99.08	0.97	0.93	11	-
GCF_000770795.1	s__Lysobacter_A dokdonensis	80.4917	548	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362405.1	s__JABFWF01 sp013362405	80.4472	458	1311	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:53:12,697] [INFO] GTDB search result was written to GCF_016613535.2_ASM1661353v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:53:12,697] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:53:12,700] [INFO] DFAST_QC result json was written to GCF_016613535.2_ASM1661353v2_genomic.fna/dqc_result.json
[2024-01-25 19:53:12,701] [INFO] DFAST_QC completed!
[2024-01-25 19:53:12,701] [INFO] Total running time: 0h1m52s