[2023-06-19 09:16:55,786] [INFO] DFAST_QC pipeline started.
[2023-06-19 09:16:55,795] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 09:16:55,796] [INFO] DQC Reference Directory: /var/lib/cwl/stgbbb00906-aaa8-4b4c-8df1-3d448d64e8cc/dqc_reference
[2023-06-19 09:16:57,441] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 09:16:57,442] [INFO] Task started: Prodigal
[2023-06-19 09:16:57,442] [INFO] Running command: gunzip -c /var/lib/cwl/stgab62869e-7fe4-4102-8f76-fe7e55c72490/GCA_014378295.1_ASM1437829v1_genomic.fna.gz | prodigal -d GCA_014378295.1_ASM1437829v1_genomic.fna/cds.fna -a GCA_014378295.1_ASM1437829v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 09:17:03,595] [INFO] Task succeeded: Prodigal
[2023-06-19 09:17:03,596] [INFO] Task started: HMMsearch
[2023-06-19 09:17:03,596] [INFO] Running command: hmmsearch --tblout GCA_014378295.1_ASM1437829v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbbb00906-aaa8-4b4c-8df1-3d448d64e8cc/dqc_reference/reference_markers.hmm GCA_014378295.1_ASM1437829v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 09:17:03,827] [INFO] Task succeeded: HMMsearch
[2023-06-19 09:17:03,828] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgab62869e-7fe4-4102-8f76-fe7e55c72490/GCA_014378295.1_ASM1437829v1_genomic.fna.gz]
[2023-06-19 09:17:03,860] [INFO] Query marker FASTA was written to GCA_014378295.1_ASM1437829v1_genomic.fna/markers.fasta
[2023-06-19 09:17:03,860] [INFO] Task started: Blastn
[2023-06-19 09:17:03,861] [INFO] Running command: blastn -query GCA_014378295.1_ASM1437829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbb00906-aaa8-4b4c-8df1-3d448d64e8cc/dqc_reference/reference_markers.fasta -out GCA_014378295.1_ASM1437829v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:17:04,435] [INFO] Task succeeded: Blastn
[2023-06-19 09:17:04,442] [INFO] Selected 22 target genomes.
[2023-06-19 09:17:04,443] [INFO] Target genome list was writen to GCA_014378295.1_ASM1437829v1_genomic.fna/target_genomes.txt
[2023-06-19 09:17:04,448] [INFO] Task started: fastANI
[2023-06-19 09:17:04,449] [INFO] Running command: fastANI --query /var/lib/cwl/stgab62869e-7fe4-4102-8f76-fe7e55c72490/GCA_014378295.1_ASM1437829v1_genomic.fna.gz --refList GCA_014378295.1_ASM1437829v1_genomic.fna/target_genomes.txt --output GCA_014378295.1_ASM1437829v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 09:17:20,329] [INFO] Task succeeded: fastANI
[2023-06-19 09:17:20,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbbb00906-aaa8-4b4c-8df1-3d448d64e8cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 09:17:20,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbbb00906-aaa8-4b4c-8df1-3d448d64e8cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 09:17:20,344] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 09:17:20,345] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 09:17:20,345] [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 oryziterrae	strain=YC6267	GCA_000747135.1	498055	498055	type	True	79.2277	207	433	95	below_threshold
Arenimonas oryziterrae	strain=DSM 21050	GCA_000420545.1	498055	498055	type	True	79.2271	207	433	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	78.6864	197	433	95	below_threshold
Arenimonas soli	strain=CGMCC 1.15905	GCA_014643775.1	2269504	2269504	type	True	78.6625	187	433	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	78.6171	173	433	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	78.5956	192	433	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	78.5045	197	433	95	below_threshold
Lysobacter ruishenii	strain=CGMCC 1.10136	GCA_007830115.1	686800	686800	type	True	78.0668	121	433	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	77.8276	123	433	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	77.6393	124	433	95	below_threshold
Thermomonas fusca	strain=DSM 15424	GCA_000423885.1	215690	215690	type	True	77.5858	117	433	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	77.5715	122	433	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	77.5419	128	433	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	77.5307	103	433	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	77.5001	124	433	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	77.4901	126	433	95	below_threshold
Pseudoxanthomonas spadix	strain=DSM 18855	GCA_003703395.1	415229	415229	type	True	77.2273	101	433	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	75.7905	51	433	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 09:17:20,348] [INFO] DFAST Taxonomy check result was written to GCA_014378295.1_ASM1437829v1_genomic.fna/tc_result.tsv
[2023-06-19 09:17:20,349] [INFO] ===== Taxonomy check completed =====
