[2024-01-24 11:12:48,714] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:48,718] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:48,718] [INFO] DQC Reference Directory: /var/lib/cwl/stg0256daec-4d28-4efb-88dc-4a4d65ef0e97/dqc_reference
[2024-01-24 11:12:49,910] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:49,911] [INFO] Task started: Prodigal
[2024-01-24 11:12:49,911] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1f00a79-03b3-4641-81e1-16c6755bb3ba/GCF_005849285.1_ASM584928v1_genomic.fna.gz | prodigal -d GCF_005849285.1_ASM584928v1_genomic.fna/cds.fna -a GCF_005849285.1_ASM584928v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:59,351] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:59,351] [INFO] Task started: HMMsearch
[2024-01-24 11:12:59,352] [INFO] Running command: hmmsearch --tblout GCF_005849285.1_ASM584928v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0256daec-4d28-4efb-88dc-4a4d65ef0e97/dqc_reference/reference_markers.hmm GCF_005849285.1_ASM584928v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:59,593] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:59,594] [INFO] Found 6/6 markers.
[2024-01-24 11:12:59,623] [INFO] Query marker FASTA was written to GCF_005849285.1_ASM584928v1_genomic.fna/markers.fasta
[2024-01-24 11:12:59,624] [INFO] Task started: Blastn
[2024-01-24 11:12:59,624] [INFO] Running command: blastn -query GCF_005849285.1_ASM584928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0256daec-4d28-4efb-88dc-4a4d65ef0e97/dqc_reference/reference_markers.fasta -out GCF_005849285.1_ASM584928v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:00,359] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:00,364] [INFO] Selected 26 target genomes.
[2024-01-24 11:13:00,365] [INFO] Target genome list was writen to GCF_005849285.1_ASM584928v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:00,605] [INFO] Task started: fastANI
[2024-01-24 11:13:00,606] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1f00a79-03b3-4641-81e1-16c6755bb3ba/GCF_005849285.1_ASM584928v1_genomic.fna.gz --refList GCF_005849285.1_ASM584928v1_genomic.fna/target_genomes.txt --output GCF_005849285.1_ASM584928v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:20,398] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:20,399] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0256daec-4d28-4efb-88dc-4a4d65ef0e97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:20,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0256daec-4d28-4efb-88dc-4a4d65ef0e97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:20,412] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:20,413] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:20,413] [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
Luteithermobacter gelatinilyticus	strain=MEBiC09520	GCA_005849285.1	2582913	2582913	type	True	100.0	1048	1048	95	conclusive
Emcibacter nanhaiensis	strain=MCCC 1A06723	GCA_006385175.1	1505037	1505037	type	True	77.8927	346	1048	95	below_threshold
Paremcibacter congregatus	strain=ZYL	GCA_002740695.1	2043170	2043170	type	True	76.7428	139	1048	95	below_threshold
Paremcibacter congregatus	strain=ZYLT	GCA_006385135.1	2043170	2043170	type	True	76.6771	138	1048	95	below_threshold
Kordiimonas marina	strain=A6E486	GCA_023006325.1	2872312	2872312	type	True	76.1573	52	1048	95	below_threshold
Iodidimonas muriae	strain=JCM 17843	GCA_014647255.1	261467	261467	type	True	75.9071	53	1048	95	below_threshold
Iodidimonas gelatinilytica	strain=Hi-2	GCA_008579125.1	1236966	1236966	type	True	75.5737	58	1048	95	below_threshold
Sneathiella chinensis	strain=LMG23452	GCA_012720115.1	349750	349750	type	True	75.5195	53	1048	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:20,415] [INFO] DFAST Taxonomy check result was written to GCF_005849285.1_ASM584928v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:20,416] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:20,416] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:20,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0256daec-4d28-4efb-88dc-4a4d65ef0e97/dqc_reference/checkm_data
[2024-01-24 11:13:20,417] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:20,452] [INFO] Task started: CheckM
[2024-01-24 11:13:20,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005849285.1_ASM584928v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005849285.1_ASM584928v1_genomic.fna/checkm_input GCF_005849285.1_ASM584928v1_genomic.fna/checkm_result
[2024-01-24 11:13:53,248] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:53,250] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:53,275] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:53,275] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:53,276] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005849285.1_ASM584928v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:53,276] [INFO] Task started: Blastn
[2024-01-24 11:13:53,277] [INFO] Running command: blastn -query GCF_005849285.1_ASM584928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0256daec-4d28-4efb-88dc-4a4d65ef0e97/dqc_reference/reference_markers_gtdb.fasta -out GCF_005849285.1_ASM584928v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:54,536] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:54,541] [INFO] Selected 25 target genomes.
[2024-01-24 11:13:54,541] [INFO] Target genome list was writen to GCF_005849285.1_ASM584928v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:54,599] [INFO] Task started: fastANI
[2024-01-24 11:13:54,600] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1f00a79-03b3-4641-81e1-16c6755bb3ba/GCF_005849285.1_ASM584928v1_genomic.fna.gz --refList GCF_005849285.1_ASM584928v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005849285.1_ASM584928v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:10,238] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:10,253] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:10,253] [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_005849285.1	s__Luteithermobacter gelatinilyticus	100.0	1048	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Luteithermobacter	95.0	99.04	99.04	0.96	0.96	2	conclusive
GCF_006385175.1	s__Emcibacter nanhaiensis	77.9379	347	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Emcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385135.1	s__Paremcibacter congregatus	76.7895	138	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002749135.1	s__Paremcibacter sp002749135	76.6465	106	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401455.1	s__Paremcibacter sp002401455	76.5897	91	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051815.1	s__Paremcibacter sp011051815	76.4214	68	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152755.1	s__Paremcibacter sp013152755	76.0641	113	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647255.1	s__Iodidimonas muriae	75.9071	53	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Rhodothalassiaceae;g__Iodidimonas	95.0	97.25	95.88	0.95	0.93	4	-
GCF_002195995.1	s__Inquilinus limosus_C	75.6414	55	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012720115.1	s__Sneathiella chinensis	75.5195	53	1048	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Sneathiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:10,255] [INFO] GTDB search result was written to GCF_005849285.1_ASM584928v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:10,255] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:10,258] [INFO] DFAST_QC result json was written to GCF_005849285.1_ASM584928v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:10,258] [INFO] DFAST_QC completed!
[2024-01-24 11:14:10,258] [INFO] Total running time: 0h1m22s