[2024-01-24 15:10:19,838] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:19,841] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:19,841] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe642d27-8ab4-48b6-ad2d-7545c6d34d29/dqc_reference
[2024-01-24 15:10:22,718] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:22,719] [INFO] Task started: Prodigal
[2024-01-24 15:10:22,720] [INFO] Running command: gunzip -c /var/lib/cwl/stgdda3f69a-3473-457b-8d1c-d1f78039ae29/GCF_008124885.1_ASM812488v1_genomic.fna.gz | prodigal -d GCF_008124885.1_ASM812488v1_genomic.fna/cds.fna -a GCF_008124885.1_ASM812488v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:42,755] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:42,756] [INFO] Task started: HMMsearch
[2024-01-24 15:10:42,756] [INFO] Running command: hmmsearch --tblout GCF_008124885.1_ASM812488v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe642d27-8ab4-48b6-ad2d-7545c6d34d29/dqc_reference/reference_markers.hmm GCF_008124885.1_ASM812488v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:43,052] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:43,056] [INFO] Found 6/6 markers.
[2024-01-24 15:10:43,099] [INFO] Query marker FASTA was written to GCF_008124885.1_ASM812488v1_genomic.fna/markers.fasta
[2024-01-24 15:10:43,100] [INFO] Task started: Blastn
[2024-01-24 15:10:43,100] [INFO] Running command: blastn -query GCF_008124885.1_ASM812488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe642d27-8ab4-48b6-ad2d-7545c6d34d29/dqc_reference/reference_markers.fasta -out GCF_008124885.1_ASM812488v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:43,697] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:43,700] [INFO] Selected 18 target genomes.
[2024-01-24 15:10:43,701] [INFO] Target genome list was writen to GCF_008124885.1_ASM812488v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:43,709] [INFO] Task started: fastANI
[2024-01-24 15:10:43,710] [INFO] Running command: fastANI --query /var/lib/cwl/stgdda3f69a-3473-457b-8d1c-d1f78039ae29/GCF_008124885.1_ASM812488v1_genomic.fna.gz --refList GCF_008124885.1_ASM812488v1_genomic.fna/target_genomes.txt --output GCF_008124885.1_ASM812488v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:58,963] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:58,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe642d27-8ab4-48b6-ad2d-7545c6d34d29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:58,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe642d27-8ab4-48b6-ad2d-7545c6d34d29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:58,976] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:58,976] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:58,976] [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 composti Yoo et al. 2007 non Ten et al. 2007	strain=DSM 18850	GCA_008124885.1	415956	415956	type	True	100.0	1433	1436	95	conclusive
Sphingobacterium faecale	strain=C459-1	GCA_016746095.1	2803775	2803775	type	True	79.3959	102	1436	95	below_threshold
Sphingobacterium corticibacterium	strain=30C10-4-7	GCA_004208525.1	2484746	2484746	type	True	78.7205	199	1436	95	below_threshold
Sphingobacterium phlebotomi	strain=SSI9	GCA_008180195.1	2605433	2605433	type	True	78.6163	210	1436	95	below_threshold
Sphingobacterium chungjuense	strain=IMCC25678	GCA_011316935.1	2675553	2675553	type	True	78.5665	78	1436	95	below_threshold
Sphingobacterium wenxiniae	strain=DSM 22789	GCA_900116225.1	683125	683125	type	True	78.5299	174	1436	95	below_threshold
Sphingobacterium deserti	strain=ACCC 05744	GCA_000757725.1	1229276	1229276	type	True	78.4933	197	1436	95	below_threshold
Sphingobacterium micropteri	strain=DN00404	GCA_014692515.1	2763501	2763501	type	True	78.4027	218	1436	95	below_threshold
Sphingobacterium endophyticum	strain=NYYP31	GCA_009733535.1	2546448	2546448	type	True	78.3902	88	1436	95	below_threshold
Sphingobacterium spiritivorum	strain=FDAARGOS_1144	GCA_016725645.1	258	258	suspected-type	True	78.3165	104	1436	95	below_threshold
Sphingobacterium spiritivorum	strain=ATCC 33861	GCA_000143765.1	258	258	suspected-type	True	78.3122	103	1436	95	below_threshold
Sphingobacterium paucimobilis	strain=HER1398	GCA_000416985.1	1385985	1385985	type	True	78.1538	96	1436	95	below_threshold
Sphingobacterium spiritivorum	strain=NCTC11386	GCA_900457435.1	258	258	suspected-type	True	78.0869	105	1436	95	below_threshold
Sphingobacterium olei	strain=HAL-9	GCA_005048855.1	2571155	2571155	type	True	78.0581	121	1436	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:58,983] [INFO] DFAST Taxonomy check result was written to GCF_008124885.1_ASM812488v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:58,983] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:58,983] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:58,984] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe642d27-8ab4-48b6-ad2d-7545c6d34d29/dqc_reference/checkm_data
[2024-01-24 15:10:58,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:59,037] [INFO] Task started: CheckM
[2024-01-24 15:10:59,038] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008124885.1_ASM812488v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008124885.1_ASM812488v1_genomic.fna/checkm_input GCF_008124885.1_ASM812488v1_genomic.fna/checkm_result
[2024-01-24 15:11:59,710] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:59,711] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:59,733] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:59,734] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:59,734] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008124885.1_ASM812488v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:59,735] [INFO] Task started: Blastn
[2024-01-24 15:11:59,735] [INFO] Running command: blastn -query GCF_008124885.1_ASM812488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe642d27-8ab4-48b6-ad2d-7545c6d34d29/dqc_reference/reference_markers_gtdb.fasta -out GCF_008124885.1_ASM812488v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:00,619] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:00,626] [INFO] Selected 20 target genomes.
[2024-01-24 15:12:00,626] [INFO] Target genome list was writen to GCF_008124885.1_ASM812488v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:00,650] [INFO] Task started: fastANI
[2024-01-24 15:12:00,650] [INFO] Running command: fastANI --query /var/lib/cwl/stgdda3f69a-3473-457b-8d1c-d1f78039ae29/GCF_008124885.1_ASM812488v1_genomic.fna.gz --refList GCF_008124885.1_ASM812488v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008124885.1_ASM812488v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:16,504] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:16,523] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:16,523] [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_008124885.1	s__Sphingobacterium composti_A	100.0	1433	1436	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_011043555.1	s__Sphingobacterium sp011043555	80.4812	232	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016746095.1	s__Sphingobacterium sp016746095	79.3752	101	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004208525.1	s__Sphingobacterium sp004208525	78.752	195	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180195.1	s__Sphingobacterium phlebotomi	78.6623	206	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116225.1	s__Sphingobacterium wenxiniae	78.5311	175	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757725.1	s__Sphingobacterium deserti	78.5022	197	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733535.1	s__Sphingobacterium endophyticum	78.4748	84	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692515.1	s__Sphingobacterium sp014692515	78.4177	215	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000143765.1	s__Sphingobacterium spiritivorum	78.3443	101	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_014653155.1	s__Sphingobacterium griseoflavum	78.1606	228	1436	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000416985.1	s__Sphingobacterium paucimobilis	78.1346	94	1436	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	78.0152	122	1436	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 15:12:16,525] [INFO] GTDB search result was written to GCF_008124885.1_ASM812488v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:16,525] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:16,529] [INFO] DFAST_QC result json was written to GCF_008124885.1_ASM812488v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:16,530] [INFO] DFAST_QC completed!
[2024-01-24 15:12:16,530] [INFO] Total running time: 0h1m57s