[2023-06-19 09:28:45,196] [INFO] DFAST_QC pipeline started.
[2023-06-19 09:28:45,199] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 09:28:45,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg7406e6a7-d66a-44c5-aeee-083dadf64759/dqc_reference
[2023-06-19 09:28:46,940] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 09:28:46,942] [INFO] Task started: Prodigal
[2023-06-19 09:28:46,942] [INFO] Running command: gunzip -c /var/lib/cwl/stg2329c7d7-099e-461b-8a69-08ee5672257e/GCA_018334015.1_ASM1833401v1_genomic.fna.gz | prodigal -d GCA_018334015.1_ASM1833401v1_genomic.fna/cds.fna -a GCA_018334015.1_ASM1833401v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 09:28:53,989] [INFO] Task succeeded: Prodigal
[2023-06-19 09:28:53,990] [INFO] Task started: HMMsearch
[2023-06-19 09:28:53,990] [INFO] Running command: hmmsearch --tblout GCA_018334015.1_ASM1833401v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7406e6a7-d66a-44c5-aeee-083dadf64759/dqc_reference/reference_markers.hmm GCA_018334015.1_ASM1833401v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 09:28:54,230] [INFO] Task succeeded: HMMsearch
[2023-06-19 09:28:54,232] [INFO] Found 6/6 markers.
[2023-06-19 09:28:54,254] [INFO] Query marker FASTA was written to GCA_018334015.1_ASM1833401v1_genomic.fna/markers.fasta
[2023-06-19 09:28:54,255] [INFO] Task started: Blastn
[2023-06-19 09:28:54,255] [INFO] Running command: blastn -query GCA_018334015.1_ASM1833401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7406e6a7-d66a-44c5-aeee-083dadf64759/dqc_reference/reference_markers.fasta -out GCA_018334015.1_ASM1833401v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:28:55,317] [INFO] Task succeeded: Blastn
[2023-06-19 09:28:55,323] [INFO] Selected 26 target genomes.
[2023-06-19 09:28:55,323] [INFO] Target genome list was writen to GCA_018334015.1_ASM1833401v1_genomic.fna/target_genomes.txt
[2023-06-19 09:28:55,326] [INFO] Task started: fastANI
[2023-06-19 09:28:55,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg2329c7d7-099e-461b-8a69-08ee5672257e/GCA_018334015.1_ASM1833401v1_genomic.fna.gz --refList GCA_018334015.1_ASM1833401v1_genomic.fna/target_genomes.txt --output GCA_018334015.1_ASM1833401v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 09:29:13,474] [INFO] Task succeeded: fastANI
[2023-06-19 09:29:13,475] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7406e6a7-d66a-44c5-aeee-083dadf64759/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 09:29:13,475] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7406e6a7-d66a-44c5-aeee-083dadf64759/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 09:29:13,495] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 09:29:13,496] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 09:29:13,496] [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 metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	80.1953	417	733	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	80.1253	418	733	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	80.1126	391	733	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	79.8096	399	733	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	79.7737	398	733	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	79.7652	388	733	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	79.7416	363	733	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	79.587	354	733	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	79.5139	392	733	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	79.5131	305	733	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	79.5102	376	733	95	below_threshold
Arenimonas donghaensis	strain=HO3-R19	GCA_000743535.1	375061	375061	type	True	79.508	368	733	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	79.5037	336	733	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	79.4518	378	733	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	79.4289	346	733	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	79.4239	336	733	95	below_threshold
Arenimonas fontis	strain=3729k	GCA_008386465.1	2608255	2608255	type	True	79.3625	357	733	95	below_threshold
Lysobacter maris	strain=KCTC 42381	GCA_006546735.2	1605891	1605891	type	True	79.2979	326	733	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	79.2541	342	733	95	below_threshold
