[2024-01-24 12:31:04,570] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:04,572] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:04,572] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb2bb65d-30a7-4604-97fd-07f051c918fa/dqc_reference
[2024-01-24 12:31:05,816] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:05,817] [INFO] Task started: Prodigal
[2024-01-24 12:31:05,817] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbcf071c-8ca9-494e-b07c-8177f7cf04ac/GCF_003610355.1_ASM361035v1_genomic.fna.gz | prodigal -d GCF_003610355.1_ASM361035v1_genomic.fna/cds.fna -a GCF_003610355.1_ASM361035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:34,977] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:34,978] [INFO] Task started: HMMsearch
[2024-01-24 12:31:34,978] [INFO] Running command: hmmsearch --tblout GCF_003610355.1_ASM361035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb2bb65d-30a7-4604-97fd-07f051c918fa/dqc_reference/reference_markers.hmm GCF_003610355.1_ASM361035v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:35,331] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:35,334] [INFO] Found 6/6 markers.
[2024-01-24 12:31:35,392] [INFO] Query marker FASTA was written to GCF_003610355.1_ASM361035v1_genomic.fna/markers.fasta
[2024-01-24 12:31:35,393] [INFO] Task started: Blastn
[2024-01-24 12:31:35,393] [INFO] Running command: blastn -query GCF_003610355.1_ASM361035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb2bb65d-30a7-4604-97fd-07f051c918fa/dqc_reference/reference_markers.fasta -out GCF_003610355.1_ASM361035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:36,020] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:36,023] [INFO] Selected 11 target genomes.
[2024-01-24 12:31:36,024] [INFO] Target genome list was writen to GCF_003610355.1_ASM361035v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:36,039] [INFO] Task started: fastANI
[2024-01-24 12:31:36,040] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbcf071c-8ca9-494e-b07c-8177f7cf04ac/GCF_003610355.1_ASM361035v1_genomic.fna.gz --refList GCF_003610355.1_ASM361035v1_genomic.fna/target_genomes.txt --output GCF_003610355.1_ASM361035v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:48,558] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:48,558] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb2bb65d-30a7-4604-97fd-07f051c918fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:48,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb2bb65d-30a7-4604-97fd-07f051c918fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:48,570] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:48,570] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:48,570] [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 detergens	strain=CECT 7938	GCA_003610355.1	1145106	1145106	type	True	100.0	2238	2238	95	conclusive
Sphingobacterium puteale	strain=M05W1-28	GCA_003627955.1	2420510	2420510	type	True	86.9449	1405	2238	95	below_threshold
Sphingobacterium athyrii	strain=M46	GCA_003071065.1	2152717	2152717	type	True	86.1683	1435	2238	95	below_threshold
Sphingobacterium prati	strain=arapr2	GCA_013167215.1	2737006	2737006	type	True	85.4653	1275	2238	95	below_threshold
Sphingobacterium paramultivorum	strain=w15	GCA_009660355.1	2886510	2886510	type	True	81.4866	938	2238	95	below_threshold
Sphingobacterium siyangense	strain=CGMCC 1.6855	GCA_007830445.1	459529	459529	type	True	81.367	851	2238	95	below_threshold
Sphingobacterium multivorum	strain=NCTC11343	GCA_900457465.1	28454	28454	type	True	81.189	875	2238	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:48,572] [INFO] DFAST Taxonomy check result was written to GCF_003610355.1_ASM361035v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:48,572] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:48,573] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:48,573] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb2bb65d-30a7-4604-97fd-07f051c918fa/dqc_reference/checkm_data
[2024-01-24 12:31:48,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:48,637] [INFO] Task started: CheckM
[2024-01-24 12:31:48,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003610355.1_ASM361035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003610355.1_ASM361035v1_genomic.fna/checkm_input GCF_003610355.1_ASM361035v1_genomic.fna/checkm_result
[2024-01-24 12:33:09,471] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:09,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:09,497] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:09,498] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:09,498] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003610355.1_ASM361035v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:09,499] [INFO] Task started: Blastn
[2024-01-24 12:33:09,499] [INFO] Running command: blastn -query GCF_003610355.1_ASM361035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb2bb65d-30a7-4604-97fd-07f051c918fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_003610355.1_ASM361035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:10,309] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:10,313] [INFO] Selected 10 target genomes.
[2024-01-24 12:33:10,314] [INFO] Target genome list was writen to GCF_003610355.1_ASM361035v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:10,322] [INFO] Task started: fastANI
[2024-01-24 12:33:10,322] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbcf071c-8ca9-494e-b07c-8177f7cf04ac/GCF_003610355.1_ASM361035v1_genomic.fna.gz --refList GCF_003610355.1_ASM361035v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003610355.1_ASM361035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:23,719] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:23,732] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:23,732] [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_003610355.1	s__Sphingobacterium detergens	100.0	2238	2238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002000245.1	s__Sphingobacterium sp002000245	88.2609	1451	2238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627955.1	s__Sphingobacterium puteale	86.9447	1405	2238	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	86.4529	1447	2238	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	86.1849	1433	2238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.91	97.66	0.85	0.84	3	-
GCA_002472835.1	s__Sphingobacterium sp002472835	84.8865	1260	2238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	95.27	95.27	0.83	0.83	2	-
GCF_017908035.1	s__Sphingobacterium tabacisoli	77.6207	136	2238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852525.1	s__Pedobacter sp003852525	76.2171	64	2238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129215.1	s__Pedobacter caeni	76.1368	63	2238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:23,734] [INFO] GTDB search result was written to GCF_003610355.1_ASM361035v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:23,735] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:23,738] [INFO] DFAST_QC result json was written to GCF_003610355.1_ASM361035v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:23,738] [INFO] DFAST_QC completed!
[2024-01-24 12:33:23,738] [INFO] Total running time: 0h2m19s