[2023-06-29 08:34:29,655] [INFO] DFAST_QC pipeline started.
[2023-06-29 08:34:29,660] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 08:34:29,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg66eda85a-3749-46c2-9fa9-c1d154c1ac81/dqc_reference
[2023-06-29 08:34:32,198] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 08:34:32,199] [INFO] Task started: Prodigal
[2023-06-29 08:34:32,199] [INFO] Running command: gunzip -c /var/lib/cwl/stg9bc00b44-fa77-49c5-9bd1-c18a4d0b5e36/GCA_020200315.1_ASM2020031v1_genomic.fna.gz | prodigal -d GCA_020200315.1_ASM2020031v1_genomic.fna/cds.fna -a GCA_020200315.1_ASM2020031v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 08:34:37,665] [INFO] Task succeeded: Prodigal
[2023-06-29 08:34:37,666] [INFO] Task started: HMMsearch
[2023-06-29 08:34:37,666] [INFO] Running command: hmmsearch --tblout GCA_020200315.1_ASM2020031v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66eda85a-3749-46c2-9fa9-c1d154c1ac81/dqc_reference/reference_markers.hmm GCA_020200315.1_ASM2020031v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 08:34:37,902] [INFO] Task succeeded: HMMsearch
[2023-06-29 08:34:37,903] [INFO] Found 6/6 markers.
[2023-06-29 08:34:37,930] [INFO] Query marker FASTA was written to GCA_020200315.1_ASM2020031v1_genomic.fna/markers.fasta
[2023-06-29 08:34:37,931] [INFO] Task started: Blastn
[2023-06-29 08:34:37,931] [INFO] Running command: blastn -query GCA_020200315.1_ASM2020031v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66eda85a-3749-46c2-9fa9-c1d154c1ac81/dqc_reference/reference_markers.fasta -out GCA_020200315.1_ASM2020031v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:34:38,786] [INFO] Task succeeded: Blastn
[2023-06-29 08:34:38,791] [INFO] Selected 20 target genomes.
[2023-06-29 08:34:38,792] [INFO] Target genome list was writen to GCA_020200315.1_ASM2020031v1_genomic.fna/target_genomes.txt
[2023-06-29 08:34:38,800] [INFO] Task started: fastANI
[2023-06-29 08:34:38,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bc00b44-fa77-49c5-9bd1-c18a4d0b5e36/GCA_020200315.1_ASM2020031v1_genomic.fna.gz --refList GCA_020200315.1_ASM2020031v1_genomic.fna/target_genomes.txt --output GCA_020200315.1_ASM2020031v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 08:34:48,803] [INFO] Task succeeded: fastANI
[2023-06-29 08:34:48,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66eda85a-3749-46c2-9fa9-c1d154c1ac81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 08:34:48,804] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66eda85a-3749-46c2-9fa9-c1d154c1ac81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 08:34:48,823] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 08:34:48,823] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 08:34:48,823] [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
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	79.5196	295	627	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	79.449	322	627	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	79.2306	314	627	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	79.1325	271	627	95	below_threshold
Sphingomonas jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	79.0687	272	627	95	below_threshold
Sphingomonas astaxanthinifaciens	strain=DSM 22298	GCA_000711715.1	407019	407019	type	True	79.0107	303	627	95	below_threshold
Sphingomonas kaistensis	strain=DSM 16846	GCA_011927725.1	298708	298708	type	True	78.7767	271	627	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	78.5646	279	627	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	78.3831	245	627	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_024721585.1	1582356	1582356	type	True	78.2014	217	627	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	78.1862	239	627	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_022953075.1	1582356	1582356	type	True	78.1616	221	627	95	below_threshold
Sphingomonas xanthus	strain=AE3	GCA_007998985.1	2594473	2594473	type	True	78.0997	211	627	95	below_threshold
Sphingomicrobium astaxanthinifaciens	strain=JCM 18551	GCA_022865105.1	1227949	1227949	type	True	78.078	227	627	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	78.0217	236	627	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	77.8812	216	627	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	77.6519	183	627	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	77.6511	183	627	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	77.5823	203	627	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	77.4302	200	627	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 08:34:48,825] [INFO] DFAST Taxonomy check result was written to GCA_020200315.1_ASM2020031v1_genomic.fna/tc_result.tsv
[2023-06-29 08:34:48,826] [INFO] ===== Taxonomy check completed =====
[2023-06-29 08:34:48,826] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 08:34:48,826] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66eda85a-3749-46c2-9fa9-c1d154c1ac81/dqc_reference/checkm_data
