[2024-01-24 12:44:50,906] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:50,908] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:50,908] [INFO] DQC Reference Directory: /var/lib/cwl/stg94968381-3422-45a9-a89c-1f6bca1bd3d1/dqc_reference
[2024-01-24 12:44:52,150] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:52,151] [INFO] Task started: Prodigal
[2024-01-24 12:44:52,152] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d618dbe-0a3e-4ee7-a76c-9fbfc1e87796/GCF_019802285.1_ASM1980228v1_genomic.fna.gz | prodigal -d GCF_019802285.1_ASM1980228v1_genomic.fna/cds.fna -a GCF_019802285.1_ASM1980228v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:01,394] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:01,395] [INFO] Task started: HMMsearch
[2024-01-24 12:45:01,395] [INFO] Running command: hmmsearch --tblout GCF_019802285.1_ASM1980228v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94968381-3422-45a9-a89c-1f6bca1bd3d1/dqc_reference/reference_markers.hmm GCF_019802285.1_ASM1980228v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:01,641] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:01,643] [INFO] Found 6/6 markers.
[2024-01-24 12:45:01,672] [INFO] Query marker FASTA was written to GCF_019802285.1_ASM1980228v1_genomic.fna/markers.fasta
[2024-01-24 12:45:01,673] [INFO] Task started: Blastn
[2024-01-24 12:45:01,673] [INFO] Running command: blastn -query GCF_019802285.1_ASM1980228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94968381-3422-45a9-a89c-1f6bca1bd3d1/dqc_reference/reference_markers.fasta -out GCF_019802285.1_ASM1980228v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:02,582] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:02,585] [INFO] Selected 12 target genomes.
[2024-01-24 12:45:02,586] [INFO] Target genome list was writen to GCF_019802285.1_ASM1980228v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:02,604] [INFO] Task started: fastANI
[2024-01-24 12:45:02,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d618dbe-0a3e-4ee7-a76c-9fbfc1e87796/GCF_019802285.1_ASM1980228v1_genomic.fna.gz --refList GCF_019802285.1_ASM1980228v1_genomic.fna/target_genomes.txt --output GCF_019802285.1_ASM1980228v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:11,260] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:11,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94968381-3422-45a9-a89c-1f6bca1bd3d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:11,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94968381-3422-45a9-a89c-1f6bca1bd3d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:11,271] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:11,272] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:11,272] [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 antarcticus	strain=GW1-59	GCA_019802285.1	2862543	2862543	type	True	100.0	925	925	95	conclusive
Lysobacter avium	strain=H23M41	GCA_015209745.1	2781023	2781023	type	True	88.9141	832	925	95	below_threshold
Lysobacter ciconiae	strain=H21R20	GCA_015209725.1	2781022	2781022	type	True	88.4011	804	925	95	below_threshold
Lysobacter concretionis	strain=Ko07	GCA_000768345.1	262325	262325	type	True	82.814	623	925	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	81.3087	531	925	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	80.8758	520	925	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	80.5285	475	925	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	80.5081	488	925	95	below_threshold
Lysobacter spongiicola	strain=DSM 21749	GCA_900167055.1	435289	435289	type	True	80.2784	500	925	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	80.1682	521	925	95	below_threshold
Lysobacter aestuarii	strain=JCM 31130	GCA_006546775.1	1706195	1706195	type	True	79.9083	429	925	95	below_threshold
Lysobacter antibioticus	strain=ATCC 29479	GCA_001442535.1	84531	84531	type	True	79.7743	480	925	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:11,273] [INFO] DFAST Taxonomy check result was written to GCF_019802285.1_ASM1980228v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:11,274] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:11,274] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:11,274] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94968381-3422-45a9-a89c-1f6bca1bd3d1/dqc_reference/checkm_data
[2024-01-24 12:45:11,275] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:11,309] [INFO] Task started: CheckM
[2024-01-24 12:45:11,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019802285.1_ASM1980228v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019802285.1_ASM1980228v1_genomic.fna/checkm_input GCF_019802285.1_ASM1980228v1_genomic.fna/checkm_result
[2024-01-24 12:45:44,865] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:44,867] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:44,890] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:44,890] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:44,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019802285.1_ASM1980228v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:44,891] [INFO] Task started: Blastn
[2024-01-24 12:45:44,891] [INFO] Running command: blastn -query GCF_019802285.1_ASM1980228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94968381-3422-45a9-a89c-1f6bca1bd3d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_019802285.1_ASM1980228v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:46,507] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:46,511] [INFO] Selected 11 target genomes.
[2024-01-24 12:45:46,511] [INFO] Target genome list was writen to GCF_019802285.1_ASM1980228v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:46,520] [INFO] Task started: fastANI
[2024-01-24 12:45:46,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d618dbe-0a3e-4ee7-a76c-9fbfc1e87796/GCF_019802285.1_ASM1980228v1_genomic.fna.gz --refList GCF_019802285.1_ASM1980228v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019802285.1_ASM1980228v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:54,113] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:54,126] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:45:54,126] [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_000855665.1	s__Lysobacter sp000855665	92.9453	817	925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015209765.1	s__Lysobacter sp015209765	88.8585	824	925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.00	98.00	0.93	0.93	2	-
GCF_015209725.1	s__Lysobacter sp015209725	88.3998	804	925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.91	96.91	0.94	0.94	2	-
GCF_000768345.1	s__Lysobacter concretionis	82.8414	621	925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000768335.1	s__Lysobacter arseniciresistens	81.322	530	925	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	80.8798	519	925	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	80.4952	490	925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900167055.1	s__Lysobacter spongiicola	80.294	499	925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442535.1	s__Lysobacter antibioticus	79.7738	480	925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.45	98.45	0.94	0.94	2	-
GCA_017302075.1	s__Thermomonas sp017302075	79.3135	365	925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367355.1	s__Lysobacter sp003367355	78.6475	344	925	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:54,128] [INFO] GTDB search result was written to GCF_019802285.1_ASM1980228v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:54,128] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:54,132] [INFO] DFAST_QC result json was written to GCF_019802285.1_ASM1980228v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:54,132] [INFO] DFAST_QC completed!
[2024-01-24 12:45:54,132] [INFO] Total running time: 0h1m3s