[2024-01-24 12:40:07,041] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:07,043] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:07,043] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a396d12-67f6-46d3-b6ce-3d0dfb6942d6/dqc_reference
[2024-01-24 12:40:08,310] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:08,311] [INFO] Task started: Prodigal
[2024-01-24 12:40:08,311] [INFO] Running command: gunzip -c /var/lib/cwl/stg47b6efbb-6993-4ea4-9774-fbaba70d360b/GCF_000153705.1_ASM15370v1_genomic.fna.gz | prodigal -d GCF_000153705.1_ASM15370v1_genomic.fna/cds.fna -a GCF_000153705.1_ASM15370v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:18,739] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:18,740] [INFO] Task started: HMMsearch
[2024-01-24 12:40:18,740] [INFO] Running command: hmmsearch --tblout GCF_000153705.1_ASM15370v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a396d12-67f6-46d3-b6ce-3d0dfb6942d6/dqc_reference/reference_markers.hmm GCF_000153705.1_ASM15370v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:18,952] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:18,953] [INFO] Found 6/6 markers.
[2024-01-24 12:40:18,984] [INFO] Query marker FASTA was written to GCF_000153705.1_ASM15370v1_genomic.fna/markers.fasta
[2024-01-24 12:40:18,984] [INFO] Task started: Blastn
[2024-01-24 12:40:18,984] [INFO] Running command: blastn -query GCF_000153705.1_ASM15370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a396d12-67f6-46d3-b6ce-3d0dfb6942d6/dqc_reference/reference_markers.fasta -out GCF_000153705.1_ASM15370v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:19,896] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:19,900] [INFO] Selected 16 target genomes.
[2024-01-24 12:40:19,900] [INFO] Target genome list was writen to GCF_000153705.1_ASM15370v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:19,906] [INFO] Task started: fastANI
[2024-01-24 12:40:19,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg47b6efbb-6993-4ea4-9774-fbaba70d360b/GCF_000153705.1_ASM15370v1_genomic.fna.gz --refList GCF_000153705.1_ASM15370v1_genomic.fna/target_genomes.txt --output GCF_000153705.1_ASM15370v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:32,953] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:32,953] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a396d12-67f6-46d3-b6ce-3d0dfb6942d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:32,953] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a396d12-67f6-46d3-b6ce-3d0dfb6942d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:32,966] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:32,967] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:32,967] [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
Fulvimarina pelagi	strain=HTCC2506	GCA_000153705.1	217511	217511	type	True	100.0	1266	1267	95	conclusive
Fulvimarina pelagi	strain=DSM 15513	GCA_001463845.1	217511	217511	type	True	99.9752	1230	1267	95	conclusive
Fulvimarina endophytica	strain=85	GCA_003403015.1	2293836	2293836	type	True	79.8855	618	1267	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	78.5958	460	1267	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	78.5011	447	1267	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_001463825.1	182270	182270	type	True	78.4793	438	1267	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	78.4751	455	1267	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_000421645.1	182270	182270	type	True	78.4496	440	1267	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	78.3983	462	1267	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	78.387	421	1267	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	78.2864	410	1267	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	78.2011	416	1267	95	below_threshold
Aureimonas pseudogalii	strain=DSM 102238	GCA_014196835.1	1744844	1744844	type	True	77.7798	326	1267	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	76.9371	205	1267	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.7662	186	1267	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	76.755	187	1267	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:32,969] [INFO] DFAST Taxonomy check result was written to GCF_000153705.1_ASM15370v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:32,970] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:32,970] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:32,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a396d12-67f6-46d3-b6ce-3d0dfb6942d6/dqc_reference/checkm_data
[2024-01-24 12:40:32,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:33,009] [INFO] Task started: CheckM
[2024-01-24 12:40:33,009] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000153705.1_ASM15370v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000153705.1_ASM15370v1_genomic.fna/checkm_input GCF_000153705.1_ASM15370v1_genomic.fna/checkm_result
[2024-01-24 12:41:05,947] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:05,948] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:05,965] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:05,966] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:05,966] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000153705.1_ASM15370v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:05,966] [INFO] Task started: Blastn
[2024-01-24 12:41:05,966] [INFO] Running command: blastn -query GCF_000153705.1_ASM15370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a396d12-67f6-46d3-b6ce-3d0dfb6942d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000153705.1_ASM15370v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:07,625] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:07,628] [INFO] Selected 14 target genomes.
[2024-01-24 12:41:07,629] [INFO] Target genome list was writen to GCF_000153705.1_ASM15370v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:07,637] [INFO] Task started: fastANI
[2024-01-24 12:41:07,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg47b6efbb-6993-4ea4-9774-fbaba70d360b/GCF_000153705.1_ASM15370v1_genomic.fna.gz --refList GCF_000153705.1_ASM15370v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000153705.1_ASM15370v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:19,973] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:19,985] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:19,985] [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_000153705.1	s__Fulvimarina pelagi	100.0	1266	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Fulvimarina	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003403015.1	s__Fulvimarina endophytica	79.8854	618	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Fulvimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176465.1	s__Fulvimarina manganoxydans	78.9442	484	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Fulvimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088275.1	s__Jiella sp002088275	78.6722	468	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153465.1	s__Aurantimonas manganoxydans	78.5788	447	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	99.99	99.99	1.00	1.00	2	-
GCF_017815135.1	s__Jiella sp017815135	78.5734	424	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353515.1	s__Jiella sp017353515	78.4661	456	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500815.1	s__Jiella pacifica	78.4139	460	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500835.1	s__Aurantimonas aggregata	78.3868	421	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700095.1	s__Jiella sp002700095	78.3279	445	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196845.1	s__Aurantimonas endophytica	78.1961	416	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001475935.1	s__Aureimonas ureilytica_A	77.5775	247	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	96.93	96.78	0.87	0.86	4	-
GCF_016919405.1	s__Ensifer sp000799055	77.4301	217	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	97.37	96.05	0.91	0.88	3	-
GCF_007004135.1	s__Rhizobium_A straminoryzae	77.2605	172	1267	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	98.62	98.62	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:19,987] [INFO] GTDB search result was written to GCF_000153705.1_ASM15370v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:19,987] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:19,991] [INFO] DFAST_QC result json was written to GCF_000153705.1_ASM15370v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:19,991] [INFO] DFAST_QC completed!
[2024-01-24 12:41:19,991] [INFO] Total running time: 0h1m13s