[2023-06-29 08:34:48,827] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 08:34:48,857] [INFO] Task started: CheckM
[2023-06-29 08:34:48,857] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020200315.1_ASM2020031v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020200315.1_ASM2020031v1_genomic.fna/checkm_input GCA_020200315.1_ASM2020031v1_genomic.fna/checkm_result
[2023-06-29 08:35:13,169] [INFO] Task succeeded: CheckM
[2023-06-29 08:35:13,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 08:35:13,190] [INFO] ===== Completeness check finished =====
[2023-06-29 08:35:13,191] [INFO] ===== Start GTDB Search =====
[2023-06-29 08:35:13,191] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020200315.1_ASM2020031v1_genomic.fna/markers.fasta)
[2023-06-29 08:35:13,191] [INFO] Task started: Blastn
[2023-06-29 08:35:13,192] [INFO] Running command: blastn -query GCA_020200315.1_ASM2020031v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66eda85a-3749-46c2-9fa9-c1d154c1ac81/dqc_reference/reference_markers_gtdb.fasta -out GCA_020200315.1_ASM2020031v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 08:35:14,667] [INFO] Task succeeded: Blastn
[2023-06-29 08:35:14,673] [INFO] Selected 23 target genomes.
[2023-06-29 08:35:14,673] [INFO] Target genome list was writen to GCA_020200315.1_ASM2020031v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 08:35:14,747] [INFO] Task started: fastANI
[2023-06-29 08:35:14,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bc00b44-fa77-49c5-9bd1-c18a4d0b5e36/GCA_020200315.1_ASM2020031v1_genomic.fna.gz --refList GCA_020200315.1_ASM2020031v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020200315.1_ASM2020031v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 08:35:25,964] [INFO] Task succeeded: fastANI
[2023-06-29 08:35:25,985] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 08:35:25,986] [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_003499275.1	s__Sphingomicrobium mesophila	79.5026	296	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363895.1	s__Sphingomicrobium ginsengisoli	79.4115	325	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011053295.1	s__Sphingomicrobium sp011053295	79.3727	236	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970925.1	s__Sphingomicrobium sp003970925	79.2306	314	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014396585.1	s__Sphingomicrobium rhizophilum	79.1157	272	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013816785.1	s__Sphingomicrobium sp013816785	79.0558	291	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927725.1	s__Sphingomicrobium kaistense	78.7771	271	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806285.1	s__Sphingomicrobium sp902806285	78.5031	243	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242355.1	s__Sphingomicrobium sp019242355	78.4744	221	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720245.1	s__Sphingomicrobium sp009720245	78.3831	245	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806265.1	s__Sphingomicrobium sp902806265	78.3431	239	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177405.1	s__Allosphingosinicella indica	78.2777	237	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247755.1	s__Sphingomicrobium sp019247755	78.1926	155	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812805.1	s__Sphingomicrobium sp013812805	78.1757	213	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007998985.1	s__Sphingomicrobium xanthus	78.0997	211	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806275.1	s__Sphingomicrobium sp902806275	78.0366	181	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515075.1	s__Sphingomonas gilva	77.9805	238	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129465.1	s__Allosphingosinicella humi	77.9119	214	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806315.1	s__Allosphingosinicella sp902806315	77.9115	186	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341505.2	s__Sphingomonas sp004341505	77.6992	190	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_004135605.1	s__Sphingomonas desiccabilis	77.669	182	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004792685.1	s__Sphingomonas gei	77.5666	204	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002796605.1	s__Sphingomonas sp002796605	77.4155	201	627	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 08:35:25,988] [INFO] GTDB search result was written to GCA_020200315.1_ASM2020031v1_genomic.fna/result_gtdb.tsv
[2023-06-29 08:35:25,988] [INFO] ===== GTDB Search completed =====
[2023-06-29 08:35:25,996] [INFO] DFAST_QC result json was written to GCA_020200315.1_ASM2020031v1_genomic.fna/dqc_result.json
[2023-06-29 08:35:25,997] [INFO] DFAST_QC completed!
[2023-06-29 08:35:25,997] [INFO] Total running time: 0h0m56s