[2024-01-24 13:43:26,913] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:43:26,917] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:43:26,917] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a1cdc34-4a17-4d48-a5a1-0502767d5ee1/dqc_reference
[2024-01-24 13:43:28,111] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:43:28,112] [INFO] Task started: Prodigal
[2024-01-24 13:43:28,112] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2f75c7f-7fb8-48aa-8796-9edfadda3747/GCF_014284335.1_ASM1428433v1_genomic.fna.gz | prodigal -d GCF_014284335.1_ASM1428433v1_genomic.fna/cds.fna -a GCF_014284335.1_ASM1428433v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:47,415] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:47,416] [INFO] Task started: HMMsearch
[2024-01-24 13:43:47,416] [INFO] Running command: hmmsearch --tblout GCF_014284335.1_ASM1428433v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a1cdc34-4a17-4d48-a5a1-0502767d5ee1/dqc_reference/reference_markers.hmm GCF_014284335.1_ASM1428433v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:47,690] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:47,691] [INFO] Found 6/6 markers.
[2024-01-24 13:43:47,738] [INFO] Query marker FASTA was written to GCF_014284335.1_ASM1428433v1_genomic.fna/markers.fasta
[2024-01-24 13:43:47,738] [INFO] Task started: Blastn
[2024-01-24 13:43:47,738] [INFO] Running command: blastn -query GCF_014284335.1_ASM1428433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a1cdc34-4a17-4d48-a5a1-0502767d5ee1/dqc_reference/reference_markers.fasta -out GCF_014284335.1_ASM1428433v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:48,453] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:48,456] [INFO] Selected 18 target genomes.
[2024-01-24 13:43:48,457] [INFO] Target genome list was writen to GCF_014284335.1_ASM1428433v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:48,466] [INFO] Task started: fastANI
[2024-01-24 13:43:48,466] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2f75c7f-7fb8-48aa-8796-9edfadda3747/GCF_014284335.1_ASM1428433v1_genomic.fna.gz --refList GCF_014284335.1_ASM1428433v1_genomic.fna/target_genomes.txt --output GCF_014284335.1_ASM1428433v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:44:04,324] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:04,325] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a1cdc34-4a17-4d48-a5a1-0502767d5ee1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:44:04,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a1cdc34-4a17-4d48-a5a1-0502767d5ee1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:44:04,338] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:44:04,338] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:44:04,338] [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
Undibacterium hunanense	strain=CY18W	GCA_014284335.1	2762292	2762292	type	True	100.0	2059	2063	95	conclusive
Undibacterium pigrum	strain=DSM 19792	GCA_003201815.1	401470	401470	type	True	82.419	1202	2063	95	below_threshold
Undibacterium umbellatum	strain=NL8W	GCA_014284125.1	2762300	2762300	type	True	82.0183	1129	2063	95	below_threshold
Undibacterium aquatile	strain=CCTCC AB 2015119	GCA_014699135.1	1537398	1537398	type	True	78.8002	431	2063	95	below_threshold
Undibacterium rivi	strain=FT147W	GCA_018139565.1	2828729	2828729	type	True	78.748	431	2063	95	below_threshold
Undibacterium griseum	strain=FT31W	GCA_014284195.1	2762295	2762295	type	True	78.7355	420	2063	95	below_threshold
Undibacterium jejuense	strain=KACC 12607	GCA_014284255.1	1344949	1344949	type	True	78.6691	353	2063	95	below_threshold
Undibacterium curvum	strain=CY22W	GCA_014284235.1	2762294	2762294	type	True	78.6008	490	2063	95	below_threshold
Undibacterium crateris	strain=B2R-29	GCA_010078235.1	2528175	2528175	type	True	78.5478	468	2063	95	below_threshold
Undibacterium oligocarboniphilum	strain=EM 1	GCA_013377855.1	666702	666702	type	True	78.5382	392	2063	95	below_threshold
Undibacterium rugosum	strain=CY7W	GCA_014284365.1	2762291	2762291	type	True	78.4937	428	2063	95	below_threshold
Herminiimonas fonticola	strain=DSM 18555	GCA_004361795.1	303380	303380	type	True	77.4417	192	2063	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	77.0502	208	2063	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	76.9758	162	2063	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	76.7148	220	2063	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	76.6793	180	2063	95	below_threshold
Noviherbaspirillum saxi	strain=K1R23-30	GCA_003591035.1	2320863	2320863	type	True	76.6186	199	2063	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	76.5197	153	2063	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:44:04,340] [INFO] DFAST Taxonomy check result was written to GCF_014284335.1_ASM1428433v1_genomic.fna/tc_result.tsv
[2024-01-24 13:44:04,341] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:44:04,341] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:44:04,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a1cdc34-4a17-4d48-a5a1-0502767d5ee1/dqc_reference/checkm_data
[2024-01-24 13:44:04,342] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:44:04,397] [INFO] Task started: CheckM
[2024-01-24 13:44:04,397] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014284335.1_ASM1428433v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014284335.1_ASM1428433v1_genomic.fna/checkm_input GCF_014284335.1_ASM1428433v1_genomic.fna/checkm_result
[2024-01-24 13:45:00,816] [INFO] Task succeeded: CheckM
[2024-01-24 13:45:00,817] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:45:00,833] [INFO] ===== Completeness check finished =====
[2024-01-24 13:45:00,833] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:45:00,833] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014284335.1_ASM1428433v1_genomic.fna/markers.fasta)
[2024-01-24 13:45:00,833] [INFO] Task started: Blastn
[2024-01-24 13:45:00,833] [INFO] Running command: blastn -query GCF_014284335.1_ASM1428433v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a1cdc34-4a17-4d48-a5a1-0502767d5ee1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014284335.1_ASM1428433v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:02,003] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:02,007] [INFO] Selected 6 target genomes.
[2024-01-24 13:45:02,007] [INFO] Target genome list was writen to GCF_014284335.1_ASM1428433v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:45:02,016] [INFO] Task started: fastANI
[2024-01-24 13:45:02,016] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2f75c7f-7fb8-48aa-8796-9edfadda3747/GCF_014284335.1_ASM1428433v1_genomic.fna.gz --refList GCF_014284335.1_ASM1428433v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014284335.1_ASM1428433v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:45:11,433] [INFO] Task succeeded: fastANI
[2024-01-24 13:45:11,439] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:45:11,439] [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_014284335.1	s__Undibacterium sp014284335	100.0	2059	2063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016200895.1	s__Undibacterium sp016200895	82.5324	1112	2063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201815.1	s__Undibacterium pigrum	82.4284	1202	2063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009937975.1	s__Undibacterium sp009937975	82.3628	1252	2063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009937955.1	s__Undibacterium sp009937955	82.206	1292	2063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284125.1	s__Undibacterium sp014284125	82.0209	1130	2063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:45:11,440] [INFO] GTDB search result was written to GCF_014284335.1_ASM1428433v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:45:11,441] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:45:11,444] [INFO] DFAST_QC result json was written to GCF_014284335.1_ASM1428433v1_genomic.fna/dqc_result.json
[2024-01-24 13:45:11,444] [INFO] DFAST_QC completed!
[2024-01-24 13:45:11,444] [INFO] Total running time: 0h1m45s