[2024-01-25 17:49:05,623] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:49:05,624] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:49:05,624] [INFO] DQC Reference Directory: /var/lib/cwl/stg13fb4e6e-36f7-4e43-b2ff-51fab93ff675/dqc_reference
[2024-01-25 17:49:06,807] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:49:06,808] [INFO] Task started: Prodigal
[2024-01-25 17:49:06,808] [INFO] Running command: gunzip -c /var/lib/cwl/stgba1457b1-3a0d-4245-8079-72e76207e8e8/GCF_016464365.1_ASM1646436v1_genomic.fna.gz | prodigal -d GCF_016464365.1_ASM1646436v1_genomic.fna/cds.fna -a GCF_016464365.1_ASM1646436v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:49:16,050] [INFO] Task succeeded: Prodigal
[2024-01-25 17:49:16,050] [INFO] Task started: HMMsearch
[2024-01-25 17:49:16,050] [INFO] Running command: hmmsearch --tblout GCF_016464365.1_ASM1646436v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13fb4e6e-36f7-4e43-b2ff-51fab93ff675/dqc_reference/reference_markers.hmm GCF_016464365.1_ASM1646436v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:49:16,258] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:49:16,259] [INFO] Found 6/6 markers.
[2024-01-25 17:49:16,289] [INFO] Query marker FASTA was written to GCF_016464365.1_ASM1646436v1_genomic.fna/markers.fasta
[2024-01-25 17:49:16,289] [INFO] Task started: Blastn
[2024-01-25 17:49:16,289] [INFO] Running command: blastn -query GCF_016464365.1_ASM1646436v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13fb4e6e-36f7-4e43-b2ff-51fab93ff675/dqc_reference/reference_markers.fasta -out GCF_016464365.1_ASM1646436v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:17,093] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:17,096] [INFO] Selected 30 target genomes.
[2024-01-25 17:49:17,096] [INFO] Target genome list was writen to GCF_016464365.1_ASM1646436v1_genomic.fna/target_genomes.txt
[2024-01-25 17:49:17,107] [INFO] Task started: fastANI
[2024-01-25 17:49:17,107] [INFO] Running command: fastANI --query /var/lib/cwl/stgba1457b1-3a0d-4245-8079-72e76207e8e8/GCF_016464365.1_ASM1646436v1_genomic.fna.gz --refList GCF_016464365.1_ASM1646436v1_genomic.fna/target_genomes.txt --output GCF_016464365.1_ASM1646436v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:49:36,724] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:36,724] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13fb4e6e-36f7-4e43-b2ff-51fab93ff675/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:49:36,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13fb4e6e-36f7-4e43-b2ff-51fab93ff675/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:49:36,742] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:49:36,742] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:49:36,742] [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
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	78.2004	215	1168	95	below_threshold
Rhizorhabdus dicambivorans	strain=Ndbn-20	GCA_002355275.1	1850238	1850238	type	True	78.0758	251	1168	95	below_threshold
Sphingobium cloacae	strain=NBRC 102517	GCA_001591285.1	120107	120107	type	True	78.0657	207	1168	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	77.8949	203	1168	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_014199595.1	172044	172044	type	True	77.8393	189	1168	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.8017	228	1168	95	below_threshold
Sphingomonas yabuuchiae	strain=DSM 14562	GCA_017052455.1	172044	172044	type	True	77.65	192	1168	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	77.5749	227	1168	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.5624	201	1168	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.5588	252	1168	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	77.5175	213	1168	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	77.4698	240	1168	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	77.4231	169	1168	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	77.4018	176	1168	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	77.3813	186	1168	95	below_threshold
Polymorphobacter multimanifer	strain=JCM 18140	GCA_014647295.1	1070431	1070431	type	True	77.3627	213	1168	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	77.3325	171	1168	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	77.3195	198	1168	95	below_threshold
Polymorphobacter multimanifer	strain=DSM 102189	GCA_014205635.1	1070431	1070431	type	True	77.3084	238	1168	95	below_threshold
Sphingomonas gellani	strain=S6-262	GCA_900110035.1	1166340	1166340	type	True	77.3047	168	1168	95	below_threshold
Sphingomonas lutea	strain=KCTC 23642	GCA_021497585.1	1045317	1045317	type	True	77.3028	117	1168	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.279	227	1168	95	below_threshold
Croceicoccus marinus	strain=E4A9	GCA_001661675.2	450378	450378	type	True	77.2633	176	1168	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	77.2099	247	1168	95	below_threshold
