[2024-01-24 12:47:12,303] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:12,305] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:12,306] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b94f8b3-f800-44ce-9f80-d240c3c1eb8b/dqc_reference
[2024-01-24 12:47:13,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:13,664] [INFO] Task started: Prodigal
[2024-01-24 12:47:13,664] [INFO] Running command: gunzip -c /var/lib/cwl/stgae1b02ef-6c45-402e-937c-5ddbb2ed301b/GCF_011065485.1_ASM1106548v1_genomic.fna.gz | prodigal -d GCF_011065485.1_ASM1106548v1_genomic.fna/cds.fna -a GCF_011065485.1_ASM1106548v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:28,330] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:28,330] [INFO] Task started: HMMsearch
[2024-01-24 12:47:28,330] [INFO] Running command: hmmsearch --tblout GCF_011065485.1_ASM1106548v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b94f8b3-f800-44ce-9f80-d240c3c1eb8b/dqc_reference/reference_markers.hmm GCF_011065485.1_ASM1106548v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:28,660] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:28,661] [INFO] Found 6/6 markers.
[2024-01-24 12:47:28,705] [INFO] Query marker FASTA was written to GCF_011065485.1_ASM1106548v1_genomic.fna/markers.fasta
[2024-01-24 12:47:28,706] [INFO] Task started: Blastn
[2024-01-24 12:47:28,706] [INFO] Running command: blastn -query GCF_011065485.1_ASM1106548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b94f8b3-f800-44ce-9f80-d240c3c1eb8b/dqc_reference/reference_markers.fasta -out GCF_011065485.1_ASM1106548v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:29,642] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:29,645] [INFO] Selected 14 target genomes.
[2024-01-24 12:47:29,646] [INFO] Target genome list was writen to GCF_011065485.1_ASM1106548v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:29,653] [INFO] Task started: fastANI
[2024-01-24 12:47:29,653] [INFO] Running command: fastANI --query /var/lib/cwl/stgae1b02ef-6c45-402e-937c-5ddbb2ed301b/GCF_011065485.1_ASM1106548v1_genomic.fna.gz --refList GCF_011065485.1_ASM1106548v1_genomic.fna/target_genomes.txt --output GCF_011065485.1_ASM1106548v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:47,582] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:47,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b94f8b3-f800-44ce-9f80-d240c3c1eb8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:47,583] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b94f8b3-f800-44ce-9f80-d240c3c1eb8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:47,595] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:47:47,595] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:47:47,595] [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 contaminans	strain=Lac-M11	GCA_011065485.1	2703882	2703882	type	True	100.0	1735	1736	95	inconclusive
Rahnella laticis	strain=SAP-17	GCA_015644585.1	2787622	2787622	type	True	95.2489	1565	1736	95	inconclusive
Rahnella variigena	strain=CIP 105588	GCA_003610915.1	574964	574964	type	True	86.972	1369	1736	95	below_threshold
Rahnella variigena	strain=CIP 105588	GCA_003602185.1	574964	574964	type	True	86.9312	1366	1736	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	86.8861	1376	1736	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	86.8745	1384	1736	95	below_threshold
Rahnella victoriana	strain=DSM 27397	GCA_004330295.1	1510570	1510570	type	True	86.8344	1377	1736	95	below_threshold
Rahnella woolbedingensis	strain=DSM 27399	GCA_003602095.1	1510574	1510574	type	True	86.8259	1364	1736	95	below_threshold
Rahnella bruchi	strain=DSM 27398	GCA_003614975.1	1510573	1510573	type	True	86.7108	1389	1736	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	85.7215	1314	1736	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	85.6307	1180	1736	95	below_threshold
Rahnella inusitata	strain=DSM 30078	GCA_003602055.1	58169	58169	type	True	85.4937	1288	1736	95	below_threshold
Rahnella inusitata	strain=DSM 30078	GCA_003263515.1	58169	58169	type	True	85.4125	1270	1736	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.3061	585	1736	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:47,597] [INFO] DFAST Taxonomy check result was written to GCF_011065485.1_ASM1106548v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:47,597] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:47,597] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:47,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b94f8b3-f800-44ce-9f80-d240c3c1eb8b/dqc_reference/checkm_data
[2024-01-24 12:47:47,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:47,650] [INFO] Task started: CheckM
[2024-01-24 12:47:47,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011065485.1_ASM1106548v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011065485.1_ASM1106548v1_genomic.fna/checkm_input GCF_011065485.1_ASM1106548v1_genomic.fna/checkm_result
[2024-01-24 12:48:34,708] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:34,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:34,733] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:34,734] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:34,734] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011065485.1_ASM1106548v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:34,734] [INFO] Task started: Blastn
[2024-01-24 12:48:34,734] [INFO] Running command: blastn -query GCF_011065485.1_ASM1106548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b94f8b3-f800-44ce-9f80-d240c3c1eb8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_011065485.1_ASM1106548v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:36,131] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:36,135] [INFO] Selected 13 target genomes.
[2024-01-24 12:48:36,136] [INFO] Target genome list was writen to GCF_011065485.1_ASM1106548v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:36,147] [INFO] Task started: fastANI
[2024-01-24 12:48:36,147] [INFO] Running command: fastANI --query /var/lib/cwl/stgae1b02ef-6c45-402e-937c-5ddbb2ed301b/GCF_011065485.1_ASM1106548v1_genomic.fna.gz --refList GCF_011065485.1_ASM1106548v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011065485.1_ASM1106548v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:52,577] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:52,588] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:52,589] [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	95.2489	1565	1736	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	92.0341	1460	1736	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	90.4746	1458	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610915.1	s__Rahnella variigena	86.9629	1370	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	97.86	97.35	0.92	0.89	8	-
GCF_019049625.1	s__Rahnella sp019049625	86.8833	1377	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049675.1	s__Rahnella sp019049675	86.8778	1383	1736	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	86.8344	1377	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	98.74	98.62	0.94	0.93	5	-
GCF_003602095.1	s__Rahnella woolbedingensis	86.8332	1363	1736	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	86.7036	1390	1736	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	86.3392	1365	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	99.19	98.40	0.95	0.89	21	-
GCF_000241955.1	s__Rahnella aquatilis	86.2393	1326	1736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	99.30	98.90	0.94	0.91	4	-
GCF_001422575.1	s__Rahnella sp001422575	85.7123	1314	1736	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	85.4113	1270	1736	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 12:48:52,591] [INFO] GTDB search result was written to GCF_011065485.1_ASM1106548v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:52,591] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:52,595] [INFO] DFAST_QC result json was written to GCF_011065485.1_ASM1106548v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:52,595] [INFO] DFAST_QC completed!
[2024-01-24 12:48:52,595] [INFO] Total running time: 0h1m40s