[2024-01-24 13:09:51,748] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:51,751] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:51,751] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc7d9e68-c8f1-416c-a23b-ec3ca0f48db9/dqc_reference
[2024-01-24 13:09:53,196] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:53,197] [INFO] Task started: Prodigal
[2024-01-24 13:09:53,197] [INFO] Running command: gunzip -c /var/lib/cwl/stg524a97b7-0dcb-4611-bbb6-72c322ee6826/GCF_004342685.1_ASM434268v1_genomic.fna.gz | prodigal -d GCF_004342685.1_ASM434268v1_genomic.fna/cds.fna -a GCF_004342685.1_ASM434268v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:08,954] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:08,955] [INFO] Task started: HMMsearch
[2024-01-24 13:10:08,955] [INFO] Running command: hmmsearch --tblout GCF_004342685.1_ASM434268v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc7d9e68-c8f1-416c-a23b-ec3ca0f48db9/dqc_reference/reference_markers.hmm GCF_004342685.1_ASM434268v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:09,265] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:09,266] [INFO] Found 6/6 markers.
[2024-01-24 13:10:09,314] [INFO] Query marker FASTA was written to GCF_004342685.1_ASM434268v1_genomic.fna/markers.fasta
[2024-01-24 13:10:09,315] [INFO] Task started: Blastn
[2024-01-24 13:10:09,315] [INFO] Running command: blastn -query GCF_004342685.1_ASM434268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc7d9e68-c8f1-416c-a23b-ec3ca0f48db9/dqc_reference/reference_markers.fasta -out GCF_004342685.1_ASM434268v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:09,936] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:09,940] [INFO] Selected 16 target genomes.
[2024-01-24 13:10:09,940] [INFO] Target genome list was writen to GCF_004342685.1_ASM434268v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:09,945] [INFO] Task started: fastANI
[2024-01-24 13:10:09,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg524a97b7-0dcb-4611-bbb6-72c322ee6826/GCF_004342685.1_ASM434268v1_genomic.fna.gz --refList GCF_004342685.1_ASM434268v1_genomic.fna/target_genomes.txt --output GCF_004342685.1_ASM434268v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:21,101] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:21,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc7d9e68-c8f1-416c-a23b-ec3ca0f48db9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:21,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc7d9e68-c8f1-416c-a23b-ec3ca0f48db9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:21,118] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:21,119] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:21,119] [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 alimentarium	strain=DSM 22362	GCA_004342685.1	797292	797292	type	True	99.9999	1139	1144	95	conclusive
Sphingobacterium litopenaei	strain=DN04309	GCA_014692495.1	2763500	2763500	type	True	81.0962	489	1144	95	below_threshold
Sphingobacterium bovisgrunnientis	strain=KCTC 52685	GCA_009829085.1	1874697	1874697	type	True	81.0828	465	1144	95	below_threshold
Sphingobacterium cavernae	strain=5.0403-2	GCA_008520265.1	2592657	2592657	type	True	80.889	488	1144	95	below_threshold
Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007	strain=KCTC 12578	GCA_009829075.1	363260	363260	type	True	80.7785	459	1144	95	below_threshold
Sphingobacterium rhinopitheci	strain=WQ 047	GCA_022627575.1	2781960	2781960	type	True	79.0137	247	1144	95	below_threshold
Sphingobacterium nematocida	strain=DSM 24091	GCA_900168125.1	1513896	1513896	type	True	78.7801	179	1144	95	below_threshold
Sphingobacterium mizutaii	strain=NCTC12149	GCA_900187125.1	1010	1010	type	True	78.6193	154	1144	95	below_threshold
Sphingobacterium mizutaii	strain=NBRC 14946	GCA_007990895.1	1010	1010	type	True	78.5364	149	1144	95	below_threshold
Sphingobacterium detergens	strain=CECT 7938	GCA_003610355.1	1145106	1145106	type	True	78.4697	147	1144	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:21,123] [INFO] DFAST Taxonomy check result was written to GCF_004342685.1_ASM434268v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:21,123] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:21,124] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:21,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc7d9e68-c8f1-416c-a23b-ec3ca0f48db9/dqc_reference/checkm_data
[2024-01-24 13:10:21,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:21,163] [INFO] Task started: CheckM
[2024-01-24 13:10:21,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004342685.1_ASM434268v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004342685.1_ASM434268v1_genomic.fna/checkm_input GCF_004342685.1_ASM434268v1_genomic.fna/checkm_result
[2024-01-24 13:11:09,038] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:09,039] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:09,059] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:09,059] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:09,060] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004342685.1_ASM434268v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:09,060] [INFO] Task started: Blastn
[2024-01-24 13:11:09,060] [INFO] Running command: blastn -query GCF_004342685.1_ASM434268v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc7d9e68-c8f1-416c-a23b-ec3ca0f48db9/dqc_reference/reference_markers_gtdb.fasta -out GCF_004342685.1_ASM434268v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:09,859] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:09,863] [INFO] Selected 20 target genomes.
[2024-01-24 13:11:09,863] [INFO] Target genome list was writen to GCF_004342685.1_ASM434268v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:09,881] [INFO] Task started: fastANI
[2024-01-24 13:11:09,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg524a97b7-0dcb-4611-bbb6-72c322ee6826/GCF_004342685.1_ASM434268v1_genomic.fna.gz --refList GCF_004342685.1_ASM434268v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004342685.1_ASM434268v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:24,778] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:24,794] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:24,794] [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_004342685.1	s__Sphingobacterium alimentarium	99.9999	1139	1144	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_009829085.1	s__Sphingobacterium bovisgrunnientis	81.0865	466	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	96.1642	N/A	N/A	N/A	N/A	1	-
GCF_008520265.1	s__Sphingobacterium cavernae	80.9106	486	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	96.1642	N/A	N/A	N/A	N/A	1	-
GCF_011043515.1	s__Sphingobacterium sp011043515	80.8682	463	1144	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	80.7652	461	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014219015.1	s__Sphingobacterium sp002476975	79.0409	166	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.27	97.88	0.91	0.89	5	-
GCF_007830445.1	s__Sphingobacterium siyangense	78.8997	143	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	96.51	95.59	0.80	0.78	14	-
GCF_900168125.1	s__Sphingobacterium nematocida	78.7916	178	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011007365.1	s__Sphingobacterium sp011007365	78.6852	178	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.58	99.33	0.95	0.93	4	-
GCF_017834055.1	s__Sphingobacterium sp002429765	78.6203	115	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.80	97.10	0.89	0.87	5	-
GCF_900187125.1	s__Sphingobacterium mizutaii	78.6107	154	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.36	98.08	0.96	0.87	4	-
GCF_003610355.1	s__Sphingobacterium detergens	78.497	146	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005048855.1	s__Sphingobacterium olei	78.446	189	1144	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	78.0969	120	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000783305.1	s__Sphingobacterium sp000783305	77.9408	107	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001586775.1	s__Sphingobacterium sp001586775	77.8626	98	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011043525.1	s__Sphingobacterium sp011043525	77.8006	113	1144	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 13:11:24,796] [INFO] GTDB search result was written to GCF_004342685.1_ASM434268v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:24,796] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:24,800] [INFO] DFAST_QC result json was written to GCF_004342685.1_ASM434268v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:24,800] [INFO] DFAST_QC completed!
[2024-01-24 13:11:24,800] [INFO] Total running time: 0h1m33s