[2023-06-05 10:33:51,797] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:33:51,798] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:33:51,798] [INFO] DQC Reference Directory: /var/lib/cwl/stg222ccae7-7d57-4c17-8876-52d0d9879871/dqc_reference
[2023-06-05 10:33:52,888] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:33:52,889] [INFO] Task started: Prodigal
[2023-06-05 10:33:52,889] [INFO] Running command: gunzip -c /var/lib/cwl/stg778024ba-1d44-4c67-a14e-28c1b97b519f/GCA_001830245.1_ASM183024v1_genomic.fna.gz | prodigal -d GCA_001830245.1_ASM183024v1_genomic.fna/cds.fna -a GCA_001830245.1_ASM183024v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:34:00,917] [INFO] Task succeeded: Prodigal
[2023-06-05 10:34:00,917] [INFO] Task started: HMMsearch
[2023-06-05 10:34:00,917] [INFO] Running command: hmmsearch --tblout GCA_001830245.1_ASM183024v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg222ccae7-7d57-4c17-8876-52d0d9879871/dqc_reference/reference_markers.hmm GCA_001830245.1_ASM183024v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:34:01,116] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:34:01,117] [INFO] Found 6/6 markers.
[2023-06-05 10:34:01,143] [INFO] Query marker FASTA was written to GCA_001830245.1_ASM183024v1_genomic.fna/markers.fasta
[2023-06-05 10:34:01,143] [INFO] Task started: Blastn
[2023-06-05 10:34:01,143] [INFO] Running command: blastn -query GCA_001830245.1_ASM183024v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg222ccae7-7d57-4c17-8876-52d0d9879871/dqc_reference/reference_markers.fasta -out GCA_001830245.1_ASM183024v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:34:02,054] [INFO] Task succeeded: Blastn
[2023-06-05 10:34:02,057] [INFO] Selected 23 target genomes.
[2023-06-05 10:34:02,058] [INFO] Target genome list was writen to GCA_001830245.1_ASM183024v1_genomic.fna/target_genomes.txt
[2023-06-05 10:34:02,066] [INFO] Task started: fastANI
[2023-06-05 10:34:02,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg778024ba-1d44-4c67-a14e-28c1b97b519f/GCA_001830245.1_ASM183024v1_genomic.fna.gz --refList GCA_001830245.1_ASM183024v1_genomic.fna/target_genomes.txt --output GCA_001830245.1_ASM183024v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:34:19,156] [INFO] Task succeeded: fastANI
[2023-06-05 10:34:19,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg222ccae7-7d57-4c17-8876-52d0d9879871/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:34:19,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg222ccae7-7d57-4c17-8876-52d0d9879871/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:34:19,170] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:34:19,170] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 10:34:19,170] [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 arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	83.4643	613	948	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	82.5255	606	948	95	below_threshold
Lysobacter maris	strain=KCTC 42381	GCA_006546735.2	1605891	1605891	type	True	82.4969	553	948	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	82.2892	630	948	95	below_threshold
Lysobacter spongiae	strain=119BY6-57	GCA_014145325.1	2025720	2025720	type	True	81.8103	605	948	95	below_threshold
Lysobacter alkalisoli	strain=SJ-36	GCA_006547045.1	2591633	2591633	type	True	81.8055	577	948	95	below_threshold
Lysobacter defluvii	strain=IMMIB APB-9	GCA_000769985.1	391738	391738	type	True	81.7524	443	948	95	below_threshold
Lysobacter psychrotolerans	strain=ZS60	GCA_003719825.1	1327343	1327343	type	True	81.7171	586	948	95	below_threshold
Lysobacter defluvii	strain=DSM 18482	GCA_000423325.1	391738	391738	type	True	81.6885	539	948	95	below_threshold
Lysobacter spongiicola	strain=DSM 21749	GCA_900167055.1	435289	435289	type	True	81.6771	582	948	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	81.5949	603	948	95	below_threshold
Lysobacter solisilvae	strain=R19	GCA_016613535.2	2763317	2763317	type	True	81.4211	579	948	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	81.2934	534	948	95	below_threshold
Pseudoxanthomonas koreensis	strain=KCTC 12208	GCA_010093225.1	266061	266061	type	True	81.2434	525	948	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	81.0457	604	948	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	80.9622	531	948	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	80.8562	540	948	95	below_threshold
Pseudoxanthomonas mexicana	strain=DSM 17121	GCA_010093385.1	128785	128785	type	True	80.7084	524	948	95	below_threshold
Pseudoxanthomonas daejeonensis	strain=DSM 17801	GCA_010093205.1	266062	266062	type	True	80.6314	535	948	95	below_threshold
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	80.5749	540	948	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	80.4848	477	948	95	below_threshold
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	80.4848	531	948	95	below_threshold
