[2024-01-24 14:10:15,938] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:10:15,940] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:10:15,940] [INFO] DQC Reference Directory: /var/lib/cwl/stg663803c6-54f5-44dc-94c6-c1ab685997cb/dqc_reference
[2024-01-24 14:10:17,260] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:10:17,261] [INFO] Task started: Prodigal
[2024-01-24 14:10:17,261] [INFO] Running command: gunzip -c /var/lib/cwl/stg11c0db4c-70f2-4828-9f93-b4714eb2dd63/GCF_009660355.1_ASM966035v1_genomic.fna.gz | prodigal -d GCF_009660355.1_ASM966035v1_genomic.fna/cds.fna -a GCF_009660355.1_ASM966035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:10:46,243] [INFO] Task succeeded: Prodigal
[2024-01-24 14:10:46,244] [INFO] Task started: HMMsearch
[2024-01-24 14:10:46,244] [INFO] Running command: hmmsearch --tblout GCF_009660355.1_ASM966035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg663803c6-54f5-44dc-94c6-c1ab685997cb/dqc_reference/reference_markers.hmm GCF_009660355.1_ASM966035v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:10:46,614] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:10:46,615] [INFO] Found 6/6 markers.
[2024-01-24 14:10:46,671] [INFO] Query marker FASTA was written to GCF_009660355.1_ASM966035v1_genomic.fna/markers.fasta
[2024-01-24 14:10:46,671] [INFO] Task started: Blastn
[2024-01-24 14:10:46,671] [INFO] Running command: blastn -query GCF_009660355.1_ASM966035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg663803c6-54f5-44dc-94c6-c1ab685997cb/dqc_reference/reference_markers.fasta -out GCF_009660355.1_ASM966035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:10:47,290] [INFO] Task succeeded: Blastn
[2024-01-24 14:10:47,293] [INFO] Selected 14 target genomes.
[2024-01-24 14:10:47,294] [INFO] Target genome list was writen to GCF_009660355.1_ASM966035v1_genomic.fna/target_genomes.txt
[2024-01-24 14:10:47,299] [INFO] Task started: fastANI
[2024-01-24 14:10:47,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg11c0db4c-70f2-4828-9f93-b4714eb2dd63/GCF_009660355.1_ASM966035v1_genomic.fna.gz --refList GCF_009660355.1_ASM966035v1_genomic.fna/target_genomes.txt --output GCF_009660355.1_ASM966035v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:11:03,872] [INFO] Task succeeded: fastANI
[2024-01-24 14:11:03,873] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg663803c6-54f5-44dc-94c6-c1ab685997cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:11:03,874] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg663803c6-54f5-44dc-94c6-c1ab685997cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:11:03,884] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:11:03,884] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:11:03,884] [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 paramultivorum	strain=w15	GCA_009660355.1	2886510	2886510	type	True	100.0	2187	2190	95	inconclusive
Sphingobacterium siyangense	strain=CGMCC 1.6855	GCA_007830445.1	459529	459529	type	True	95.5493	1635	2190	95	inconclusive
Sphingobacterium multivorum	strain=FDAARGOS_1203	GCA_016894225.1	28454	28454	type	True	91.9331	1538	2190	95	below_threshold
Sphingobacterium multivorum	strain=NCTC11343	GCA_900457465.1	28454	28454	type	True	91.9126	1543	2190	95	below_threshold
Sphingobacterium puteale	strain=M05W1-28	GCA_003627955.1	2420510	2420510	type	True	81.85	968	2190	95	below_threshold
Sphingobacterium detergens	strain=CECT 7938	GCA_003610355.1	1145106	1145106	type	True	81.55	916	2190	95	below_threshold
Sphingobacterium prati	strain=arapr2	GCA_013167215.1	2737006	2737006	type	True	81.3214	936	2190	95	below_threshold
Sphingobacterium athyrii	strain=M46	GCA_003071065.1	2152717	2152717	type	True	81.264	991	2190	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:11:03,885] [INFO] DFAST Taxonomy check result was written to GCF_009660355.1_ASM966035v1_genomic.fna/tc_result.tsv
[2024-01-24 14:11:03,886] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:11:03,886] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:11:03,886] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg663803c6-54f5-44dc-94c6-c1ab685997cb/dqc_reference/checkm_data
[2024-01-24 14:11:03,887] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:11:03,947] [INFO] Task started: CheckM
[2024-01-24 14:11:03,947] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009660355.1_ASM966035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009660355.1_ASM966035v1_genomic.fna/checkm_input GCF_009660355.1_ASM966035v1_genomic.fna/checkm_result
[2024-01-24 14:12:22,782] [INFO] Task succeeded: CheckM
[2024-01-24 14:12:22,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:12:22,807] [INFO] ===== Completeness check finished =====
[2024-01-24 14:12:22,808] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:12:22,808] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009660355.1_ASM966035v1_genomic.fna/markers.fasta)
[2024-01-24 14:12:22,809] [INFO] Task started: Blastn
[2024-01-24 14:12:22,809] [INFO] Running command: blastn -query GCF_009660355.1_ASM966035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg663803c6-54f5-44dc-94c6-c1ab685997cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_009660355.1_ASM966035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:23,599] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:23,603] [INFO] Selected 12 target genomes.
[2024-01-24 14:12:23,603] [INFO] Target genome list was writen to GCF_009660355.1_ASM966035v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:12:23,655] [INFO] Task started: fastANI
[2024-01-24 14:12:23,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg11c0db4c-70f2-4828-9f93-b4714eb2dd63/GCF_009660355.1_ASM966035v1_genomic.fna.gz --refList GCF_009660355.1_ASM966035v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009660355.1_ASM966035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:12:35,198] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:35,211] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:12:35,211] [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_007830445.1	s__Sphingobacterium siyangense	95.5448	1635	2190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	96.51	95.59	0.80	0.78	14	conclusive
GCF_900457465.1	s__Sphingobacterium multivorum	91.9194	1542	2190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.58	95.36	0.86	0.75	43	-
GCA_002420705.1	s__Sphingobacterium sp002420705	87.3094	1436	2190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002500745.1	s__Sphingobacterium sp002500745	86.4832	1222	2190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.61	98.61	0.89	0.89	2	-
GCF_017834055.1	s__Sphingobacterium sp002429765	85.1141	1324	2190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.80	97.10	0.89	0.87	5	-
GCA_002454415.1	s__Sphingobacterium sp002454415	83.424	1008	2190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003071065.1	s__Sphingobacterium athyrii	81.2544	992	2190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.91	97.66	0.85	0.84	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:12:35,212] [INFO] GTDB search result was written to GCF_009660355.1_ASM966035v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:12:35,213] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:12:35,215] [INFO] DFAST_QC result json was written to GCF_009660355.1_ASM966035v1_genomic.fna/dqc_result.json
[2024-01-24 14:12:35,216] [INFO] DFAST_QC completed!
[2024-01-24 14:12:35,216] [INFO] Total running time: 0h2m19s