[2024-01-25 18:04:05,548] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:04:05,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:04:05,549] [INFO] DQC Reference Directory: /var/lib/cwl/stga6fbeafd-ad24-48b3-bebe-d8c54939a8b2/dqc_reference
[2024-01-25 18:04:06,694] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:04:06,694] [INFO] Task started: Prodigal
[2024-01-25 18:04:06,695] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb16d3aa-3623-4d3b-9b92-fb092dee680a/GCF_014352855.1_ASM1435285v1_genomic.fna.gz | prodigal -d GCF_014352855.1_ASM1435285v1_genomic.fna/cds.fna -a GCF_014352855.1_ASM1435285v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:04:13,290] [INFO] Task succeeded: Prodigal
[2024-01-25 18:04:13,290] [INFO] Task started: HMMsearch
[2024-01-25 18:04:13,290] [INFO] Running command: hmmsearch --tblout GCF_014352855.1_ASM1435285v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6fbeafd-ad24-48b3-bebe-d8c54939a8b2/dqc_reference/reference_markers.hmm GCF_014352855.1_ASM1435285v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:04:13,489] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:04:13,490] [INFO] Found 6/6 markers.
[2024-01-25 18:04:13,514] [INFO] Query marker FASTA was written to GCF_014352855.1_ASM1435285v1_genomic.fna/markers.fasta
[2024-01-25 18:04:13,514] [INFO] Task started: Blastn
[2024-01-25 18:04:13,514] [INFO] Running command: blastn -query GCF_014352855.1_ASM1435285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6fbeafd-ad24-48b3-bebe-d8c54939a8b2/dqc_reference/reference_markers.fasta -out GCF_014352855.1_ASM1435285v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:14,432] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:14,435] [INFO] Selected 20 target genomes.
[2024-01-25 18:04:14,435] [INFO] Target genome list was writen to GCF_014352855.1_ASM1435285v1_genomic.fna/target_genomes.txt
[2024-01-25 18:04:14,456] [INFO] Task started: fastANI
[2024-01-25 18:04:14,456] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb16d3aa-3623-4d3b-9b92-fb092dee680a/GCF_014352855.1_ASM1435285v1_genomic.fna.gz --refList GCF_014352855.1_ASM1435285v1_genomic.fna/target_genomes.txt --output GCF_014352855.1_ASM1435285v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:04:26,444] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:26,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6fbeafd-ad24-48b3-bebe-d8c54939a8b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:04:26,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6fbeafd-ad24-48b3-bebe-d8c54939a8b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:04:26,457] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:04:26,457] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:04:26,457] [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 sabuli	strain=sand1-3	GCA_014352855.1	2764186	2764186	type	True	100.0	837	837	95	conclusive
Sphingomonas sinipercae	strain=HDW15C	GCA_011302055.1	2714944	2714944	type	True	80.1393	412	837	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	79.7363	422	837	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_014396785.1	1045317	1045317	type	True	79.6796	427	837	95	below_threshold
Sphingomonas jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	79.6473	367	837	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	79.4657	376	837	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	79.3965	367	837	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	79.2743	385	837	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	79.2684	338	837	95	below_threshold
Sphingomonas kaistensis	strain=DSM 16846	GCA_011927725.1	298708	298708	type	True	79.0624	372	837	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	78.8344	391	837	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.4136	269	837	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	78.3777	276	837	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.2629	264	837	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	78.1239	299	837	95	below_threshold
Sphingomonas asaccharolytica	strain=NBRC 15499	GCA_001598355.1	40681	40681	type	True	77.9435	247	837	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	77.8605	261	837	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	77.6258	249	837	95	below_threshold
Sphingomonas prati	strain=DSM 103336	GCA_014199405.1	1843237	1843237	type	True	77.5163	218	837	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	77.4735	221	837	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:04:26,459] [INFO] DFAST Taxonomy check result was written to GCF_014352855.1_ASM1435285v1_genomic.fna/tc_result.tsv
[2024-01-25 18:04:26,459] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:04:26,459] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:04:26,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6fbeafd-ad24-48b3-bebe-d8c54939a8b2/dqc_reference/checkm_data
[2024-01-25 18:04:26,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:04:26,487] [INFO] Task started: CheckM
[2024-01-25 18:04:26,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014352855.1_ASM1435285v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014352855.1_ASM1435285v1_genomic.fna/checkm_input GCF_014352855.1_ASM1435285v1_genomic.fna/checkm_result
[2024-01-25 18:04:49,400] [INFO] Task succeeded: CheckM
[2024-01-25 18:04:49,400] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:04:49,416] [INFO] ===== Completeness check finished =====
[2024-01-25 18:04:49,416] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:04:49,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014352855.1_ASM1435285v1_genomic.fna/markers.fasta)
[2024-01-25 18:04:49,416] [INFO] Task started: Blastn
[2024-01-25 18:04:49,416] [INFO] Running command: blastn -query GCF_014352855.1_ASM1435285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6fbeafd-ad24-48b3-bebe-d8c54939a8b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014352855.1_ASM1435285v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:51,254] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:51,257] [INFO] Selected 21 target genomes.
[2024-01-25 18:04:51,257] [INFO] Target genome list was writen to GCF_014352855.1_ASM1435285v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:04:51,280] [INFO] Task started: fastANI
[2024-01-25 18:04:51,280] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb16d3aa-3623-4d3b-9b92-fb092dee680a/GCF_014352855.1_ASM1435285v1_genomic.fna.gz --refList GCF_014352855.1_ASM1435285v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014352855.1_ASM1435285v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:05:02,984] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:03,000] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:05:03,001] [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_014352855.1	s__Sphingomicrobium sp014352855	100.0	837	837	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_011302055.1	s__Sphingomicrobium sinipercae	80.1256	413	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053295.1	s__Sphingomicrobium sp011053295	79.7231	297	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014396785.1	s__Sphingomicrobium lutea	79.7108	424	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000585415.1	s__Sphingomicrobium jaspsi	79.661	366	837	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	79.4094	366	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013817375.1	s__Sphingomicrobium sp013817375	79.3766	344	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620665.1	s__Sphingomicrobium sp000620665	79.375	385	837	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	79.2871	306	837	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	79.2621	339	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097155.1	s__Sphingomicrobium sp003097155	79.1264	410	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873475.1	s__Sphingomicrobium sp014873475	79.0711	355	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013816595.1	s__Sphingomicrobium sp013816595	78.8752	269	837	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	78.8619	389	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361785.1	s__Sphingomicrobium sp013361785	78.8005	265	837	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	78.6366	296	837	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	78.3305	312	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016765.1	s__Rhizorhabdus wittichii	78.1008	319	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_900167915.1	s__Rhizorhabdus histidinilytica	78.099	301	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.24	99.18	0.90	0.89	3	-
GCF_000632225.1	s__Sphingomonas sp000632225	78.0213	285	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903642285.1	s__Sphingomonas sp903642285	77.2187	198	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:05:03,002] [INFO] GTDB search result was written to GCF_014352855.1_ASM1435285v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:05:03,003] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:05:03,009] [INFO] DFAST_QC result json was written to GCF_014352855.1_ASM1435285v1_genomic.fna/dqc_result.json
[2024-01-25 18:05:03,009] [INFO] DFAST_QC completed!
[2024-01-25 18:05:03,009] [INFO] Total running time: 0h0m57s