[2024-01-24 11:05:25,463] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:25,464] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:25,464] [INFO] DQC Reference Directory: /var/lib/cwl/stg079f6f8e-6818-4349-9da9-7b5d5c5d5a83/dqc_reference
[2024-01-24 11:05:26,792] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,793] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,793] [INFO] Running command: gunzip -c /var/lib/cwl/stg165ae91e-4340-48dc-9000-7a7f64e1accb/GCF_003071065.1_ASM307106v1_genomic.fna.gz | prodigal -d GCF_003071065.1_ASM307106v1_genomic.fna/cds.fna -a GCF_003071065.1_ASM307106v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:57,187] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:57,187] [INFO] Task started: HMMsearch
[2024-01-24 11:05:57,187] [INFO] Running command: hmmsearch --tblout GCF_003071065.1_ASM307106v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg079f6f8e-6818-4349-9da9-7b5d5c5d5a83/dqc_reference/reference_markers.hmm GCF_003071065.1_ASM307106v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:57,583] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:57,585] [INFO] Found 6/6 markers.
[2024-01-24 11:05:57,646] [INFO] Query marker FASTA was written to GCF_003071065.1_ASM307106v1_genomic.fna/markers.fasta
[2024-01-24 11:05:57,646] [INFO] Task started: Blastn
[2024-01-24 11:05:57,646] [INFO] Running command: blastn -query GCF_003071065.1_ASM307106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg079f6f8e-6818-4349-9da9-7b5d5c5d5a83/dqc_reference/reference_markers.fasta -out GCF_003071065.1_ASM307106v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:58,285] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:58,288] [INFO] Selected 11 target genomes.
[2024-01-24 11:05:58,288] [INFO] Target genome list was writen to GCF_003071065.1_ASM307106v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:58,293] [INFO] Task started: fastANI
[2024-01-24 11:05:58,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg165ae91e-4340-48dc-9000-7a7f64e1accb/GCF_003071065.1_ASM307106v1_genomic.fna.gz --refList GCF_003071065.1_ASM307106v1_genomic.fna/target_genomes.txt --output GCF_003071065.1_ASM307106v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:11,688] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:11,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg079f6f8e-6818-4349-9da9-7b5d5c5d5a83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:11,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg079f6f8e-6818-4349-9da9-7b5d5c5d5a83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:11,704] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:11,704] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:11,704] [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
Sphingobacterium athyrii	strain=M46	GCA_003071065.1	2152717	2152717	type	True	100.0	2275	2275	95	conclusive
Sphingobacterium puteale	strain=M05W1-28	GCA_003627955.1	2420510	2420510	type	True	91.7784	1711	2275	95	below_threshold
Sphingobacterium prati	strain=arapr2	GCA_013167215.1	2737006	2737006	type	True	87.9937	1489	2275	95	below_threshold
Sphingobacterium detergens	strain=CECT 7938	GCA_003610355.1	1145106	1145106	type	True	86.1134	1428	2275	95	below_threshold
Sphingobacterium siyangense	strain=CGMCC 1.6855	GCA_007830445.1	459529	459529	type	True	81.277	932	2275	95	below_threshold
Sphingobacterium multivorum	strain=FDAARGOS_1203	GCA_016894225.1	28454	28454	type	True	81.2405	892	2275	95	below_threshold
Sphingobacterium paramultivorum	strain=w15	GCA_009660355.1	2886510	2886510	type	True	81.0957	983	2275	95	below_threshold
Sphingobacterium thalpophilum	strain=NCTC11429	GCA_901482695.1	259	259	type	True	80.9278	828	2275	95	below_threshold
Sphingobacterium rhinopitheci	strain=WQ 047	GCA_022627575.1	2781960	2781960	type	True	78.1767	128	2275	95	below_threshold
Sphingobacterium faecale	strain=C459-1	GCA_016746095.1	2803775	2803775	type	True	78.1313	114	2275	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:11,706] [INFO] DFAST Taxonomy check result was written to GCF_003071065.1_ASM307106v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:11,706] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:11,707] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:11,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg079f6f8e-6818-4349-9da9-7b5d5c5d5a83/dqc_reference/checkm_data
[2024-01-24 11:06:11,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:11,772] [INFO] Task started: CheckM
[2024-01-24 11:06:11,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003071065.1_ASM307106v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003071065.1_ASM307106v1_genomic.fna/checkm_input GCF_003071065.1_ASM307106v1_genomic.fna/checkm_result
[2024-01-24 11:07:34,905] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:34,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:34,929] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:34,930] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:34,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003071065.1_ASM307106v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:34,931] [INFO] Task started: Blastn
[2024-01-24 11:07:34,931] [INFO] Running command: blastn -query GCF_003071065.1_ASM307106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg079f6f8e-6818-4349-9da9-7b5d5c5d5a83/dqc_reference/reference_markers_gtdb.fasta -out GCF_003071065.1_ASM307106v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:35,768] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:35,775] [INFO] Selected 7 target genomes.
[2024-01-24 11:07:35,776] [INFO] Target genome list was writen to GCF_003071065.1_ASM307106v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:35,781] [INFO] Task started: fastANI
[2024-01-24 11:07:35,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg165ae91e-4340-48dc-9000-7a7f64e1accb/GCF_003071065.1_ASM307106v1_genomic.fna.gz --refList GCF_003071065.1_ASM307106v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003071065.1_ASM307106v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:47,269] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:47,282] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:47,282] [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_003071065.1	s__Sphingobacterium athyrii	100.0	2275	2275	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.91	97.66	0.85	0.84	3	conclusive
GCF_003627955.1	s__Sphingobacterium puteale	91.7834	1710	2275	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933815.1	s__Sphingobacterium sp002933815	91.2308	1586	2275	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002472835.1	s__Sphingobacterium sp002472835	88.5008	1461	2275	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	95.27	95.27	0.83	0.83	2	-
GCF_003610355.1	s__Sphingobacterium detergens	86.1363	1424	2275	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000245.1	s__Sphingobacterium sp002000245	84.8555	1324	2275	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830445.1	s__Sphingobacterium siyangense	81.2789	930	2275	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	96.51	95.59	0.80	0.78	14	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:47,283] [INFO] GTDB search result was written to GCF_003071065.1_ASM307106v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:47,284] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:47,287] [INFO] DFAST_QC result json was written to GCF_003071065.1_ASM307106v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:47,287] [INFO] DFAST_QC completed!
[2024-01-24 11:07:47,287] [INFO] Total running time: 0h2m22s