[2024-01-24 13:39:59,695] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:39:59,698] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:39:59,699] [INFO] DQC Reference Directory: /var/lib/cwl/stgf760bf98-0543-4850-9003-1b665e061dc3/dqc_reference
[2024-01-24 13:40:01,004] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:01,005] [INFO] Task started: Prodigal
[2024-01-24 13:40:01,006] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6489338-866b-482f-8618-f5f1846034f7/GCF_009733535.1_ASM973353v1_genomic.fna.gz | prodigal -d GCF_009733535.1_ASM973353v1_genomic.fna/cds.fna -a GCF_009733535.1_ASM973353v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:18,596] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:18,596] [INFO] Task started: HMMsearch
[2024-01-24 13:40:18,596] [INFO] Running command: hmmsearch --tblout GCF_009733535.1_ASM973353v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf760bf98-0543-4850-9003-1b665e061dc3/dqc_reference/reference_markers.hmm GCF_009733535.1_ASM973353v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:18,928] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:18,929] [INFO] Found 6/6 markers.
[2024-01-24 13:40:18,972] [INFO] Query marker FASTA was written to GCF_009733535.1_ASM973353v1_genomic.fna/markers.fasta
[2024-01-24 13:40:18,973] [INFO] Task started: Blastn
[2024-01-24 13:40:18,973] [INFO] Running command: blastn -query GCF_009733535.1_ASM973353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf760bf98-0543-4850-9003-1b665e061dc3/dqc_reference/reference_markers.fasta -out GCF_009733535.1_ASM973353v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:19,610] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:19,615] [INFO] Selected 18 target genomes.
[2024-01-24 13:40:19,615] [INFO] Target genome list was writen to GCF_009733535.1_ASM973353v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:19,625] [INFO] Task started: fastANI
[2024-01-24 13:40:19,625] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6489338-866b-482f-8618-f5f1846034f7/GCF_009733535.1_ASM973353v1_genomic.fna.gz --refList GCF_009733535.1_ASM973353v1_genomic.fna/target_genomes.txt --output GCF_009733535.1_ASM973353v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:33,375] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:33,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf760bf98-0543-4850-9003-1b665e061dc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:33,377] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf760bf98-0543-4850-9003-1b665e061dc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:33,390] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:33,390] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:33,390] [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 endophyticum	strain=NYYP31	GCA_009733535.1	2546448	2546448	type	True	100.0	1551	1554	95	conclusive
Sphingobacterium soli	strain=CGMCC 1.15966	GCA_014644335.1	1914757	1914757	type	True	80.9446	716	1554	95	below_threshold
Sphingobacterium soli	strain=DSM 101679	GCA_014138555.1	1914757	1914757	type	True	80.9326	717	1554	95	below_threshold
Sphingobacterium mizutaii	strain=NCTC12149	GCA_900187125.1	1010	1010	type	True	80.7062	678	1554	95	below_threshold
Sphingobacterium mizutaii	strain=NBRC 14946	GCA_007990895.1	1010	1010	type	True	80.6858	658	1554	95	below_threshold
Sphingobacterium mizutaii	strain=DSM 11724	GCA_900102835.1	1010	1010	type	True	80.6495	673	1554	95	below_threshold
Sphingobacterium lactis	strain=DSM 22361	GCA_011046555.1	797291	797291	type	True	79.3139	347	1554	95	below_threshold
Sphingobacterium lactis	strain=DSM 22361	GCA_900107985.1	797291	797291	type	True	79.2796	348	1554	95	below_threshold
Sphingobacterium corticibacter	strain=2c-3	GCA_003076635.1	2171749	2171749	type	True	78.4343	131	1554	95	below_threshold
Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007	strain=KCTC 12578	GCA_009829075.1	363260	363260	type	True	77.9856	172	1554	95	below_threshold
Sphingobacterium chungjuense	strain=IMCC25678	GCA_011316935.1	2675553	2675553	type	True	77.4955	112	1554	95	below_threshold
Sphingobacterium hungaricum	strain=KB22	GCA_015210005.1	2082723	2082723	type	True	77.4001	160	1554	95	below_threshold
Sphingobacterium prati	strain=arapr2	GCA_013167215.1	2737006	2737006	type	True	77.2833	139	1554	95	below_threshold
Pedobacter agri	strain=PB92	GCA_000258495.1	454586	454586	type	True	76.2491	51	1554	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:33,392] [INFO] DFAST Taxonomy check result was written to GCF_009733535.1_ASM973353v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:33,392] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:33,392] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:33,393] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf760bf98-0543-4850-9003-1b665e061dc3/dqc_reference/checkm_data
[2024-01-24 13:40:33,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:33,437] [INFO] Task started: CheckM
[2024-01-24 13:40:33,438] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009733535.1_ASM973353v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009733535.1_ASM973353v1_genomic.fna/checkm_input GCF_009733535.1_ASM973353v1_genomic.fna/checkm_result
[2024-01-24 13:41:28,776] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:28,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:28,797] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:28,798] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:28,798] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009733535.1_ASM973353v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:28,799] [INFO] Task started: Blastn
[2024-01-24 13:41:28,799] [INFO] Running command: blastn -query GCF_009733535.1_ASM973353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf760bf98-0543-4850-9003-1b665e061dc3/dqc_reference/reference_markers_gtdb.fasta -out GCF_009733535.1_ASM973353v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:29,624] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:29,629] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:29,629] [INFO] Target genome list was writen to GCF_009733535.1_ASM973353v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:29,639] [INFO] Task started: fastANI
[2024-01-24 13:41:29,640] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6489338-866b-482f-8618-f5f1846034f7/GCF_009733535.1_ASM973353v1_genomic.fna.gz --refList GCF_009733535.1_ASM973353v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009733535.1_ASM973353v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:40,711] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:40,724] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:40,724] [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_009733535.1	s__Sphingobacterium endophyticum	100.0	1551	1554	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_901472535.1	s__Sphingobacterium daejeonense	81.0095	725	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.25	97.25	0.90	0.90	2	-
GCF_900187125.1	s__Sphingobacterium mizutaii	80.7062	678	1554	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	80.6844	684	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.27	97.88	0.91	0.89	5	-
GCA_002245855.1	s__Sphingobacterium cellulitidis	80.5555	711	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.02	97.95	0.91	0.90	4	-
GCF_011046555.1	s__Sphingobacterium lactis	79.2916	348	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008274825.1	s__Sphingobacterium hotanense	78.8224	294	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.82	97.82	0.91	0.91	2	-
GCA_002322865.1	s__Sphingobacterium sp002322865	78.6819	290	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009557615.1	s__Sphingobacterium sp009557615	78.576	287	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003076635.1	s__Sphingobacterium sp003076635	78.4641	130	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829075.1	s__Sphingobacterium composti	77.9856	172	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011316935.1	s__Sphingobacterium sp011316935	77.5204	111	1554	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015210005.1	s__Sphingobacterium sp015210005	77.4179	159	1554	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 13:41:40,726] [INFO] GTDB search result was written to GCF_009733535.1_ASM973353v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:40,727] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:40,732] [INFO] DFAST_QC result json was written to GCF_009733535.1_ASM973353v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:40,733] [INFO] DFAST_QC completed!
[2024-01-24 13:41:40,733] [INFO] Total running time: 0h1m41s