[2023-06-19 09:17:20,349] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 09:17:20,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbbb00906-aaa8-4b4c-8df1-3d448d64e8cc/dqc_reference/checkm_data
[2023-06-19 09:17:20,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 09:17:20,378] [INFO] Task started: CheckM
[2023-06-19 09:17:20,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014378295.1_ASM1437829v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014378295.1_ASM1437829v1_genomic.fna/checkm_input GCA_014378295.1_ASM1437829v1_genomic.fna/checkm_result
[2023-06-19 09:17:44,234] [INFO] Task succeeded: CheckM
[2023-06-19 09:17:44,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.61%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 09:17:44,263] [INFO] ===== Completeness check finished =====
[2023-06-19 09:17:44,264] [INFO] ===== Start GTDB Search =====
[2023-06-19 09:17:44,264] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014378295.1_ASM1437829v1_genomic.fna/markers.fasta)
[2023-06-19 09:17:44,264] [INFO] Task started: Blastn
[2023-06-19 09:17:44,265] [INFO] Running command: blastn -query GCA_014378295.1_ASM1437829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbbb00906-aaa8-4b4c-8df1-3d448d64e8cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_014378295.1_ASM1437829v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 09:17:44,930] [INFO] Task succeeded: Blastn
[2023-06-19 09:17:44,936] [INFO] Selected 22 target genomes.
[2023-06-19 09:17:44,936] [INFO] Target genome list was writen to GCA_014378295.1_ASM1437829v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 09:17:44,949] [INFO] Task started: fastANI
[2023-06-19 09:17:44,949] [INFO] Running command: fastANI --query /var/lib/cwl/stgab62869e-7fe4-4102-8f76-fe7e55c72490/GCA_014378295.1_ASM1437829v1_genomic.fna.gz --refList GCA_014378295.1_ASM1437829v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014378295.1_ASM1437829v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 09:17:58,093] [INFO] Task succeeded: fastANI
[2023-06-19 09:17:58,111] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 09:17:58,111] [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_001801685.1	s__Arenimonas sp001801685	83.8233	336	433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420545.1	s__Arenimonas oryziterrae	79.2271	207	433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007993735.1	s__Arenimonas daejeonensis	78.9865	186	433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265115.1	s__Arenimonas terrae	78.6864	197	433	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	78.6171	173	433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747155.1	s__Arenimonas metalli	78.5956	192	433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638745.1	s__Arenimonas maotaiensis	78.4814	129	433	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	78.2719	168	433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497545.1	s__Arenimonas sp003497545	78.2458	134	433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.43	99.43	0.81	0.81	2	-
GCF_007830115.1	s__Lysobacter ruishenii	78.0668	121	433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018122625.2	s__Coralloluteibacterium stylophorae	77.7106	122	433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Coralloluteibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014395425.1	s__Thermomonas brevis	77.5545	129	433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006476065.1	s__Luteimonas_B lumbrici	77.5307	103	433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202935.1	s__Rehaibacterium terrae	77.4893	138	433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Rehaibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004284655.1	s__Pseudoxanthomonas_A spadix_A	77.4612	121	433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	98.46	98.41	0.91	0.91	3	-
GCA_018333835.1	s__Silanimonas sp018333835	77.3309	92	433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Silanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003703395.1	s__Pseudoxanthomonas_A spadix	77.2273	101	433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.25	98.51	0.95	0.90	3	-
GCF_900112425.1	s__Variovorax sp900112425	75.8729	59	433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	99.32	98.64	0.96	0.91	3	-
--------------------------------------------------------------------------------
[2023-06-19 09:17:58,113] [INFO] GTDB search result was written to GCA_014378295.1_ASM1437829v1_genomic.fna/result_gtdb.tsv
[2023-06-19 09:17:58,113] [INFO] ===== GTDB Search completed =====
[2023-06-19 09:17:58,118] [INFO] DFAST_QC result json was written to GCA_014378295.1_ASM1437829v1_genomic.fna/dqc_result.json
[2023-06-19 09:17:58,119] [INFO] DFAST_QC completed!
[2023-06-19 09:17:58,119] [INFO] Total running time: 0h1m2s