[2024-01-24 13:17:14,377] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:14,379] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:14,379] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bf3f280-8249-43ad-9ab2-c1d41f8ee60b/dqc_reference
[2024-01-24 13:17:15,722] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,722] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,723] [INFO] Running command: gunzip -c /var/lib/cwl/stg4fbc1082-3992-40aa-bd7c-5de76cedbae3/GCF_003054045.1_ASM305404v1_genomic.fna.gz | prodigal -d GCF_003054045.1_ASM305404v1_genomic.fna/cds.fna -a GCF_003054045.1_ASM305404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:36,211] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:36,212] [INFO] Task started: HMMsearch
[2024-01-24 13:17:36,212] [INFO] Running command: hmmsearch --tblout GCF_003054045.1_ASM305404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bf3f280-8249-43ad-9ab2-c1d41f8ee60b/dqc_reference/reference_markers.hmm GCF_003054045.1_ASM305404v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:36,539] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:36,541] [INFO] Found 6/6 markers.
[2024-01-24 13:17:36,587] [INFO] Query marker FASTA was written to GCF_003054045.1_ASM305404v1_genomic.fna/markers.fasta
[2024-01-24 13:17:36,587] [INFO] Task started: Blastn
[2024-01-24 13:17:36,587] [INFO] Running command: blastn -query GCF_003054045.1_ASM305404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bf3f280-8249-43ad-9ab2-c1d41f8ee60b/dqc_reference/reference_markers.fasta -out GCF_003054045.1_ASM305404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:37,205] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:37,209] [INFO] Selected 19 target genomes.
[2024-01-24 13:17:37,209] [INFO] Target genome list was writen to GCF_003054045.1_ASM305404v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:37,215] [INFO] Task started: fastANI
[2024-01-24 13:17:37,215] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fbc1082-3992-40aa-bd7c-5de76cedbae3/GCF_003054045.1_ASM305404v1_genomic.fna.gz --refList GCF_003054045.1_ASM305404v1_genomic.fna/target_genomes.txt --output GCF_003054045.1_ASM305404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:53,497] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:53,498] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bf3f280-8249-43ad-9ab2-c1d41f8ee60b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:53,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bf3f280-8249-43ad-9ab2-c1d41f8ee60b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:53,516] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:53,516] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:53,516] [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 faecium	strain=DSM 11690	GCA_003054045.1	34087	34087	type	True	100.0	1754	1754	95	conclusive
Sphingobacterium faecium	strain=NBRC 15299	GCA_007990875.1	34087	34087	type	True	99.9821	1728	1754	95	conclusive
Sphingobacterium multivorum	strain=FDAARGOS_1203	GCA_016894225.1	28454	28454	type	True	78.3861	241	1754	95	below_threshold
Sphingobacterium multivorum	strain=NCTC11343	GCA_900457465.1	28454	28454	type	True	78.3424	242	1754	95	below_threshold
Sphingobacterium paramultivorum	strain=w15	GCA_009660355.1	2886510	2886510	type	True	78.2106	248	1754	95	below_threshold
Sphingobacterium lumbrici	strain=1.3611	GCA_006476045.1	2559600	2559600	type	True	78.2001	131	1754	95	below_threshold
Sphingobacterium puteale	strain=M05W1-28	GCA_003627955.1	2420510	2420510	type	True	78.0813	237	1754	95	below_threshold
Sphingobacterium olei	strain=HAL-9	GCA_005048855.1	2571155	2571155	type	True	78.0012	142	1754	95	below_threshold
Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007	strain=KCTC 12578	GCA_009829075.1	363260	363260	type	True	78.0011	163	1754	95	below_threshold
Sphingobacterium litopenaei	strain=DN04309	GCA_014692495.1	2763500	2763500	type	True	77.9906	169	1754	95	below_threshold
Sphingobacterium siyangense	strain=CGMCC 1.6855	GCA_007830445.1	459529	459529	type	True	77.9827	254	1754	95	below_threshold
Sphingobacterium rhinopitheci	strain=WQ 047	GCA_022627575.1	2781960	2781960	type	True	77.9764	177	1754	95	below_threshold
Sphingobacterium alkalisoli	strain=Y3L14	GCA_005049105.1	1874115	1874115	type	True	77.9227	144	1754	95	below_threshold
Sphingobacterium alkalisoli	strain=CGMCC 1.15782	GCA_014643675.1	1874115	1874115	type	True	77.8839	141	1754	95	below_threshold
Sphingobacterium nematocida	strain=DSM 24091	GCA_900168125.1	1513896	1513896	type	True	77.7433	137	1754	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:53,518] [INFO] DFAST Taxonomy check result was written to GCF_003054045.1_ASM305404v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:53,518] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:53,518] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:53,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bf3f280-8249-43ad-9ab2-c1d41f8ee60b/dqc_reference/checkm_data
[2024-01-24 13:17:53,519] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:53,572] [INFO] Task started: CheckM
[2024-01-24 13:17:53,572] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003054045.1_ASM305404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003054045.1_ASM305404v1_genomic.fna/checkm_input GCF_003054045.1_ASM305404v1_genomic.fna/checkm_result
[2024-01-24 13:18:52,765] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:52,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:52,783] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:52,783] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:52,783] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003054045.1_ASM305404v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:52,784] [INFO] Task started: Blastn
[2024-01-24 13:18:52,784] [INFO] Running command: blastn -query GCF_003054045.1_ASM305404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bf3f280-8249-43ad-9ab2-c1d41f8ee60b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003054045.1_ASM305404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:53,585] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:53,587] [INFO] Selected 11 target genomes.
[2024-01-24 13:18:53,588] [INFO] Target genome list was writen to GCF_003054045.1_ASM305404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:53,614] [INFO] Task started: fastANI
[2024-01-24 13:18:53,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fbc1082-3992-40aa-bd7c-5de76cedbae3/GCF_003054045.1_ASM305404v1_genomic.fna.gz --refList GCF_003054045.1_ASM305404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003054045.1_ASM305404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:03,976] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:03,993] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:03,993] [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_003054045.1	s__Sphingobacterium faecium	100.0	1754	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.76	97.52	0.94	0.88	3	conclusive
GCA_000938735.2	s__Sphingobacterium sp000938735	92.8222	1341	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.17	98.17	0.81	0.81	2	-
GCF_012030425.1	s__Sphingobacterium kitahiroshimense	84.0326	1144	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.48	96.84	0.85	0.82	6	-
GCF_000747525.1	s__Sphingobacterium sp000747525	81.9376	849	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017942165.1	s__Sphingobacterium sp017942165	78.9157	173	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011043515.1	s__Sphingobacterium sp011043515	78.0662	163	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.84	98.84	0.89	0.89	2	-
GCF_009829075.1	s__Sphingobacterium composti	77.9994	161	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017834055.1	s__Sphingobacterium sp002429765	77.9443	224	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.80	97.10	0.89	0.87	5	-
GCF_002933815.1	s__Sphingobacterium sp002933815	77.9042	249	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002245855.1	s__Sphingobacterium cellulitidis	77.636	151	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.02	97.95	0.91	0.90	4	-
GCA_002454415.1	s__Sphingobacterium sp002454415	77.5753	211	1754	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 13:19:03,994] [INFO] GTDB search result was written to GCF_003054045.1_ASM305404v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:03,995] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:03,998] [INFO] DFAST_QC result json was written to GCF_003054045.1_ASM305404v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:03,998] [INFO] DFAST_QC completed!
[2024-01-24 13:19:03,999] [INFO] Total running time: 0h1m50s