[2024-01-24 15:18:18,982] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:18,984] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:18,984] [INFO] DQC Reference Directory: /var/lib/cwl/stgecaeedda-dcb2-41d1-9a61-f23786671dbd/dqc_reference
[2024-01-24 15:18:20,225] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:20,226] [INFO] Task started: Prodigal
[2024-01-24 15:18:20,227] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7d7725d-7a64-4a3d-a845-d7dc1ac8ebf1/GCF_000429065.1_ASM42906v1_genomic.fna.gz | prodigal -d GCF_000429065.1_ASM42906v1_genomic.fna/cds.fna -a GCF_000429065.1_ASM42906v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:27,990] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:27,991] [INFO] Task started: HMMsearch
[2024-01-24 15:18:27,991] [INFO] Running command: hmmsearch --tblout GCF_000429065.1_ASM42906v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgecaeedda-dcb2-41d1-9a61-f23786671dbd/dqc_reference/reference_markers.hmm GCF_000429065.1_ASM42906v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:28,228] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:28,230] [INFO] Found 6/6 markers.
[2024-01-24 15:18:28,257] [INFO] Query marker FASTA was written to GCF_000429065.1_ASM42906v1_genomic.fna/markers.fasta
[2024-01-24 15:18:28,257] [INFO] Task started: Blastn
[2024-01-24 15:18:28,257] [INFO] Running command: blastn -query GCF_000429065.1_ASM42906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecaeedda-dcb2-41d1-9a61-f23786671dbd/dqc_reference/reference_markers.fasta -out GCF_000429065.1_ASM42906v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:29,244] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:29,248] [INFO] Selected 22 target genomes.
[2024-01-24 15:18:29,249] [INFO] Target genome list was writen to GCF_000429065.1_ASM42906v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:29,294] [INFO] Task started: fastANI
[2024-01-24 15:18:29,295] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7d7725d-7a64-4a3d-a845-d7dc1ac8ebf1/GCF_000429065.1_ASM42906v1_genomic.fna.gz --refList GCF_000429065.1_ASM42906v1_genomic.fna/target_genomes.txt --output GCF_000429065.1_ASM42906v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:43,038] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:43,039] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgecaeedda-dcb2-41d1-9a61-f23786671dbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:43,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgecaeedda-dcb2-41d1-9a61-f23786671dbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:43,060] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:18:43,060] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:18:43,061] [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
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	81.1635	478	873	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	81.0072	439	873	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	80.9987	506	873	95	below_threshold
Arenimonas fontis	strain=3729k	GCA_008386465.1	2608255	2608255	type	True	80.3447	452	873	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	80.2357	506	873	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	80.2221	442	873	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	80.1706	471	873	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	80.0768	487	873	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	80.0213	494	873	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	80.0121	473	873	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	79.9451	417	873	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	79.9451	461	873	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	79.9444	412	873	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	79.8046	429	873	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	79.8012	448	873	95	below_threshold
Arenimonas soli	strain=CGMCC 1.15905	GCA_014643775.1	2269504	2269504	type	True	79.7957	465	873	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	79.6821	406	873	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	79.5479	442	873	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	79.5396	454	873	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	79.3997	428	873	95	below_threshold
Stenotrophomonas acidaminiphila	strain=JCM 13310	GCA_001431595.1	128780	128780	type	True	78.9748	418	873	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	78.8755	425	873	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:43,062] [INFO] DFAST Taxonomy check result was written to GCF_000429065.1_ASM42906v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:43,063] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:43,063] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:43,063] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgecaeedda-dcb2-41d1-9a61-f23786671dbd/dqc_reference/checkm_data
[2024-01-24 15:18:43,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:43,095] [INFO] Task started: CheckM
[2024-01-24 15:18:43,096] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429065.1_ASM42906v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429065.1_ASM42906v1_genomic.fna/checkm_input GCF_000429065.1_ASM42906v1_genomic.fna/checkm_result
[2024-01-24 15:19:15,418] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:15,419] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:15,446] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:15,446] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:15,447] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429065.1_ASM42906v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:15,447] [INFO] Task started: Blastn
[2024-01-24 15:19:15,447] [INFO] Running command: blastn -query GCF_000429065.1_ASM42906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecaeedda-dcb2-41d1-9a61-f23786671dbd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429065.1_ASM42906v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:17,426] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:17,430] [INFO] Selected 13 target genomes.
[2024-01-24 15:19:17,430] [INFO] Target genome list was writen to GCF_000429065.1_ASM42906v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:17,439] [INFO] Task started: fastANI
[2024-01-24 15:19:17,439] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7d7725d-7a64-4a3d-a845-d7dc1ac8ebf1/GCF_000429065.1_ASM42906v1_genomic.fna.gz --refList GCF_000429065.1_ASM42906v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429065.1_ASM42906v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:26,712] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:26,726] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:26,726] [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_000429065.1	s__Silanimonas lenta	100.0	869	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Silanimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018333835.1	s__Silanimonas sp018333835	84.8272	531	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Silanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003449515.1	s__Silanimonas sp003449515	83.2266	394	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Silanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018334015.1	s__Silanimonas sp018334015	83.1058	546	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Silanimonas	95.0	99.95	99.95	0.95	0.95	2	-
GCF_000747075.1	s__Arenimonas malthae	81.1624	478	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024235.1	s__Arenimonas caeni	81.0243	504	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	81.0167	438	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Vulcaniibacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265115.1	s__Arenimonas terrae	80.2239	507	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093135.1	s__Pseudoxanthomonas taiwanensis	80.1497	448	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.04	99.04	0.90	0.90	2	-
GCF_000559025.1	s__Luteimonas huabeiensis	80.0709	488	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426365.1	s__Arenimonas composti	80.0394	471	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_018122625.2	s__Coralloluteibacterium stylophorae	79.5224	457	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Coralloluteibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008017755.1	s__VRTS01 sp008017755	79.2033	386	873	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__VRTS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:26,732] [INFO] GTDB search result was written to GCF_000429065.1_ASM42906v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:26,732] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:26,736] [INFO] DFAST_QC result json was written to GCF_000429065.1_ASM42906v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:26,736] [INFO] DFAST_QC completed!
[2024-01-24 15:19:26,736] [INFO] Total running time: 0h1m8s