[2024-01-24 12:40:07,158] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:07,160] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:07,160] [INFO] DQC Reference Directory: /var/lib/cwl/stg607f2427-1ee6-485c-a613-de95b48e8bf4/dqc_reference
[2024-01-24 12:40:08,449] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:08,450] [INFO] Task started: Prodigal
[2024-01-24 12:40:08,450] [INFO] Running command: gunzip -c /var/lib/cwl/stg85b35a54-a373-445a-bfaa-f1a95aa61724/GCF_000420765.1_ASM42076v1_genomic.fna.gz | prodigal -d GCF_000420765.1_ASM42076v1_genomic.fna/cds.fna -a GCF_000420765.1_ASM42076v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:17,478] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:17,479] [INFO] Task started: HMMsearch
[2024-01-24 12:40:17,479] [INFO] Running command: hmmsearch --tblout GCF_000420765.1_ASM42076v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg607f2427-1ee6-485c-a613-de95b48e8bf4/dqc_reference/reference_markers.hmm GCF_000420765.1_ASM42076v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:17,671] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:17,672] [INFO] Found 6/6 markers.
[2024-01-24 12:40:17,701] [INFO] Query marker FASTA was written to GCF_000420765.1_ASM42076v1_genomic.fna/markers.fasta
[2024-01-24 12:40:17,701] [INFO] Task started: Blastn
[2024-01-24 12:40:17,701] [INFO] Running command: blastn -query GCF_000420765.1_ASM42076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg607f2427-1ee6-485c-a613-de95b48e8bf4/dqc_reference/reference_markers.fasta -out GCF_000420765.1_ASM42076v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:18,505] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:18,509] [INFO] Selected 14 target genomes.
[2024-01-24 12:40:18,509] [INFO] Target genome list was writen to GCF_000420765.1_ASM42076v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:18,515] [INFO] Task started: fastANI
[2024-01-24 12:40:18,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg85b35a54-a373-445a-bfaa-f1a95aa61724/GCF_000420765.1_ASM42076v1_genomic.fna.gz --refList GCF_000420765.1_ASM42076v1_genomic.fna/target_genomes.txt --output GCF_000420765.1_ASM42076v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:27,393] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:27,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg607f2427-1ee6-485c-a613-de95b48e8bf4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:27,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg607f2427-1ee6-485c-a613-de95b48e8bf4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:27,405] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:27,406] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:27,406] [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
Sandarakinorhabdus limnophila	strain=DSM 17366	GCA_000420765.1	210512	210512	type	True	100.0	864	865	95	conclusive
Sandarakinorhabdus oryzae	strain=NM-18	GCA_009733735.1	2675220	2675220	type	True	85.7093	638	865	95	below_threshold
Sandarakinorhabdus cyanobacteriorum	strain=TH057	GCA_002251755.1	1981098	1981098	type	True	83.6408	687	865	95	below_threshold
Sandarakinorhabdus rubra	strain=MO-4	GCA_010994245.1	2672568	2672568	type	True	83.1993	522	865	95	below_threshold
Polymorphobacter fuscus	strain=DSM 105347	GCA_011927825.1	1439888	1439888	type	True	78.4769	391	865	95	below_threshold
Polymorphobacter fuscus	strain=D40P	GCA_009607675.1	1439888	1439888	type	True	78.4431	392	865	95	below_threshold
Polymorphobacter multimanifer	strain=DSM 102189	GCA_014205635.1	1070431	1070431	type	True	78.214	364	865	95	below_threshold
Polymorphobacter multimanifer	strain=JCM 18140	GCA_014647295.1	1070431	1070431	type	True	78.1504	343	865	95	below_threshold
Sphingobium quisquiliarum	strain=P25	GCA_000445065.1	538379	538379	type	True	77.3155	159	865	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.3006	233	865	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	77.0821	202	865	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	76.9005	240	865	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	76.8125	166	865	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	76.7234	185	865	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:27,408] [INFO] DFAST Taxonomy check result was written to GCF_000420765.1_ASM42076v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:27,408] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:27,408] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:27,409] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg607f2427-1ee6-485c-a613-de95b48e8bf4/dqc_reference/checkm_data
[2024-01-24 12:40:27,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:27,438] [INFO] Task started: CheckM
[2024-01-24 12:40:27,438] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000420765.1_ASM42076v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000420765.1_ASM42076v1_genomic.fna/checkm_input GCF_000420765.1_ASM42076v1_genomic.fna/checkm_result
[2024-01-24 12:40:58,058] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:58,059] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:58,079] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:58,080] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:58,080] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000420765.1_ASM42076v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:58,080] [INFO] Task started: Blastn
[2024-01-24 12:40:58,080] [INFO] Running command: blastn -query GCF_000420765.1_ASM42076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg607f2427-1ee6-485c-a613-de95b48e8bf4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000420765.1_ASM42076v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:59,544] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:59,548] [INFO] Selected 7 target genomes.
[2024-01-24 12:40:59,548] [INFO] Target genome list was writen to GCF_000420765.1_ASM42076v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:59,553] [INFO] Task started: fastANI
[2024-01-24 12:40:59,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg85b35a54-a373-445a-bfaa-f1a95aa61724/GCF_000420765.1_ASM42076v1_genomic.fna.gz --refList GCF_000420765.1_ASM42076v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000420765.1_ASM42076v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:04,628] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:04,635] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:04,635] [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_000420765.1	s__Sandarakinorhabdus limnophila	100.0	864	865	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	96.49	96.49	0.92	0.92	2	conclusive
GCA_002280855.1	s__Sandarakinorhabdus sp002280855	94.211	796	865	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	96.11	96.11	0.96	0.96	2	-
GCF_000331225.1	s__Sandarakinorhabdus sp000331225	88.1521	755	865	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733735.1	s__Sandarakinorhabdus oryzae	85.715	638	865	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970445.1	s__Sandarakinorhabdus sp018970445	83.827	667	865	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002251755.1	s__Sandarakinorhabdus cyanobacteriorum	83.6348	686	865	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	96.87	96.87	0.91	0.91	2	-
GCF_010994245.1	s__Sandarakinorhabdus rubra	83.211	521	865	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:04,636] [INFO] GTDB search result was written to GCF_000420765.1_ASM42076v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:04,637] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:04,640] [INFO] DFAST_QC result json was written to GCF_000420765.1_ASM42076v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:04,640] [INFO] DFAST_QC completed!
[2024-01-24 12:41:04,640] [INFO] Total running time: 0h0m57s