[2024-01-25 18:07:05,557] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:05,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:05,558] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd06a585-d50a-4f90-a8da-4c22362b1362/dqc_reference
[2024-01-25 18:07:06,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:06,671] [INFO] Task started: Prodigal
[2024-01-25 18:07:06,671] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc51ede7-9f1f-478c-a8db-5bc38e71ce85/GCF_009733735.1_ASM973373v1_genomic.fna.gz | prodigal -d GCF_009733735.1_ASM973373v1_genomic.fna/cds.fna -a GCF_009733735.1_ASM973373v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:07:15,054] [INFO] Task succeeded: Prodigal
[2024-01-25 18:07:15,054] [INFO] Task started: HMMsearch
[2024-01-25 18:07:15,054] [INFO] Running command: hmmsearch --tblout GCF_009733735.1_ASM973373v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd06a585-d50a-4f90-a8da-4c22362b1362/dqc_reference/reference_markers.hmm GCF_009733735.1_ASM973373v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:07:15,277] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:07:15,278] [INFO] Found 6/6 markers.
[2024-01-25 18:07:15,309] [INFO] Query marker FASTA was written to GCF_009733735.1_ASM973373v1_genomic.fna/markers.fasta
[2024-01-25 18:07:15,309] [INFO] Task started: Blastn
[2024-01-25 18:07:15,309] [INFO] Running command: blastn -query GCF_009733735.1_ASM973373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd06a585-d50a-4f90-a8da-4c22362b1362/dqc_reference/reference_markers.fasta -out GCF_009733735.1_ASM973373v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:16,171] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:16,177] [INFO] Selected 15 target genomes.
[2024-01-25 18:07:16,177] [INFO] Target genome list was writen to GCF_009733735.1_ASM973373v1_genomic.fna/target_genomes.txt
[2024-01-25 18:07:16,183] [INFO] Task started: fastANI
[2024-01-25 18:07:16,183] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc51ede7-9f1f-478c-a8db-5bc38e71ce85/GCF_009733735.1_ASM973373v1_genomic.fna.gz --refList GCF_009733735.1_ASM973373v1_genomic.fna/target_genomes.txt --output GCF_009733735.1_ASM973373v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:07:25,589] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:25,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd06a585-d50a-4f90-a8da-4c22362b1362/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:07:25,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd06a585-d50a-4f90-a8da-4c22362b1362/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:07:25,602] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:07:25,602] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:07:25,602] [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 oryzae	strain=NM-18	GCA_009733735.1	2675220	2675220	type	True	100.0	890	892	95	conclusive
Sandarakinorhabdus limnophila	strain=DSM 17366	GCA_000420765.1	210512	210512	type	True	85.5811	640	892	95	below_threshold
Sandarakinorhabdus cyanobacteriorum	strain=TH057	GCA_002251755.1	1981098	1981098	type	True	84.1884	666	892	95	below_threshold
Sandarakinorhabdus rubra	strain=MO-4	GCA_010994245.1	2672568	2672568	type	True	84.1269	538	892	95	below_threshold
Polymorphobacter fuscus	strain=DSM 105347	GCA_011927825.1	1439888	1439888	type	True	79.1294	390	892	95	below_threshold
Polymorphobacter fuscus	strain=D40P	GCA_009607675.1	1439888	1439888	type	True	79.0242	399	892	95	below_threshold
Polymorphobacter glacialis	strain=CGMCC 1.15519	GCA_014643455.1	1614636	1614636	type	True	78.5746	295	892	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.844	255	892	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	77.6117	225	892	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	77.5887	201	892	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.5225	237	892	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.4253	218	892	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	77.2009	178	892	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	77.0218	213	892	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	76.9659	195	892	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:07:25,603] [INFO] DFAST Taxonomy check result was written to GCF_009733735.1_ASM973373v1_genomic.fna/tc_result.tsv
[2024-01-25 18:07:25,604] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:07:25,604] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:07:25,604] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd06a585-d50a-4f90-a8da-4c22362b1362/dqc_reference/checkm_data
[2024-01-25 18:07:25,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:07:25,640] [INFO] Task started: CheckM
[2024-01-25 18:07:25,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009733735.1_ASM973373v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009733735.1_ASM973373v1_genomic.fna/checkm_input GCF_009733735.1_ASM973373v1_genomic.fna/checkm_result
[2024-01-25 18:07:59,334] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:59,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:59,359] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:59,359] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:59,360] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009733735.1_ASM973373v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:59,360] [INFO] Task started: Blastn
[2024-01-25 18:07:59,360] [INFO] Running command: blastn -query GCF_009733735.1_ASM973373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd06a585-d50a-4f90-a8da-4c22362b1362/dqc_reference/reference_markers_gtdb.fasta -out GCF_009733735.1_ASM973373v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:01,110] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:01,113] [INFO] Selected 7 target genomes.
[2024-01-25 18:08:01,113] [INFO] Target genome list was writen to GCF_009733735.1_ASM973373v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:08:01,121] [INFO] Task started: fastANI
[2024-01-25 18:08:01,121] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc51ede7-9f1f-478c-a8db-5bc38e71ce85/GCF_009733735.1_ASM973373v1_genomic.fna.gz --refList GCF_009733735.1_ASM973373v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009733735.1_ASM973373v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:08:06,414] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:06,420] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:08:06,420] [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_009733735.1	s__Sandarakinorhabdus oryzae	100.0	890	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000331225.1	s__Sandarakinorhabdus sp000331225	85.976	690	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420765.1	s__Sandarakinorhabdus limnophila	85.5811	640	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	96.49	96.49	0.92	0.92	2	-
GCA_002280855.1	s__Sandarakinorhabdus sp002280855	85.4696	692	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	96.11	96.11	0.96	0.96	2	-
GCF_002251755.1	s__Sandarakinorhabdus cyanobacteriorum	84.2054	665	892	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	84.0884	540	892	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	83.9617	632	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:08:06,421] [INFO] GTDB search result was written to GCF_009733735.1_ASM973373v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:08:06,422] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:08:06,439] [INFO] DFAST_QC result json was written to GCF_009733735.1_ASM973373v1_genomic.fna/dqc_result.json
[2024-01-25 18:08:06,440] [INFO] DFAST_QC completed!
[2024-01-25 18:08:06,440] [INFO] Total running time: 0h1m1s