Lysobacter ruishenii	strain=CGMCC 1.10136	GCA_007830115.1	686800	686800	type	True	79.1526	320	733	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	79.1259	383	733	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	78.991	362	733	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	78.9533	351	733	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	78.9495	352	733	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	78.7463	295	733	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	78.7179	293	733	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 09:29:13,499] [INFO] DFAST Taxonomy check result was written to GCA_018334015.1_ASM1833401v1_genomic.fna/tc_result.tsv
[2023-06-19 09:29:13,499] [INFO] ===== Taxonomy check completed =====
[2023-06-19 09:29:13,500] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 09:29:13,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7406e6a7-d66a-44c5-aeee-083dadf64759/dqc_reference/checkm_data
[2023-06-19 09:29:13,501] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 09:29:13,533] [INFO] Task started: CheckM
[2023-06-19 09:29:13,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018334015.1_ASM1833401v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018334015.1_ASM1833401v1_genomic.fna/checkm_input GCA_018334015.1_ASM1833401v1_genomic.fna/checkm_result
[2023-06-19 09:29:51,576] [INFO] Task succeeded: CheckM
[2023-06-19 09:29:51,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 09:29:51,601] [INFO] ===== Completeness check finished =====
[2023-06-19 09:29:51,602] [INFO] ===== Start GTDB Search =====
[2023-06-19 09:29:51,602] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018334015.1_ASM1833401v1_genomic.fna/markers.fasta)
[2023-06-19 09:29:51,602] [INFO] Task started: Blastn
[2023-06-19 09:29:51,602] [INFO] Running command: blastn -query GCA_018334015.1_ASM1833401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7406e6a7-d66a-44c5-aeee-083dadf64759/dqc_reference/reference_markers_gtdb.fasta -out GCA_018334015.1_ASM1833401v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:29:53,510] [INFO] Task succeeded: Blastn
[2023-06-19 09:29:53,515] [INFO] Selected 14 target genomes.
[2023-06-19 09:29:53,515] [INFO] Target genome list was writen to GCA_018334015.1_ASM1833401v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 09:29:53,521] [INFO] Task started: fastANI
[2023-06-19 09:29:53,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg2329c7d7-099e-461b-8a69-08ee5672257e/GCA_018334015.1_ASM1833401v1_genomic.fna.gz --refList GCA_018334015.1_ASM1833401v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018334015.1_ASM1833401v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 09:30:02,111] [INFO] Task succeeded: fastANI
[2023-06-19 09:30:02,131] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 09:30:02,131] [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_018334015.1	s__Silanimonas sp018334015	100.0	731	733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Silanimonas	95.0	99.95	99.95	0.95	0.95	2	conclusive
GCA_018333835.1	s__Silanimonas sp018333835	86.9325	517	733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Silanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429065.1	s__Silanimonas lenta	83.1782	545	733	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	82.6687	346	733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Silanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747155.1	s__Arenimonas metalli	80.1765	418	733	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	80.1252	418	733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747075.1	s__Arenimonas malthae	80.1128	391	733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724815.1	s__Arenimonas sp001724815	80.055	433	733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743535.1	s__Arenimonas donghaensis	79.4803	371	733	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	79.4446	334	733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.04	99.04	0.90	0.90	2	-
GCF_006337105.1	s__Thermomonas sp006337105	79.4433	345	733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014654535.1	s__Pseudomonas_S boreopolis	79.1198	327	733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudomonas_S	95.0	98.68	98.68	0.91	0.91	2	-
GCF_000559025.1	s__Luteimonas huabeiensis	79.1192	384	733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472505.1	s__Luteimonas sp000472505	79.1127	371	733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.95	99.95	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-19 09:30:02,136] [INFO] GTDB search result was written to GCA_018334015.1_ASM1833401v1_genomic.fna/result_gtdb.tsv
[2023-06-19 09:30:02,136] [INFO] ===== GTDB Search completed =====
[2023-06-19 09:30:02,143] [INFO] DFAST_QC result json was written to GCA_018334015.1_ASM1833401v1_genomic.fna/dqc_result.json
[2023-06-19 09:30:02,143] [INFO] DFAST_QC completed!
[2023-06-19 09:30:02,143] [INFO] Total running time: 0h1m17s