Novosphingopyxis iocasae	strain=PB63	GCA_014334095.1	2762729	2762729	type	True	77.1806	139	1168	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	77.1541	211	1168	95	below_threshold
Polymorphobacter glacialis	strain=CGMCC 1.15519	GCA_014643455.1	1614636	1614636	type	True	77.1429	222	1168	95	below_threshold
Pacificimonas flava	strain=DSM 107612	GCA_014202205.1	1234595	1234595	type	True	77.0909	134	1168	95	below_threshold
Pacificimonas flava	strain=JLT2015	GCA_000342165.1	1234595	1234595	type	True	77.0872	135	1168	95	below_threshold
Novosphingobium rosa	strain=NBRC 15208	GCA_001598555.1	76978	76978	type	True	77.06	208	1168	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:49:36,745] [INFO] DFAST Taxonomy check result was written to GCF_016464365.1_ASM1646436v1_genomic.fna/tc_result.tsv
[2024-01-25 17:49:36,745] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:49:36,745] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:49:36,746] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13fb4e6e-36f7-4e43-b2ff-51fab93ff675/dqc_reference/checkm_data
[2024-01-25 17:49:36,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:49:36,812] [INFO] Task started: CheckM
[2024-01-25 17:49:36,812] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016464365.1_ASM1646436v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016464365.1_ASM1646436v1_genomic.fna/checkm_input GCF_016464365.1_ASM1646436v1_genomic.fna/checkm_result
[2024-01-25 17:50:07,882] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:07,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:07,902] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:07,902] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:07,903] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016464365.1_ASM1646436v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:07,904] [INFO] Task started: Blastn
[2024-01-25 17:50:07,904] [INFO] Running command: blastn -query GCF_016464365.1_ASM1646436v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13fb4e6e-36f7-4e43-b2ff-51fab93ff675/dqc_reference/reference_markers_gtdb.fasta -out GCF_016464365.1_ASM1646436v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:09,512] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:09,549] [INFO] Selected 13 target genomes.
[2024-01-25 17:50:09,549] [INFO] Target genome list was writen to GCF_016464365.1_ASM1646436v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:09,574] [INFO] Task started: fastANI
[2024-01-25 17:50:09,574] [INFO] Running command: fastANI --query /var/lib/cwl/stgba1457b1-3a0d-4245-8079-72e76207e8e8/GCF_016464365.1_ASM1646436v1_genomic.fna.gz --refList GCF_016464365.1_ASM1646436v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016464365.1_ASM1646436v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:19,055] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:19,063] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:50:19,063] [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_016464365.1	s__Sandaracinobacter sp016464365	100.0	1165	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003248865.1	s__Sandaracinobacter sp003248865	80.9429	615	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385875.1	s__Sandaracinobacter neustonicus	80.8581	640	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandaracinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004796535.1	s__Sphingomonas_L sp004796535	77.8456	225	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014117445.1	s__GCA-014117445 sp014117445	77.8446	365	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__GCA-014117445	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199595.1	s__Sphingomonas yabuuchiae	77.8393	189	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.94	96.78	0.92	0.88	4	-
GCF_000016765.1	s__Rhizorhabdus wittichii	77.6345	259	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_007785815.1	s__Sphingomonas_G solaris	77.5886	226	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003345355.1	s__Sphingomonas sp003345355	77.5765	200	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013344685.1	s__Sphingomonas sp013344685	77.4666	243	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205635.1	s__Polymorphobacter multimanifer	77.3083	238	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	99.78	99.78	0.99	0.99	2	-
GCF_001661675.2	s__Croceicoccus marinus	77.2484	177	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	96.65	96.65	0.86	0.86	2	-
GCA_013791705.1	s__Novosphingobium sp013791705	76.7908	128	1168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.87	99.87	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:50:19,065] [INFO] GTDB search result was written to GCF_016464365.1_ASM1646436v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:19,065] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:19,070] [INFO] DFAST_QC result json was written to GCF_016464365.1_ASM1646436v1_genomic.fna/dqc_result.json
[2024-01-25 17:50:19,070] [INFO] DFAST_QC completed!
[2024-01-25 17:50:19,070] [INFO] Total running time: 0h1m13s