[2024-01-24 11:51:06,946] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,949] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,949] [INFO] DQC Reference Directory: /var/lib/cwl/stgceae6080-88e7-46e6-b5da-155b5c239d6e/dqc_reference
[2024-01-24 11:51:08,191] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:08,192] [INFO] Task started: Prodigal
[2024-01-24 11:51:08,192] [INFO] Running command: gunzip -c /var/lib/cwl/stg74244a1a-553e-41ff-a839-21137e43a117/GCF_018494035.1_ASM1849403v1_genomic.fna.gz | prodigal -d GCF_018494035.1_ASM1849403v1_genomic.fna/cds.fna -a GCF_018494035.1_ASM1849403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:14,755] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:14,756] [INFO] Task started: HMMsearch
[2024-01-24 11:51:14,756] [INFO] Running command: hmmsearch --tblout GCF_018494035.1_ASM1849403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgceae6080-88e7-46e6-b5da-155b5c239d6e/dqc_reference/reference_markers.hmm GCF_018494035.1_ASM1849403v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:15,062] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:15,064] [INFO] Found 6/6 markers.
[2024-01-24 11:51:15,097] [INFO] Query marker FASTA was written to GCF_018494035.1_ASM1849403v1_genomic.fna/markers.fasta
[2024-01-24 11:51:15,098] [INFO] Task started: Blastn
[2024-01-24 11:51:15,098] [INFO] Running command: blastn -query GCF_018494035.1_ASM1849403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgceae6080-88e7-46e6-b5da-155b5c239d6e/dqc_reference/reference_markers.fasta -out GCF_018494035.1_ASM1849403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:15,854] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:15,859] [INFO] Selected 16 target genomes.
[2024-01-24 11:51:15,860] [INFO] Target genome list was writen to GCF_018494035.1_ASM1849403v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:15,933] [INFO] Task started: fastANI
[2024-01-24 11:51:15,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg74244a1a-553e-41ff-a839-21137e43a117/GCF_018494035.1_ASM1849403v1_genomic.fna.gz --refList GCF_018494035.1_ASM1849403v1_genomic.fna/target_genomes.txt --output GCF_018494035.1_ASM1849403v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:27,429] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:27,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgceae6080-88e7-46e6-b5da-155b5c239d6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:27,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgceae6080-88e7-46e6-b5da-155b5c239d6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:27,445] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:27,445] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:27,445] [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
Rosenbergiella australiborealis	strain=CdVSA20.1	GCA_018494035.1	1544696	1544696	type	True	100.0	972	973	95	conclusive
Rosenbergiella collisarenosi	strain=8.8A	GCA_018494085.1	1544695	1544695	type	True	81.6905	535	973	95	below_threshold
Rosenbergiella nectarea	strain=8N4	GCA_900111105.1	988801	988801	type	True	81.4576	530	973	95	below_threshold
Rosenbergiella epipactidis	strain=2.1A	GCA_018494055.1	1544694	1544694	type	True	81.3673	532	973	95	below_threshold
[Pantoea] beijingensis	strain=JZB2120001	GCA_022647505.1	1324864	1324864	type	True	78.5846	114	973	95	below_threshold
Pantoea cypripedii	strain=LMG 2657	GCA_002095535.1	55209	55209	type	True	78.4033	121	973	95	below_threshold
Tatumella ptyseos	strain=ATCC 33301	GCA_000439895.1	82987	82987	type	True	78.3967	149	973	95	below_threshold
Pectobacterium quasiaquaticum	strain=A477-S1-J17	GCA_014946775.2	2774015	2774015	type	True	78.3528	86	973	95	below_threshold
Pantoea rodasii	strain=LMG 26273	GCA_002095465.1	1076549	1076549	type	True	78.334	132	973	95	below_threshold
Pectobacterium aquaticum	strain=A212-S19-A16	GCA_003382565.3	2204145	2204145	type	True	78.269	83	973	95	below_threshold
Erwinia iniecta	strain=B120	GCA_001267535.1	1560201	1560201	type	True	78.2598	124	973	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:27,452] [INFO] DFAST Taxonomy check result was written to GCF_018494035.1_ASM1849403v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:27,453] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:27,453] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:27,453] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgceae6080-88e7-46e6-b5da-155b5c239d6e/dqc_reference/checkm_data
[2024-01-24 11:51:27,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:27,490] [INFO] Task started: CheckM
[2024-01-24 11:51:27,490] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018494035.1_ASM1849403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018494035.1_ASM1849403v1_genomic.fna/checkm_input GCF_018494035.1_ASM1849403v1_genomic.fna/checkm_result
[2024-01-24 11:51:53,874] [INFO] Task succeeded: CheckM
[2024-01-24 11:51:53,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:51:53,900] [INFO] ===== Completeness check finished =====
[2024-01-24 11:51:53,901] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:51:53,901] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018494035.1_ASM1849403v1_genomic.fna/markers.fasta)
[2024-01-24 11:51:53,901] [INFO] Task started: Blastn
[2024-01-24 11:51:53,902] [INFO] Running command: blastn -query GCF_018494035.1_ASM1849403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgceae6080-88e7-46e6-b5da-155b5c239d6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_018494035.1_ASM1849403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:55,087] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:55,091] [INFO] Selected 6 target genomes.
[2024-01-24 11:51:55,092] [INFO] Target genome list was writen to GCF_018494035.1_ASM1849403v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:51:55,097] [INFO] Task started: fastANI
[2024-01-24 11:51:55,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg74244a1a-553e-41ff-a839-21137e43a117/GCF_018494035.1_ASM1849403v1_genomic.fna.gz --refList GCF_018494035.1_ASM1849403v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018494035.1_ASM1849403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:51:59,565] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:59,571] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:51:59,571] [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_018494035.1	s__Rosenbergiella australiborealis	100.0	972	973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018494085.1	s__Rosenbergiella collisarenosi	81.6739	537	973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	99.00	99.00	0.87	0.87	2	-
GCF_018494065.1	s__Rosenbergiella sp018494065	81.49	547	973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111105.1	s__Rosenbergiella nectarea	81.4667	529	973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	96.23	96.23	0.89	0.89	2	-
GCF_018494055.1	s__Rosenbergiella epipactidis	81.3701	531	973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rosenbergiella	95.0	96.28	95.56	0.88	0.85	5	-
GCF_000590885.1	s__Erwinia mallotivora	78.2088	95	973	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:51:59,573] [INFO] GTDB search result was written to GCF_018494035.1_ASM1849403v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:51:59,574] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:51:59,576] [INFO] DFAST_QC result json was written to GCF_018494035.1_ASM1849403v1_genomic.fna/dqc_result.json
[2024-01-24 11:51:59,577] [INFO] DFAST_QC completed!
[2024-01-24 11:51:59,577] [INFO] Total running time: 0h0m53s