Lysobacter bugurensis	strain=KCTC 23077	GCA_014652095.1	543356	543356	type	True	80.366	526	948	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 10:34:19,172] [INFO] DFAST Taxonomy check result was written to GCA_001830245.1_ASM183024v1_genomic.fna/tc_result.tsv
[2023-06-05 10:34:19,172] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:34:19,172] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:34:19,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg222ccae7-7d57-4c17-8876-52d0d9879871/dqc_reference/checkm_data
[2023-06-05 10:34:19,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:34:19,204] [INFO] Task started: CheckM
[2023-06-05 10:34:19,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001830245.1_ASM183024v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001830245.1_ASM183024v1_genomic.fna/checkm_input GCA_001830245.1_ASM183024v1_genomic.fna/checkm_result
[2023-06-05 10:34:45,768] [INFO] Task succeeded: CheckM
[2023-06-05 10:34:45,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 10:34:45,784] [INFO] ===== Completeness check finished =====
[2023-06-05 10:34:45,784] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:34:45,785] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001830245.1_ASM183024v1_genomic.fna/markers.fasta)
[2023-06-05 10:34:45,785] [INFO] Task started: Blastn
[2023-06-05 10:34:45,785] [INFO] Running command: blastn -query GCA_001830245.1_ASM183024v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg222ccae7-7d57-4c17-8876-52d0d9879871/dqc_reference/reference_markers_gtdb.fasta -out GCA_001830245.1_ASM183024v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:34:47,533] [INFO] Task succeeded: Blastn
[2023-06-05 10:34:47,537] [INFO] Selected 20 target genomes.
[2023-06-05 10:34:47,538] [INFO] Target genome list was writen to GCA_001830245.1_ASM183024v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:34:47,882] [INFO] Task started: fastANI
[2023-06-05 10:34:47,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg778024ba-1d44-4c67-a14e-28c1b97b519f/GCA_001830245.1_ASM183024v1_genomic.fna.gz --refList GCA_001830245.1_ASM183024v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001830245.1_ASM183024v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:35:03,384] [INFO] Task succeeded: fastANI
[2023-06-05 10:35:03,396] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 10:35:03,396] [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
GCA_001830245.1	s__Lysobacter sp001830245	100.0	943	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.71	99.71	0.92	0.92	2	conclusive
GCF_000768335.1	s__Lysobacter arseniciresistens	83.4534	614	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907164845.1	s__Lysobacter sp907164845	82.5366	605	948	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	82.0741	592	948	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	81.9775	630	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.42	98.61	0.98	0.96	4	-
GCA_013361435.1	s__Lysobacter sp013361435	81.9118	560	948	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	81.8387	603	948	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	81.8343	633	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCF_006547045.1	s__Lysobacter alkalisoli	81.8258	575	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719825.1	s__Lysobacter psychrotolerans	81.717	586	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423325.1	s__Lysobacter defluvii	81.7086	537	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009765215.1	s__Lysobacter prati	81.6047	590	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016613535.2	s__Lysobacter solisilvae_A	81.4405	577	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004357985.1	s__Luteimonas aestuarii	80.845	541	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093385.1	s__Pseudoxanthomonas_A mexicana	80.7054	525	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	96.97	96.88	0.87	0.86	4	-
GCA_014654535.1	s__Pseudomonas_S boreopolis	80.6375	539	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudomonas_S	95.0	98.68	98.68	0.91	0.91	2	-
GCF_010093445.1	s__Pseudoxanthomonas_A japonensis	80.6144	536	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	96.78	96.68	0.83	0.68	4	-
GCF_001427635.1	s__Pseudoxanthomonas_A sp001427635	80.6086	556	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014851815.1	s__Pseudoxanthomonas_A sp014851815	80.4401	537	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652095.1	s__Lysobacter bugurensis	80.3649	525	948	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 10:35:03,398] [INFO] GTDB search result was written to GCA_001830245.1_ASM183024v1_genomic.fna/result_gtdb.tsv
[2023-06-05 10:35:03,398] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:35:03,402] [INFO] DFAST_QC result json was written to GCA_001830245.1_ASM183024v1_genomic.fna/dqc_result.json
[2023-06-05 10:35:03,402] [INFO] DFAST_QC completed!
[2023-06-05 10:35:03,402] [INFO] Total running time: 0h1m12s