[2024-01-24 14:30:59,905] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:59,907] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:59,907] [INFO] DQC Reference Directory: /var/lib/cwl/stgff1c6b71-a52c-4bd4-bd9a-d200f1d82cce/dqc_reference
[2024-01-24 14:31:01,265] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:01,266] [INFO] Task started: Prodigal
[2024-01-24 14:31:01,266] [INFO] Running command: gunzip -c /var/lib/cwl/stg99feda4e-03ba-4161-9a0b-7375129e1327/GCF_004330295.1_ASM433029v1_genomic.fna.gz | prodigal -d GCF_004330295.1_ASM433029v1_genomic.fna/cds.fna -a GCF_004330295.1_ASM433029v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:16,702] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:16,702] [INFO] Task started: HMMsearch
[2024-01-24 14:31:16,702] [INFO] Running command: hmmsearch --tblout GCF_004330295.1_ASM433029v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff1c6b71-a52c-4bd4-bd9a-d200f1d82cce/dqc_reference/reference_markers.hmm GCF_004330295.1_ASM433029v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:17,053] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:17,054] [INFO] Found 6/6 markers.
[2024-01-24 14:31:17,112] [INFO] Query marker FASTA was written to GCF_004330295.1_ASM433029v1_genomic.fna/markers.fasta
[2024-01-24 14:31:17,112] [INFO] Task started: Blastn
[2024-01-24 14:31:17,112] [INFO] Running command: blastn -query GCF_004330295.1_ASM433029v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff1c6b71-a52c-4bd4-bd9a-d200f1d82cce/dqc_reference/reference_markers.fasta -out GCF_004330295.1_ASM433029v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:18,114] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:18,117] [INFO] Selected 13 target genomes.
[2024-01-24 14:31:18,117] [INFO] Target genome list was writen to GCF_004330295.1_ASM433029v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:18,122] [INFO] Task started: fastANI
[2024-01-24 14:31:18,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg99feda4e-03ba-4161-9a0b-7375129e1327/GCF_004330295.1_ASM433029v1_genomic.fna.gz --refList GCF_004330295.1_ASM433029v1_genomic.fna/target_genomes.txt --output GCF_004330295.1_ASM433029v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:35,402] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:35,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff1c6b71-a52c-4bd4-bd9a-d200f1d82cce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:35,403] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff1c6b71-a52c-4bd4-bd9a-d200f1d82cce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:35,414] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:35,414] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:35,415] [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
Rahnella victoriana	strain=DSM 27397	GCA_004330295.1	1510570	1510570	type	True	100.0	1729	1733	95	conclusive
Rahnella aquatilis	strain=CIP 78.65	GCA_000241955.1	34038	34038	suspected-type	True	89.7189	1403	1733	95	below_threshold
Rahnella aquatilis	strain=ATCC 33071	GCA_000735505.1	34038	34038	suspected-type	True	89.7135	1337	1733	95	below_threshold
Rahnella aceris	strain=SAP-19	GCA_011684115.1	2703885	2703885	type	True	89.3499	1439	1733	95	below_threshold
Rahnella variigena	strain=CIP 105588	GCA_003610915.1	574964	574964	type	True	88.974	1456	1733	95	below_threshold
Rahnella variigena	strain=CIP 105588	GCA_003602185.1	574964	574964	type	True	88.9454	1441	1733	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	88.6562	1424	1733	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	88.2734	1365	1733	95	below_threshold
Rahnella woolbedingensis	strain=DSM 27399	GCA_003602095.1	1510574	1510574	type	True	88.2342	1347	1733	95	below_threshold
Rahnella bruchi	strain=DSM 27398	GCA_003614975.1	1510573	1510573	type	True	88.1399	1382	1733	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	88.1308	1232	1733	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	86.4504	1321	1733	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.3071	644	1733	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:35,416] [INFO] DFAST Taxonomy check result was written to GCF_004330295.1_ASM433029v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:35,416] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:35,417] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:35,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff1c6b71-a52c-4bd4-bd9a-d200f1d82cce/dqc_reference/checkm_data
[2024-01-24 14:31:35,418] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:35,472] [INFO] Task started: CheckM
[2024-01-24 14:31:35,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004330295.1_ASM433029v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004330295.1_ASM433029v1_genomic.fna/checkm_input GCF_004330295.1_ASM433029v1_genomic.fna/checkm_result
[2024-01-24 14:32:21,832] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:21,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:21,854] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:21,854] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:21,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004330295.1_ASM433029v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:21,855] [INFO] Task started: Blastn
[2024-01-24 14:32:21,855] [INFO] Running command: blastn -query GCF_004330295.1_ASM433029v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff1c6b71-a52c-4bd4-bd9a-d200f1d82cce/dqc_reference/reference_markers_gtdb.fasta -out GCF_004330295.1_ASM433029v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:23,346] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:23,349] [INFO] Selected 8 target genomes.
[2024-01-24 14:32:23,349] [INFO] Target genome list was writen to GCF_004330295.1_ASM433029v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:23,355] [INFO] Task started: fastANI
[2024-01-24 14:32:23,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg99feda4e-03ba-4161-9a0b-7375129e1327/GCF_004330295.1_ASM433029v1_genomic.fna.gz --refList GCF_004330295.1_ASM433029v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004330295.1_ASM433029v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:34,286] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:34,295] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:34,296] [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_004330295.1	s__Rahnella victoriana	100.0	1729	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	98.74	98.62	0.94	0.93	5	conclusive
GCF_000241955.1	s__Rahnella aquatilis	89.7096	1404	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	99.30	98.90	0.94	0.91	4	-
GCF_011684115.1	s__Rahnella aceris	89.3513	1439	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	99.19	98.40	0.95	0.89	21	-
GCF_003610915.1	s__Rahnella variigena	88.9818	1456	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	97.86	97.35	0.92	0.89	8	-
GCF_019049675.1	s__Rahnella sp019049675	88.6562	1424	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049625.1	s__Rahnella sp019049625	88.2744	1365	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003602095.1	s__Rahnella woolbedingensis	88.2356	1346	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614975.1	s__Rahnella bruchi	88.1459	1381	1733	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:34,299] [INFO] GTDB search result was written to GCF_004330295.1_ASM433029v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:34,300] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:34,310] [INFO] DFAST_QC result json was written to GCF_004330295.1_ASM433029v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:34,311] [INFO] DFAST_QC completed!
[2024-01-24 14:32:34,311] [INFO] Total running time: 0h1m34s