[2024-01-25 18:58:35,617] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:35,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:35,619] [INFO] DQC Reference Directory: /var/lib/cwl/stg67a8ccee-5c86-4c00-8f29-469a5a14d259/dqc_reference
[2024-01-25 18:58:36,776] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:36,777] [INFO] Task started: Prodigal
[2024-01-25 18:58:36,777] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6f45f70-6c44-4675-bb56-3dc53d69cd97/GCF_000423325.1_ASM42332v1_genomic.fna.gz | prodigal -d GCF_000423325.1_ASM42332v1_genomic.fna/cds.fna -a GCF_000423325.1_ASM42332v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:44,049] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:44,050] [INFO] Task started: HMMsearch
[2024-01-25 18:58:44,050] [INFO] Running command: hmmsearch --tblout GCF_000423325.1_ASM42332v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67a8ccee-5c86-4c00-8f29-469a5a14d259/dqc_reference/reference_markers.hmm GCF_000423325.1_ASM42332v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:44,241] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:44,242] [INFO] Found 6/6 markers.
[2024-01-25 18:58:44,266] [INFO] Query marker FASTA was written to GCF_000423325.1_ASM42332v1_genomic.fna/markers.fasta
[2024-01-25 18:58:44,266] [INFO] Task started: Blastn
[2024-01-25 18:58:44,266] [INFO] Running command: blastn -query GCF_000423325.1_ASM42332v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67a8ccee-5c86-4c00-8f29-469a5a14d259/dqc_reference/reference_markers.fasta -out GCF_000423325.1_ASM42332v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:45,193] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:45,195] [INFO] Selected 14 target genomes.
[2024-01-25 18:58:45,196] [INFO] Target genome list was writen to GCF_000423325.1_ASM42332v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:45,213] [INFO] Task started: fastANI
[2024-01-25 18:58:45,214] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6f45f70-6c44-4675-bb56-3dc53d69cd97/GCF_000423325.1_ASM42332v1_genomic.fna.gz --refList GCF_000423325.1_ASM42332v1_genomic.fna/target_genomes.txt --output GCF_000423325.1_ASM42332v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:55,809] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:55,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67a8ccee-5c86-4c00-8f29-469a5a14d259/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:55,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67a8ccee-5c86-4c00-8f29-469a5a14d259/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:55,820] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:58:55,820] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:58:55,820] [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 defluvii	strain=DSM 18482	GCA_000423325.1	391738	391738	type	True	100.0	900	901	95	conclusive
Lysobacter defluvii	strain=IMMIB APB-9	GCA_000769985.1	391738	391738	type	True	99.7035	693	901	95	conclusive
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	83.6088	609	901	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	82.4871	604	901	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	82.1497	588	901	95	below_threshold
Lysobacter spongiicola	strain=DSM 21749	GCA_900167055.1	435289	435289	type	True	81.7474	576	901	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	81.6029	549	901	95	below_threshold
Lysobacter aestuarii	strain=JCM 31130	GCA_006546775.1	1706195	1706195	type	True	81.2393	497	901	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	81.1382	544	901	95	below_threshold
Lysobacter spongiae	strain=119BY6-57	GCA_014145325.1	2025720	2025720	type	True	81.1186	534	901	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	81.0782	552	901	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	80.9659	546	901	95	below_threshold
Lysobacter antarcticus	strain=GW1-59	GCA_019802285.1	2862543	2862543	type	True	80.6152	472	901	95	below_threshold
Lysobacter segetis	strain=17J68-2	GCA_004359965.1	2492394	2492394	type	True	80.1348	472	901	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:55,822] [INFO] DFAST Taxonomy check result was written to GCF_000423325.1_ASM42332v1_genomic.fna/tc_result.tsv
[2024-01-25 18:58:55,822] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:55,822] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:55,822] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67a8ccee-5c86-4c00-8f29-469a5a14d259/dqc_reference/checkm_data
[2024-01-25 18:58:55,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:55,853] [INFO] Task started: CheckM
[2024-01-25 18:58:55,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423325.1_ASM42332v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423325.1_ASM42332v1_genomic.fna/checkm_input GCF_000423325.1_ASM42332v1_genomic.fna/checkm_result
[2024-01-25 18:59:26,406] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:26,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:26,427] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:26,427] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:26,428] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423325.1_ASM42332v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:26,428] [INFO] Task started: Blastn
[2024-01-25 18:59:26,428] [INFO] Running command: blastn -query GCF_000423325.1_ASM42332v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67a8ccee-5c86-4c00-8f29-469a5a14d259/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423325.1_ASM42332v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:28,368] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:28,371] [INFO] Selected 17 target genomes.
[2024-01-25 18:59:28,371] [INFO] Target genome list was writen to GCF_000423325.1_ASM42332v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:28,390] [INFO] Task started: fastANI
[2024-01-25 18:59:28,390] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6f45f70-6c44-4675-bb56-3dc53d69cd97/GCF_000423325.1_ASM42332v1_genomic.fna.gz --refList GCF_000423325.1_ASM42332v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423325.1_ASM42332v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:41,932] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:41,943] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:59:41,943] [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_000423325.1	s__Lysobacter defluvii	100.0	900	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000768335.1	s__Lysobacter arseniciresistens	83.6122	609	901	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	82.452	607	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814555.1	s__Lysobacter tengchongensis	82.1117	591	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCA_001830245.1	s__Lysobacter sp001830245	81.8779	529	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.71	99.71	0.92	0.92	2	-
GCF_006546735.2	s__Lysobacter maris	81.8407	510	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.39	98.39	0.88	0.88	2	-
GCF_900167055.1	s__Lysobacter spongiicola	81.7229	578	901	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	81.6361	546	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000510725.1	s__Pseudoxanthomonas sp000510725	81.3656	553	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.33	99.13	0.95	0.92	5	-
GCF_000513995.1	s__Pseudoxanthomonas sp000513995	81.2612	546	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382365.1	s__Lysobacter silvisoli	81.118	545	901	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	81.0817	537	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346265.1	s__Thermomonas haemolytica	80.9906	465	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	0.99	0.99	3	-
GCA_013361435.1	s__Lysobacter sp013361435	80.9851	471	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114355.1	s__Lysobacter sp900114355	80.9521	546	901	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	80.9259	570	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCF_001429785.1	s__Lysobacter sp001429785	80.8751	531	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.47	98.45	0.97	0.97	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:59:41,945] [INFO] GTDB search result was written to GCF_000423325.1_ASM42332v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:41,945] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:41,948] [INFO] DFAST_QC result json was written to GCF_000423325.1_ASM42332v1_genomic.fna/dqc_result.json
[2024-01-25 18:59:41,949] [INFO] DFAST_QC completed!
[2024-01-25 18:59:41,949] [INFO] Total running time: 0h1m6s