[2024-01-25 19:58:50,621] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:58:50,622] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:58:50,622] [INFO] DQC Reference Directory: /var/lib/cwl/stga97d018f-dfb0-48ba-9825-6b3d044816dd/dqc_reference
[2024-01-25 19:58:51,817] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:58:51,818] [INFO] Task started: Prodigal
[2024-01-25 19:58:51,818] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f9b609e-2693-419d-97f5-aa32d67ec1c6/GCF_003449035.1_ASM344903v1_genomic.fna.gz | prodigal -d GCF_003449035.1_ASM344903v1_genomic.fna/cds.fna -a GCF_003449035.1_ASM344903v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:59:04,271] [INFO] Task succeeded: Prodigal
[2024-01-25 19:59:04,271] [INFO] Task started: HMMsearch
[2024-01-25 19:59:04,271] [INFO] Running command: hmmsearch --tblout GCF_003449035.1_ASM344903v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga97d018f-dfb0-48ba-9825-6b3d044816dd/dqc_reference/reference_markers.hmm GCF_003449035.1_ASM344903v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:59:04,523] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:59:04,524] [INFO] Found 6/6 markers.
[2024-01-25 19:59:04,558] [INFO] Query marker FASTA was written to GCF_003449035.1_ASM344903v1_genomic.fna/markers.fasta
[2024-01-25 19:59:04,558] [INFO] Task started: Blastn
[2024-01-25 19:59:04,558] [INFO] Running command: blastn -query GCF_003449035.1_ASM344903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga97d018f-dfb0-48ba-9825-6b3d044816dd/dqc_reference/reference_markers.fasta -out GCF_003449035.1_ASM344903v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:05,150] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:05,155] [INFO] Selected 21 target genomes.
[2024-01-25 19:59:05,155] [INFO] Target genome list was writen to GCF_003449035.1_ASM344903v1_genomic.fna/target_genomes.txt
[2024-01-25 19:59:05,169] [INFO] Task started: fastANI
[2024-01-25 19:59:05,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f9b609e-2693-419d-97f5-aa32d67ec1c6/GCF_003449035.1_ASM344903v1_genomic.fna.gz --refList GCF_003449035.1_ASM344903v1_genomic.fna/target_genomes.txt --output GCF_003449035.1_ASM344903v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:59:21,744] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:21,745] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga97d018f-dfb0-48ba-9825-6b3d044816dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:59:21,745] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga97d018f-dfb0-48ba-9825-6b3d044816dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:59:21,751] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:59:21,751] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:59:21,751] [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
Pedobacter indicus	strain=SM1810	GCA_003449035.1	2292082	2292082	type	True	100.0	1157	1157	95	conclusive
Sphingobacterium wenxiniae	strain=DSM 22789	GCA_900116225.1	683125	683125	type	True	78.8547	50	1157	95	below_threshold
Albibacterium bauzanense	strain=DSM 22554	GCA_004339765.1	653929	653929	type	True	78.3334	152	1157	95	below_threshold
Olivibacter domesticus	strain=DSM 18733	GCA_900109575.1	407022	407022	type	True	76.4165	55	1157	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:59:21,753] [INFO] DFAST Taxonomy check result was written to GCF_003449035.1_ASM344903v1_genomic.fna/tc_result.tsv
[2024-01-25 19:59:21,754] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:59:21,754] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:59:21,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga97d018f-dfb0-48ba-9825-6b3d044816dd/dqc_reference/checkm_data
[2024-01-25 19:59:21,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:59:21,795] [INFO] Task started: CheckM
[2024-01-25 19:59:21,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003449035.1_ASM344903v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003449035.1_ASM344903v1_genomic.fna/checkm_input GCF_003449035.1_ASM344903v1_genomic.fna/checkm_result
[2024-01-25 19:59:59,322] [INFO] Task succeeded: CheckM
[2024-01-25 19:59:59,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:59:59,340] [INFO] ===== Completeness check finished =====
[2024-01-25 19:59:59,341] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:59:59,341] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003449035.1_ASM344903v1_genomic.fna/markers.fasta)
[2024-01-25 19:59:59,341] [INFO] Task started: Blastn
[2024-01-25 19:59:59,341] [INFO] Running command: blastn -query GCF_003449035.1_ASM344903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga97d018f-dfb0-48ba-9825-6b3d044816dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_003449035.1_ASM344903v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:00,184] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:00,193] [INFO] Selected 28 target genomes.
[2024-01-25 20:00:00,193] [INFO] Target genome list was writen to GCF_003449035.1_ASM344903v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:00:00,216] [INFO] Task started: fastANI
[2024-01-25 20:00:00,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f9b609e-2693-419d-97f5-aa32d67ec1c6/GCF_003449035.1_ASM344903v1_genomic.fna.gz --refList GCF_003449035.1_ASM344903v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003449035.1_ASM344903v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:00:26,929] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:26,934] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:00:26,934] [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_003449035.1	s__Albibacterium indicum	100.0	1156	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Albibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000192845.1	s__Pseudosphingobacterium jilunii	78.9758	67	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pseudosphingobacterium	95.0	98.40	98.36	0.86	0.86	3	-
GCF_004339765.1	s__Albibacterium bauzanense	78.3818	154	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Albibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002245855.1	s__Sphingobacterium cellulitidis	77.7712	51	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.02	97.95	0.91	0.90	4	-
GCF_004368405.1	s__Pseudosphingobacterium sp004368405	77.628	54	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pseudosphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109575.1	s__Pseudosphingobacterium domesticum	76.3952	57	1157	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pseudosphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:00:26,936] [INFO] GTDB search result was written to GCF_003449035.1_ASM344903v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:00:26,936] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:00:26,938] [INFO] DFAST_QC result json was written to GCF_003449035.1_ASM344903v1_genomic.fna/dqc_result.json
[2024-01-25 20:00:26,938] [INFO] DFAST_QC completed!
[2024-01-25 20:00:26,938] [INFO] Total running time: 0h1m36s