[2024-01-24 12:36:56,562] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:56,565] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:56,565] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e3de8bc-6e09-4555-9b08-3918be4728c1/dqc_reference
[2024-01-24 12:36:57,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:57,847] [INFO] Task started: Prodigal
[2024-01-24 12:36:57,849] [INFO] Running command: gunzip -c /var/lib/cwl/stg839a16fc-e89d-476d-82c4-0a3dc1226d58/GCF_015644585.1_ASM1564458v1_genomic.fna.gz | prodigal -d GCF_015644585.1_ASM1564458v1_genomic.fna/cds.fna -a GCF_015644585.1_ASM1564458v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:13,929] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:13,929] [INFO] Task started: HMMsearch
[2024-01-24 12:37:13,929] [INFO] Running command: hmmsearch --tblout GCF_015644585.1_ASM1564458v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e3de8bc-6e09-4555-9b08-3918be4728c1/dqc_reference/reference_markers.hmm GCF_015644585.1_ASM1564458v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:14,308] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:14,309] [INFO] Found 6/6 markers.
[2024-01-24 12:37:14,359] [INFO] Query marker FASTA was written to GCF_015644585.1_ASM1564458v1_genomic.fna/markers.fasta
[2024-01-24 12:37:14,360] [INFO] Task started: Blastn
[2024-01-24 12:37:14,360] [INFO] Running command: blastn -query GCF_015644585.1_ASM1564458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e3de8bc-6e09-4555-9b08-3918be4728c1/dqc_reference/reference_markers.fasta -out GCF_015644585.1_ASM1564458v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:15,383] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:15,387] [INFO] Selected 13 target genomes.
[2024-01-24 12:37:15,387] [INFO] Target genome list was writen to GCF_015644585.1_ASM1564458v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:15,393] [INFO] Task started: fastANI
[2024-01-24 12:37:15,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg839a16fc-e89d-476d-82c4-0a3dc1226d58/GCF_015644585.1_ASM1564458v1_genomic.fna.gz --refList GCF_015644585.1_ASM1564458v1_genomic.fna/target_genomes.txt --output GCF_015644585.1_ASM1564458v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:32,105] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:32,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e3de8bc-6e09-4555-9b08-3918be4728c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:32,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e3de8bc-6e09-4555-9b08-3918be4728c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:32,118] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:37:32,118] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:37:32,118] [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 laticis	strain=SAP-17	GCA_015644585.1	2787622	2787622	type	True	100.0	1899	1899	95	inconclusive
Rahnella contaminans	strain=Lac-M11	GCA_011065485.1	2703882	2703882	type	True	95.2097	1571	1899	95	inconclusive
Rahnella victoriana	strain=DSM 27397	GCA_004330295.1	1510570	1510570	type	True	86.5609	1401	1899	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	86.3367	1363	1899	95	below_threshold
Rahnella woolbedingensis	strain=DSM 27399	GCA_003602095.1	1510574	1510574	type	True	86.2994	1357	1899	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	86.2895	1377	1899	95	below_threshold
Rahnella aquatilis	strain=CIP 78.65	GCA_000241955.1	34038	34038	suspected-type	True	86.2604	1320	1899	95	below_threshold
Rahnella aceris	strain=SAP-19	GCA_011684115.1	2703885	2703885	type	True	86.1783	1377	1899	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	85.6259	1344	1899	95	below_threshold
Rahnella inusitata	strain=DSM 30078	GCA_003602055.1	58169	58169	type	True	85.5626	1318	1899	95	below_threshold
Rahnella inusitata	strain=DSM 30078	GCA_003263515.1	58169	58169	type	True	85.5163	1293	1899	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	85.4151	1174	1899	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.2052	646	1899	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:32,120] [INFO] DFAST Taxonomy check result was written to GCF_015644585.1_ASM1564458v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:32,121] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:32,121] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:32,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e3de8bc-6e09-4555-9b08-3918be4728c1/dqc_reference/checkm_data
[2024-01-24 12:37:32,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:32,178] [INFO] Task started: CheckM
[2024-01-24 12:37:32,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015644585.1_ASM1564458v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015644585.1_ASM1564458v1_genomic.fna/checkm_input GCF_015644585.1_ASM1564458v1_genomic.fna/checkm_result
[2024-01-24 12:38:19,892] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:19,894] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:19,917] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:19,918] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:19,918] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015644585.1_ASM1564458v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:19,918] [INFO] Task started: Blastn
[2024-01-24 12:38:19,919] [INFO] Running command: blastn -query GCF_015644585.1_ASM1564458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e3de8bc-6e09-4555-9b08-3918be4728c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_015644585.1_ASM1564458v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:21,350] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:21,355] [INFO] Selected 12 target genomes.
[2024-01-24 12:38:21,355] [INFO] Target genome list was writen to GCF_015644585.1_ASM1564458v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:21,389] [INFO] Task started: fastANI
[2024-01-24 12:38:21,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg839a16fc-e89d-476d-82c4-0a3dc1226d58/GCF_015644585.1_ASM1564458v1_genomic.fna.gz --refList GCF_015644585.1_ASM1564458v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015644585.1_ASM1564458v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:37,505] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:37,516] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:37,516] [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_015644585.1	s__Rahnella laticis	100.0	1899	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	96.65	95.20	0.90	0.83	8	conclusive
GCF_002951615.1	s__Rahnella sp002951615	93.0787	1549	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002834385.1	s__Rahnella sp002834385	91.3806	1505	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004330295.1	s__Rahnella victoriana	86.5487	1403	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	98.74	98.62	0.94	0.93	5	-
GCF_003610915.1	s__Rahnella variigena	86.4435	1402	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	97.86	97.35	0.92	0.89	8	-
GCF_003602095.1	s__Rahnella woolbedingensis	86.298	1357	1899	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	86.294	1377	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241955.1	s__Rahnella aquatilis	86.2569	1321	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	99.30	98.90	0.94	0.91	4	-
GCF_003614975.1	s__Rahnella bruchi	86.1823	1362	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011684115.1	s__Rahnella aceris	86.1783	1377	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	99.19	98.40	0.95	0.89	21	-
GCF_001422575.1	s__Rahnella sp001422575	85.6193	1341	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	98.18	98.11	0.91	0.87	5	-
GCF_003263515.1	s__Rahnella inusitata	85.5128	1294	1899	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	99.32	98.94	0.97	0.94	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:37,518] [INFO] GTDB search result was written to GCF_015644585.1_ASM1564458v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:37,519] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:37,523] [INFO] DFAST_QC result json was written to GCF_015644585.1_ASM1564458v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:37,524] [INFO] DFAST_QC completed!
[2024-01-24 12:38:37,524] [INFO] Total running time: 0h1m41s