[2024-01-24 10:56:34,612] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:56:34,614] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:56:34,614] [INFO] DQC Reference Directory: /var/lib/cwl/stg1df9e94a-de22-4255-96aa-03fc7b263dc1/dqc_reference
[2024-01-24 10:56:36,718] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:56:36,719] [INFO] Task started: Prodigal
[2024-01-24 10:56:36,720] [INFO] Running command: gunzip -c /var/lib/cwl/stga02683b8-c6dc-4e45-b501-b9af4523e27d/GCF_016894225.1_ASM1689422v1_genomic.fna.gz | prodigal -d GCF_016894225.1_ASM1689422v1_genomic.fna/cds.fna -a GCF_016894225.1_ASM1689422v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:02,832] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:02,833] [INFO] Task started: HMMsearch
[2024-01-24 10:57:02,833] [INFO] Running command: hmmsearch --tblout GCF_016894225.1_ASM1689422v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1df9e94a-de22-4255-96aa-03fc7b263dc1/dqc_reference/reference_markers.hmm GCF_016894225.1_ASM1689422v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:03,161] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:03,163] [INFO] Found 6/6 markers.
[2024-01-24 10:57:03,212] [INFO] Query marker FASTA was written to GCF_016894225.1_ASM1689422v1_genomic.fna/markers.fasta
[2024-01-24 10:57:03,213] [INFO] Task started: Blastn
[2024-01-24 10:57:03,213] [INFO] Running command: blastn -query GCF_016894225.1_ASM1689422v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1df9e94a-de22-4255-96aa-03fc7b263dc1/dqc_reference/reference_markers.fasta -out GCF_016894225.1_ASM1689422v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:03,810] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:03,814] [INFO] Selected 11 target genomes.
[2024-01-24 10:57:03,814] [INFO] Target genome list was writen to GCF_016894225.1_ASM1689422v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:03,819] [INFO] Task started: fastANI
[2024-01-24 10:57:03,819] [INFO] Running command: fastANI --query /var/lib/cwl/stga02683b8-c6dc-4e45-b501-b9af4523e27d/GCF_016894225.1_ASM1689422v1_genomic.fna.gz --refList GCF_016894225.1_ASM1689422v1_genomic.fna/target_genomes.txt --output GCF_016894225.1_ASM1689422v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:17,625] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:17,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1df9e94a-de22-4255-96aa-03fc7b263dc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:17,626] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1df9e94a-de22-4255-96aa-03fc7b263dc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:17,640] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:17,640] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:17,640] [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 multivorum	strain=FDAARGOS_1203	GCA_016894225.1	28454	28454	type	True	100.0	1988	1988	95	conclusive
Sphingobacterium multivorum	strain=NCTC11343	GCA_900457465.1	28454	28454	type	True	99.9642	1979	1988	95	conclusive
Sphingobacterium siyangense	strain=CGMCC 1.6855	GCA_007830445.1	459529	459529	type	True	92.3477	1547	1988	95	below_threshold
Sphingobacterium paramultivorum	strain=w15	GCA_009660355.1	2886510	2886510	type	True	91.9242	1537	1988	95	below_threshold
Sphingobacterium puteale	strain=M05W1-28	GCA_003627955.1	2420510	2420510	type	True	81.3065	881	1988	95	below_threshold
Sphingobacterium prati	strain=arapr2	GCA_013167215.1	2737006	2737006	type	True	81.1598	855	1988	95	below_threshold
Sphingobacterium athyrii	strain=M46	GCA_003071065.1	2152717	2152717	type	True	81.1549	904	1988	95	below_threshold
Sphingobacterium detergens	strain=CECT 7938	GCA_003610355.1	1145106	1145106	type	True	81.1362	875	1988	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:17,642] [INFO] DFAST Taxonomy check result was written to GCF_016894225.1_ASM1689422v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:17,643] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:17,643] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:17,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1df9e94a-de22-4255-96aa-03fc7b263dc1/dqc_reference/checkm_data
[2024-01-24 10:57:17,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:17,703] [INFO] Task started: CheckM
[2024-01-24 10:57:17,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016894225.1_ASM1689422v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016894225.1_ASM1689422v1_genomic.fna/checkm_input GCF_016894225.1_ASM1689422v1_genomic.fna/checkm_result
[2024-01-24 10:58:30,479] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:30,480] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:30,502] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:30,502] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:30,503] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016894225.1_ASM1689422v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:30,503] [INFO] Task started: Blastn
[2024-01-24 10:58:30,503] [INFO] Running command: blastn -query GCF_016894225.1_ASM1689422v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1df9e94a-de22-4255-96aa-03fc7b263dc1/dqc_reference/reference_markers_gtdb.fasta -out GCF_016894225.1_ASM1689422v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:31,293] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:31,297] [INFO] Selected 7 target genomes.
[2024-01-24 10:58:31,297] [INFO] Target genome list was writen to GCF_016894225.1_ASM1689422v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:31,304] [INFO] Task started: fastANI
[2024-01-24 10:58:31,304] [INFO] Running command: fastANI --query /var/lib/cwl/stga02683b8-c6dc-4e45-b501-b9af4523e27d/GCF_016894225.1_ASM1689422v1_genomic.fna.gz --refList GCF_016894225.1_ASM1689422v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016894225.1_ASM1689422v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:41,470] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:41,476] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:41,476] [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_900457465.1	s__Sphingobacterium multivorum	99.9642	1979	1988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.58	95.36	0.86	0.75	43	conclusive
GCF_007830445.1	s__Sphingobacterium siyangense	92.3483	1547	1988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	96.51	95.59	0.80	0.78	14	-
GCA_002420705.1	s__Sphingobacterium sp002420705	86.9851	1315	1988	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	85.7862	1128	1988	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	84.6523	1157	1988	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	83.1766	899	1988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610355.1	s__Sphingobacterium detergens	81.1539	873	1988	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:41,480] [INFO] GTDB search result was written to GCF_016894225.1_ASM1689422v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:41,480] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:41,483] [INFO] DFAST_QC result json was written to GCF_016894225.1_ASM1689422v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:41,483] [INFO] DFAST_QC completed!
[2024-01-24 10:58:41,483] [INFO] Total running time: 0h2m7s