[2024-01-24 13:58:10,254] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,256] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,256] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc02c0cf-8175-4846-aabe-995547d0f543/dqc_reference
[2024-01-24 13:58:11,362] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,363] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,363] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3487e4b-5854-4415-9b0c-76aef16b4bab/GCF_014138555.1_ASM1413855v1_genomic.fna.gz | prodigal -d GCF_014138555.1_ASM1413855v1_genomic.fna/cds.fna -a GCF_014138555.1_ASM1413855v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:26,097] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:26,097] [INFO] Task started: HMMsearch
[2024-01-24 13:58:26,097] [INFO] Running command: hmmsearch --tblout GCF_014138555.1_ASM1413855v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc02c0cf-8175-4846-aabe-995547d0f543/dqc_reference/reference_markers.hmm GCF_014138555.1_ASM1413855v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:26,332] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:26,333] [INFO] Found 6/6 markers.
[2024-01-24 13:58:26,366] [INFO] Query marker FASTA was written to GCF_014138555.1_ASM1413855v1_genomic.fna/markers.fasta
[2024-01-24 13:58:26,367] [INFO] Task started: Blastn
[2024-01-24 13:58:26,367] [INFO] Running command: blastn -query GCF_014138555.1_ASM1413855v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc02c0cf-8175-4846-aabe-995547d0f543/dqc_reference/reference_markers.fasta -out GCF_014138555.1_ASM1413855v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:26,909] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:26,912] [INFO] Selected 9 target genomes.
[2024-01-24 13:58:26,912] [INFO] Target genome list was writen to GCF_014138555.1_ASM1413855v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:26,915] [INFO] Task started: fastANI
[2024-01-24 13:58:26,915] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3487e4b-5854-4415-9b0c-76aef16b4bab/GCF_014138555.1_ASM1413855v1_genomic.fna.gz --refList GCF_014138555.1_ASM1413855v1_genomic.fna/target_genomes.txt --output GCF_014138555.1_ASM1413855v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:34,018] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:34,018] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc02c0cf-8175-4846-aabe-995547d0f543/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:34,018] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc02c0cf-8175-4846-aabe-995547d0f543/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:34,023] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:34,024] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:34,024] [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 soli	strain=DSM 101679	GCA_014138555.1	1914757	1914757	type	True	100.0	1467	1468	95	conclusive
Sphingobacterium soli	strain=CGMCC 1.15966	GCA_014644335.1	1914757	1914757	type	True	99.998	1456	1468	95	conclusive
Sphingobacterium mizutaii	strain=NCTC12149	GCA_900187125.1	1010	1010	type	True	82.3769	872	1468	95	below_threshold
Sphingobacterium mizutaii	strain=DSM 11724	GCA_900102835.1	1010	1010	type	True	82.3478	870	1468	95	below_threshold
Sphingobacterium mizutaii	strain=NBRC 14946	GCA_007990895.1	1010	1010	type	True	82.3419	859	1468	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:34,025] [INFO] DFAST Taxonomy check result was written to GCF_014138555.1_ASM1413855v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:34,025] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:34,025] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:34,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc02c0cf-8175-4846-aabe-995547d0f543/dqc_reference/checkm_data
[2024-01-24 13:58:34,026] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:34,067] [INFO] Task started: CheckM
[2024-01-24 13:58:34,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014138555.1_ASM1413855v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014138555.1_ASM1413855v1_genomic.fna/checkm_input GCF_014138555.1_ASM1413855v1_genomic.fna/checkm_result
[2024-01-24 13:59:17,271] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:17,272] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:17,287] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:17,287] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:17,287] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014138555.1_ASM1413855v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:17,287] [INFO] Task started: Blastn
[2024-01-24 13:59:17,287] [INFO] Running command: blastn -query GCF_014138555.1_ASM1413855v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc02c0cf-8175-4846-aabe-995547d0f543/dqc_reference/reference_markers_gtdb.fasta -out GCF_014138555.1_ASM1413855v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:18,103] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:18,106] [INFO] Selected 11 target genomes.
[2024-01-24 13:59:18,106] [INFO] Target genome list was writen to GCF_014138555.1_ASM1413855v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:18,112] [INFO] Task started: fastANI
[2024-01-24 13:59:18,112] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3487e4b-5854-4415-9b0c-76aef16b4bab/GCF_014138555.1_ASM1413855v1_genomic.fna.gz --refList GCF_014138555.1_ASM1413855v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014138555.1_ASM1413855v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:27,940] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:27,947] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:27,948] [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
GCA_002245855.1	s__Sphingobacterium cellulitidis	97.9693	1321	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.02	97.95	0.91	0.90	4	conclusive
GCF_900187125.1	s__Sphingobacterium mizutaii	82.3843	870	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.36	98.08	0.96	0.87	4	-
GCF_014219015.1	s__Sphingobacterium sp002476975	81.9786	854	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.27	97.88	0.91	0.89	5	-
GCF_009733535.1	s__Sphingobacterium endophyticum	80.9007	701	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901472535.1	s__Sphingobacterium daejeonense	80.6244	675	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.25	97.25	0.90	0.90	2	-
GCF_011046555.1	s__Sphingobacterium lactis	79.0813	394	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009768885.1	s__Sphingobacterium humi	79.0131	286	1468	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	78.7756	173	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.84	98.84	0.89	0.89	2	-
GCF_002000245.1	s__Sphingobacterium sp002000245	77.8154	141	1468	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	77.6608	166	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	96.51	95.59	0.80	0.78	14	-
GCF_003054045.1	s__Sphingobacterium faecium	77.6246	154	1468	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.76	97.52	0.94	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:27,949] [INFO] GTDB search result was written to GCF_014138555.1_ASM1413855v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:27,950] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:27,952] [INFO] DFAST_QC result json was written to GCF_014138555.1_ASM1413855v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:27,952] [INFO] DFAST_QC completed!
[2024-01-24 13:59:27,952] [INFO] Total running time: 0h1m18s