[2024-01-24 12:22:07,500] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:07,504] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:07,504] [INFO] DQC Reference Directory: /var/lib/cwl/stg7989a515-93c4-45f7-b0db-6bed7460e55d/dqc_reference
[2024-01-24 12:22:08,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:08,815] [INFO] Task started: Prodigal
[2024-01-24 12:22:08,815] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a6ee3f8-2c54-4546-8a35-051676e6a7b7/GCF_000768355.1_ASM76835v1_genomic.fna.gz | prodigal -d GCF_000768355.1_ASM76835v1_genomic.fna/cds.fna -a GCF_000768355.1_ASM76835v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:20,038] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:20,039] [INFO] Task started: HMMsearch
[2024-01-24 12:22:20,039] [INFO] Running command: hmmsearch --tblout GCF_000768355.1_ASM76835v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7989a515-93c4-45f7-b0db-6bed7460e55d/dqc_reference/reference_markers.hmm GCF_000768355.1_ASM76835v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:20,321] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:20,322] [INFO] Found 6/6 markers.
[2024-01-24 12:22:20,350] [INFO] Query marker FASTA was written to GCF_000768355.1_ASM76835v1_genomic.fna/markers.fasta
[2024-01-24 12:22:20,350] [INFO] Task started: Blastn
[2024-01-24 12:22:20,350] [INFO] Running command: blastn -query GCF_000768355.1_ASM76835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7989a515-93c4-45f7-b0db-6bed7460e55d/dqc_reference/reference_markers.fasta -out GCF_000768355.1_ASM76835v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:21,301] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:21,307] [INFO] Selected 16 target genomes.
[2024-01-24 12:22:21,307] [INFO] Target genome list was writen to GCF_000768355.1_ASM76835v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:21,314] [INFO] Task started: fastANI
[2024-01-24 12:22:21,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a6ee3f8-2c54-4546-8a35-051676e6a7b7/GCF_000768355.1_ASM76835v1_genomic.fna.gz --refList GCF_000768355.1_ASM76835v1_genomic.fna/target_genomes.txt --output GCF_000768355.1_ASM76835v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:35,048] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:35,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7989a515-93c4-45f7-b0db-6bed7460e55d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:35,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7989a515-93c4-45f7-b0db-6bed7460e55d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:35,062] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:35,062] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:35,062] [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 daejeonensis	strain=GH1-9	GCA_000768355.1	346181	346181	type	True	100.0	1046	1052	95	conclusive
Lysobacter ruishenii	strain=CGMCC 1.10136	GCA_007830115.1	686800	686800	type	True	87.2139	776	1052	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	82.4453	650	1052	95	below_threshold
Lysobacter panacisoli	strain=JCM 19212	GCA_009765165.1	1255263	1255263	type	True	82.2911	607	1052	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	82.1482	616	1052	95	below_threshold
Lysobacter niastensis	strain=DSM 18481	GCA_015453285.1	380629	380629	type	True	82.067	616	1052	95	below_threshold
Lysobacter prati	strain=SYSU H10001	GCA_009765215.1	2596704	2596704	type	True	81.8604	607	1052	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	81.8414	647	1052	95	below_threshold
Lysobacter psychrotolerans	strain=ZS60	GCA_003719825.1	1327343	1327343	type	True	81.7939	601	1052	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	81.5446	597	1052	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	81.4275	551	1052	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	81.1993	594	1052	95	below_threshold
Lysobacter antibioticus	strain=ATCC 29479	GCA_001442535.1	84531	84531	type	True	81.197	611	1052	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	80.8548	546	1052	95	below_threshold
Lysobacter avium	strain=H23M41	GCA_015209745.1	2781023	2781023	type	True	80.3087	471	1052	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	80.2515	541	1052	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:35,066] [INFO] DFAST Taxonomy check result was written to GCF_000768355.1_ASM76835v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:35,066] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:35,066] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:35,067] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7989a515-93c4-45f7-b0db-6bed7460e55d/dqc_reference/checkm_data
[2024-01-24 12:22:35,068] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:35,111] [INFO] Task started: CheckM
[2024-01-24 12:22:35,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000768355.1_ASM76835v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000768355.1_ASM76835v1_genomic.fna/checkm_input GCF_000768355.1_ASM76835v1_genomic.fna/checkm_result
[2024-01-24 12:23:15,401] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:15,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:15,422] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:15,422] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:15,423] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000768355.1_ASM76835v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:15,423] [INFO] Task started: Blastn
[2024-01-24 12:23:15,423] [INFO] Running command: blastn -query GCF_000768355.1_ASM76835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7989a515-93c4-45f7-b0db-6bed7460e55d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000768355.1_ASM76835v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:17,357] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:17,361] [INFO] Selected 16 target genomes.
[2024-01-24 12:23:17,361] [INFO] Target genome list was writen to GCF_000768355.1_ASM76835v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:17,372] [INFO] Task started: fastANI
[2024-01-24 12:23:17,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a6ee3f8-2c54-4546-8a35-051676e6a7b7/GCF_000768355.1_ASM76835v1_genomic.fna.gz --refList GCF_000768355.1_ASM76835v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000768355.1_ASM76835v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:30,796] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:30,816] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:30,817] [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_000768355.1	s__Lysobacter daejeonensis	100.0	1046	1052	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_007830115.1	s__Lysobacter ruishenii	87.2139	776	1052	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	82.3213	624	1052	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	82.2816	608	1052	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	82.143	617	1052	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	81.9456	656	1052	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	81.9369	574	1052	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	81.9004	649	1052	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	81.8587	650	1052	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	81.8561	607	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017308985.1	s__Lysobacter sp017308985	81.8543	616	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106525.1	s__Lysobacter enzymogenes	81.8531	646	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.14	95.07	0.91	0.91	3	-
GCF_003719825.1	s__Lysobacter psychrotolerans	81.7971	601	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336385.2	s__Lysobacter antibioticus_A	81.7551	617	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337105.1	s__Thermomonas sp006337105	81.4115	552	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011302915.1	s__Thermomonas sp011302915	80.4461	511	1052	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:30,818] [INFO] GTDB search result was written to GCF_000768355.1_ASM76835v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:30,819] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:30,822] [INFO] DFAST_QC result json was written to GCF_000768355.1_ASM76835v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:30,823] [INFO] DFAST_QC completed!
[2024-01-24 12:23:30,823] [INFO] Total running time: 0h1m23s