[2024-01-24 14:30:30,712] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:30,715] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:30,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b2b0401-e4ff-4dd3-9111-de349e54a0e2/dqc_reference
[2024-01-24 14:30:32,016] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:32,018] [INFO] Task started: Prodigal
[2024-01-24 14:30:32,018] [INFO] Running command: gunzip -c /var/lib/cwl/stgd10f2944-3485-49f1-b64f-36885361475b/GCF_020026895.1_ASM2002689v1_genomic.fna.gz | prodigal -d GCF_020026895.1_ASM2002689v1_genomic.fna/cds.fna -a GCF_020026895.1_ASM2002689v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:42,487] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:42,487] [INFO] Task started: HMMsearch
[2024-01-24 14:30:42,487] [INFO] Running command: hmmsearch --tblout GCF_020026895.1_ASM2002689v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b2b0401-e4ff-4dd3-9111-de349e54a0e2/dqc_reference/reference_markers.hmm GCF_020026895.1_ASM2002689v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:42,770] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:42,771] [INFO] Found 6/6 markers.
[2024-01-24 14:30:42,799] [INFO] Query marker FASTA was written to GCF_020026895.1_ASM2002689v1_genomic.fna/markers.fasta
[2024-01-24 14:30:42,800] [INFO] Task started: Blastn
[2024-01-24 14:30:42,800] [INFO] Running command: blastn -query GCF_020026895.1_ASM2002689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b2b0401-e4ff-4dd3-9111-de349e54a0e2/dqc_reference/reference_markers.fasta -out GCF_020026895.1_ASM2002689v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:43,870] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:43,874] [INFO] Selected 19 target genomes.
[2024-01-24 14:30:43,874] [INFO] Target genome list was writen to GCF_020026895.1_ASM2002689v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:43,888] [INFO] Task started: fastANI
[2024-01-24 14:30:43,889] [INFO] Running command: fastANI --query /var/lib/cwl/stgd10f2944-3485-49f1-b64f-36885361475b/GCF_020026895.1_ASM2002689v1_genomic.fna.gz --refList GCF_020026895.1_ASM2002689v1_genomic.fna/target_genomes.txt --output GCF_020026895.1_ASM2002689v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:30:58,276] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:58,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b2b0401-e4ff-4dd3-9111-de349e54a0e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:30:58,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b2b0401-e4ff-4dd3-9111-de349e54a0e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:30:58,297] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:30:58,297] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:30:58,297] [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	83.6566	653	1023	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	82.9054	644	1023	95	below_threshold
Lysobacter maris	strain=KCTC 42381	GCA_006546735.2	1605891	1605891	type	True	82.6526	593	1023	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	82.3576	676	1023	95	below_threshold
Lysobacter spongiae	strain=119BY6-57	GCA_014145325.1	2025720	2025720	type	True	82.149	612	1023	95	below_threshold
Lysobacter defluvii	strain=IMMIB APB-9	GCA_000769985.1	391738	391738	type	True	82.1166	458	1023	95	below_threshold
Lysobacter niastensis	strain=DSM 18481	GCA_015453285.1	380629	380629	type	True	81.9437	634	1023	95	below_threshold
Lysobacter defluvii	strain=DSM 18482	GCA_000423325.1	391738	391738	type	True	81.9122	571	1023	95	below_threshold
Lysobacter spongiicola	strain=DSM 21749	GCA_900167055.1	435289	435289	type	True	81.8953	616	1023	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	81.7201	649	1023	95	below_threshold
Lysobacter psychrotolerans	strain=ZS60	GCA_003719825.1	1327343	1327343	type	True	81.718	607	1023	95	below_threshold
Lysobacter alkalisoli	strain=SJ-36	GCA_006547045.1	2591633	2591633	type	True	81.5941	646	1023	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	81.5718	527	1023	95	below_threshold
Lysobacter penaei	strain=SG-8	GCA_014145395.1	2759900	2759900	type	True	81.5542	562	1023	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.3756	589	1023	95	below_threshold
Luteimonas terricola	strain=BZ92r	GCA_004352845.1	645597	645597	type	True	81.3196	549	1023	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	81.2047	648	1023	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	81.0225	563	1023	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	79.6158	492	1023	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:30:58,339] [INFO] DFAST Taxonomy check result was written to GCF_020026895.1_ASM2002689v1_genomic.fna/tc_result.tsv
[2024-01-24 14:30:58,340] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:30:58,341] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:30:58,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b2b0401-e4ff-4dd3-9111-de349e54a0e2/dqc_reference/checkm_data
[2024-01-24 14:30:58,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:30:58,375] [INFO] Task started: CheckM
[2024-01-24 14:30:58,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020026895.1_ASM2002689v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020026895.1_ASM2002689v1_genomic.fna/checkm_input GCF_020026895.1_ASM2002689v1_genomic.fna/checkm_result
[2024-01-24 14:31:35,553] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:35,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:35,577] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:35,577] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:35,578] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020026895.1_ASM2002689v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:35,578] [INFO] Task started: Blastn
[2024-01-24 14:31:35,579] [INFO] Running command: blastn -query GCF_020026895.1_ASM2002689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b2b0401-e4ff-4dd3-9111-de349e54a0e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_020026895.1_ASM2002689v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:37,626] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:37,631] [INFO] Selected 17 target genomes.
[2024-01-24 14:31:37,631] [INFO] Target genome list was writen to GCF_020026895.1_ASM2002689v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:37,649] [INFO] Task started: fastANI
[2024-01-24 14:31:37,649] [INFO] Running command: fastANI --query /var/lib/cwl/stgd10f2944-3485-49f1-b64f-36885361475b/GCF_020026895.1_ASM2002689v1_genomic.fna.gz --refList GCF_020026895.1_ASM2002689v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020026895.1_ASM2002689v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:50,629] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:50,647] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:31:50,647] [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	92.8466	856	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.71	99.71	0.92	0.92	2	-
GCF_000768335.1	s__Lysobacter arseniciresistens	83.633	655	1023	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	82.8664	647	1023	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	82.6447	594	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.39	98.39	0.88	0.88	2	-
GCF_007830115.1	s__Lysobacter ruishenii	82.3531	590	1023	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	82.1615	611	1023	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	82.1168	588	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015453285.1	s__Lysobacter niastensis	81.9556	633	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167055.1	s__Lysobacter spongiicola	81.9395	612	1023	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	81.8864	573	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003719825.1	s__Lysobacter psychrotolerans	81.713	607	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006547045.1	s__Lysobacter alkalisoli	81.5995	644	1023	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	81.5623	561	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442805.1	s__Lysobacter gummosus	81.2606	621	1023	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	81.0182	563	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297225.1	s__Luteimonas_B sp004297225	80.9881	443	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014654535.1	s__Pseudomonas_S boreopolis	80.8784	552	1023	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudomonas_S	95.0	98.68	98.68	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:50,649] [INFO] GTDB search result was written to GCF_020026895.1_ASM2002689v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:50,650] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:50,654] [INFO] DFAST_QC result json was written to GCF_020026895.1_ASM2002689v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:50,654] [INFO] DFAST_QC completed!
[2024-01-24 14:31:50,654] [INFO] Total running time: 0h1m20s