[2024-01-25 20:14:21,022] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:21,023] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:21,024] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf55e189-66e3-4f0e-a52c-f994867d1062/dqc_reference
[2024-01-25 20:14:22,153] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:22,154] [INFO] Task started: Prodigal
[2024-01-25 20:14:22,154] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a9a48ac-afcc-4b8b-b900-0a81a1cbd79f/GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/cds.fna -a GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:39,667] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:39,668] [INFO] Task started: HMMsearch
[2024-01-25 20:14:39,668] [INFO] Running command: hmmsearch --tblout GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf55e189-66e3-4f0e-a52c-f994867d1062/dqc_reference/reference_markers.hmm GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:39,904] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:39,905] [INFO] Found 6/6 markers.
[2024-01-25 20:14:39,936] [INFO] Query marker FASTA was written to GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:14:39,936] [INFO] Task started: Blastn
[2024-01-25 20:14:39,937] [INFO] Running command: blastn -query GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf55e189-66e3-4f0e-a52c-f994867d1062/dqc_reference/reference_markers.fasta -out GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:40,511] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:40,514] [INFO] Selected 15 target genomes.
[2024-01-25 20:14:40,514] [INFO] Target genome list was writen to GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:14:40,521] [INFO] Task started: fastANI
[2024-01-25 20:14:40,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a9a48ac-afcc-4b8b-b900-0a81a1cbd79f/GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna.gz --refList GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:51,925] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:51,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf55e189-66e3-4f0e-a52c-f994867d1062/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:51,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf55e189-66e3-4f0e-a52c-f994867d1062/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:51,934] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:14:51,934] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:51,934] [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 lactis	strain=DSM 22361	GCA_900107985.1	797291	797291	type	True	100.0	1321	1321	95	conclusive
Sphingobacterium lactis	strain=DSM 22361	GCA_011046555.1	797291	797291	type	True	99.9998	1320	1321	95	conclusive
Sphingobacterium spiritivorum	strain=ATCC 33861	GCA_000143765.1	258	258	suspected-type	True	79.6558	128	1321	95	below_threshold
Sphingobacterium endophyticum	strain=NYYP31	GCA_009733535.1	2546448	2546448	type	True	79.5427	332	1321	95	below_threshold
Sphingobacterium mizutaii	strain=NCTC12149	GCA_900187125.1	1010	1010	type	True	79.3827	406	1321	95	below_threshold
Sphingobacterium mizutaii	strain=NBRC 14946	GCA_007990895.1	1010	1010	type	True	79.3803	388	1321	95	below_threshold
Sphingobacterium soli	strain=DSM 101679	GCA_014138555.1	1914757	1914757	type	True	79.2921	388	1321	95	below_threshold
Sphingobacterium mizutaii	strain=DSM 11724	GCA_900102835.1	1010	1010	type	True	79.2596	399	1321	95	below_threshold
Sphingobacterium soli	strain=CGMCC 1.15966	GCA_014644335.1	1914757	1914757	type	True	79.2447	383	1321	95	below_threshold
Sphingobacterium humi	strain=JCM 31225	GCA_009768885.1	1796905	1796905	type	True	78.6628	314	1321	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:51,935] [INFO] DFAST Taxonomy check result was written to GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:14:51,936] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:51,936] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:51,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf55e189-66e3-4f0e-a52c-f994867d1062/dqc_reference/checkm_data
[2024-01-25 20:14:51,937] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:51,978] [INFO] Task started: CheckM
[2024-01-25 20:14:51,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/checkm_input GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:15:41,843] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:41,844] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:41,859] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:41,859] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:41,859] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:15:41,860] [INFO] Task started: Blastn
[2024-01-25 20:15:41,860] [INFO] Running command: blastn -query GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf55e189-66e3-4f0e-a52c-f994867d1062/dqc_reference/reference_markers_gtdb.fasta -out GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:42,679] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:42,683] [INFO] Selected 15 target genomes.
[2024-01-25 20:15:42,683] [INFO] Target genome list was writen to GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:42,697] [INFO] Task started: fastANI
[2024-01-25 20:15:42,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a9a48ac-afcc-4b8b-b900-0a81a1cbd79f/GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna.gz --refList GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:53,399] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:53,406] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:53,406] [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_011046555.1	s__Sphingobacterium lactis	99.9998	1320	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014219015.1	s__Sphingobacterium sp002476975	79.6954	428	1321	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	79.5367	401	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.02	97.95	0.91	0.90	4	-
GCF_009733535.1	s__Sphingobacterium endophyticum	79.5272	333	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187125.1	s__Sphingobacterium mizutaii	79.3746	406	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.36	98.08	0.96	0.87	4	-
GCA_002322865.1	s__Sphingobacterium sp002322865	79.1725	338	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004526235.1	s__Sphingobacterium sp002734245	79.1241	364	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.34	97.34	0.89	0.89	2	-
GCF_009768885.1	s__Sphingobacterium humi	78.6764	313	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354335.1	s__Sphingobacterium sp002354335	78.6282	266	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274825.1	s__Sphingobacterium hotanense	78.5632	277	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.82	97.82	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:53,408] [INFO] GTDB search result was written to GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:53,409] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:53,412] [INFO] DFAST_QC result json was written to GCF_900107985.1_IMG-taxon_2675903147_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:15:53,412] [INFO] DFAST_QC completed!
[2024-01-25 20:15:53,412] [INFO] Total running time: 0h1m32s