[2024-01-25 18:09:50,698] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:50,701] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:50,701] [INFO] DQC Reference Directory: /var/lib/cwl/stg47dde50a-dbaf-4b63-af66-aa894d269049/dqc_reference
[2024-01-25 18:09:51,806] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:51,806] [INFO] Task started: Prodigal
[2024-01-25 18:09:51,806] [INFO] Running command: gunzip -c /var/lib/cwl/stg95a3bc8b-7f21-478c-b411-e7d51271f063/GCF_000585415.1_ASM58541v1_genomic.fna.gz | prodigal -d GCF_000585415.1_ASM58541v1_genomic.fna/cds.fna -a GCF_000585415.1_ASM58541v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:58,546] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:58,547] [INFO] Task started: HMMsearch
[2024-01-25 18:09:58,547] [INFO] Running command: hmmsearch --tblout GCF_000585415.1_ASM58541v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47dde50a-dbaf-4b63-af66-aa894d269049/dqc_reference/reference_markers.hmm GCF_000585415.1_ASM58541v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:58,799] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:58,800] [INFO] Found 6/6 markers.
[2024-01-25 18:09:58,834] [INFO] Query marker FASTA was written to GCF_000585415.1_ASM58541v1_genomic.fna/markers.fasta
[2024-01-25 18:09:58,835] [INFO] Task started: Blastn
[2024-01-25 18:09:58,835] [INFO] Running command: blastn -query GCF_000585415.1_ASM58541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47dde50a-dbaf-4b63-af66-aa894d269049/dqc_reference/reference_markers.fasta -out GCF_000585415.1_ASM58541v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:59,759] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:59,762] [INFO] Selected 16 target genomes.
[2024-01-25 18:09:59,763] [INFO] Target genome list was writen to GCF_000585415.1_ASM58541v1_genomic.fna/target_genomes.txt
[2024-01-25 18:09:59,782] [INFO] Task started: fastANI
[2024-01-25 18:09:59,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg95a3bc8b-7f21-478c-b411-e7d51271f063/GCF_000585415.1_ASM58541v1_genomic.fna.gz --refList GCF_000585415.1_ASM58541v1_genomic.fna/target_genomes.txt --output GCF_000585415.1_ASM58541v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:08,788] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:08,789] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47dde50a-dbaf-4b63-af66-aa894d269049/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:08,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47dde50a-dbaf-4b63-af66-aa894d269049/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:08,800] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:10:08,800] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:10:08,800] [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 jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	100.0	849	849	95	conclusive
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	80.449	433	849	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	80.006	405	849	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	79.774	412	849	95	below_threshold
Sphingomonas xanthus	strain=AE3	GCA_007998985.1	2594473	2594473	type	True	79.6094	419	849	95	below_threshold
Sphingomonas edaphi	strain=DAC4	GCA_003583725.1	2315689	2315689	type	True	79.3994	401	849	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	79.3955	360	849	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	79.3423	394	849	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_022953075.1	1582356	1582356	type	True	79.2259	360	849	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_024721585.1	1582356	1582356	type	True	79.1104	364	849	95	below_threshold
Sphingomonas piscis	strain=HDW15B	GCA_011300455.1	2714943	2714943	type	True	78.97	298	849	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	78.6376	288	849	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	78.6296	247	849	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	78.6165	245	849	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	78.2679	261	849	95	below_threshold
Sphingomonas dokdonensis	strain=DSM 21029	GCA_002197685.1	344880	344880	type	True	78.1783	245	849	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:08,802] [INFO] DFAST Taxonomy check result was written to GCF_000585415.1_ASM58541v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:08,802] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:08,802] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:08,803] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47dde50a-dbaf-4b63-af66-aa894d269049/dqc_reference/checkm_data
[2024-01-25 18:10:08,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:08,834] [INFO] Task started: CheckM
[2024-01-25 18:10:08,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000585415.1_ASM58541v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000585415.1_ASM58541v1_genomic.fna/checkm_input GCF_000585415.1_ASM58541v1_genomic.fna/checkm_result
[2024-01-25 18:10:32,558] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:32,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:32,576] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:32,576] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:32,577] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000585415.1_ASM58541v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:32,577] [INFO] Task started: Blastn
[2024-01-25 18:10:32,577] [INFO] Running command: blastn -query GCF_000585415.1_ASM58541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47dde50a-dbaf-4b63-af66-aa894d269049/dqc_reference/reference_markers_gtdb.fasta -out GCF_000585415.1_ASM58541v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:34,421] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:34,426] [INFO] Selected 17 target genomes.
[2024-01-25 18:10:34,426] [INFO] Target genome list was writen to GCF_000585415.1_ASM58541v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:34,450] [INFO] Task started: fastANI
[2024-01-25 18:10:34,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg95a3bc8b-7f21-478c-b411-e7d51271f063/GCF_000585415.1_ASM58541v1_genomic.fna.gz --refList GCF_000585415.1_ASM58541v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000585415.1_ASM58541v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:44,006] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:44,016] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:44,017] [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_000585415.1	s__Sphingomicrobium jaspsi	100.0	849	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014396585.1	s__Sphingomicrobium rhizophilum	80.462	433	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003499275.1	s__Sphingomicrobium mesophila	79.9921	406	849	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	79.7736	412	849	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	79.75	312	849	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	79.6211	418	849	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	79.5541	403	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583725.1	s__Sphingomicrobium edaphi	79.4049	401	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011301715.1	s__Sphingomicrobium sp011301715	79.197	336	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011300455.1	s__Sphingomicrobium piscis	78.97	298	849	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	78.8223	254	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135605.1	s__Sphingomonas desiccabilis	78.6129	248	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000016765.1	s__Rhizorhabdus wittichii	78.6008	342	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCA_019247755.1	s__Sphingomicrobium sp019247755	78.3916	216	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341505.2	s__Sphingomonas sp004341505	78.2737	271	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_002197685.1	s__Sphingomonas dokdonensis	78.1686	245	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151485.1	s__Allosphingosinicella sp004151485	77.9628	241	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:44,018] [INFO] GTDB search result was written to GCF_000585415.1_ASM58541v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:44,018] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:44,022] [INFO] DFAST_QC result json was written to GCF_000585415.1_ASM58541v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:44,022] [INFO] DFAST_QC completed!
[2024-01-25 18:10:44,022] [INFO] Total running time: 0h0m53s