[2024-01-24 13:08:58,489] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:08:58,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:08:58,491] [INFO] DQC Reference Directory: /var/lib/cwl/stgacec509e-12d0-4be4-9792-2d40c33f137c/dqc_reference
[2024-01-24 13:08:59,713] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:08:59,714] [INFO] Task started: Prodigal
[2024-01-24 13:08:59,714] [INFO] Running command: gunzip -c /var/lib/cwl/stgd59ebe71-4dde-40b7-8771-a5f9ba930e5a/GCF_019049655.1_ASM1904965v1_genomic.fna.gz | prodigal -d GCF_019049655.1_ASM1904965v1_genomic.fna/cds.fna -a GCF_019049655.1_ASM1904965v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:15,473] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:15,474] [INFO] Task started: HMMsearch
[2024-01-24 13:09:15,474] [INFO] Running command: hmmsearch --tblout GCF_019049655.1_ASM1904965v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacec509e-12d0-4be4-9792-2d40c33f137c/dqc_reference/reference_markers.hmm GCF_019049655.1_ASM1904965v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:15,776] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:15,778] [INFO] Found 6/6 markers.
[2024-01-24 13:09:15,824] [INFO] Query marker FASTA was written to GCF_019049655.1_ASM1904965v1_genomic.fna/markers.fasta
[2024-01-24 13:09:15,825] [INFO] Task started: Blastn
[2024-01-24 13:09:15,825] [INFO] Running command: blastn -query GCF_019049655.1_ASM1904965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacec509e-12d0-4be4-9792-2d40c33f137c/dqc_reference/reference_markers.fasta -out GCF_019049655.1_ASM1904965v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:16,725] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:16,730] [INFO] Selected 14 target genomes.
[2024-01-24 13:09:16,731] [INFO] Target genome list was writen to GCF_019049655.1_ASM1904965v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:16,780] [INFO] Task started: fastANI
[2024-01-24 13:09:16,780] [INFO] Running command: fastANI --query /var/lib/cwl/stgd59ebe71-4dde-40b7-8771-a5f9ba930e5a/GCF_019049655.1_ASM1904965v1_genomic.fna.gz --refList GCF_019049655.1_ASM1904965v1_genomic.fna/target_genomes.txt --output GCF_019049655.1_ASM1904965v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:33,551] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:33,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacec509e-12d0-4be4-9792-2d40c33f137c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:33,552] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacec509e-12d0-4be4-9792-2d40c33f137c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:33,565] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:33,565] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:33,566] [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 rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	100.0	1802	1804	95	conclusive
Rahnella inusitata	strain=DSM 30078	GCA_003602055.1	58169	58169	type	True	87.99	1391	1804	95	below_threshold
Rahnella inusitata	strain=DSM 30078	GCA_003263515.1	58169	58169	type	True	87.9299	1385	1804	95	below_threshold
Rahnella victoriana	strain=DSM 27397	GCA_004330295.1	1510570	1510570	type	True	86.4255	1326	1804	95	below_threshold
Rahnella variigena	strain=CIP 105588	GCA_003610915.1	574964	574964	type	True	86.3228	1352	1804	95	below_threshold
Rahnella variigena	strain=CIP 105588	GCA_003602185.1	574964	574964	type	True	86.2989	1324	1804	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	86.2897	1323	1804	95	below_threshold
Rahnella woolbedingensis	strain=DSM 27399	GCA_003602095.1	1510574	1510574	type	True	86.2162	1276	1804	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	86.1783	1331	1804	95	below_threshold
Rahnella bruchi	strain=DSM 27398	GCA_003614975.1	1510573	1510573	type	True	86.0839	1306	1804	95	below_threshold
Rahnella laticis	strain=SAP-17	GCA_015644585.1	2787622	2787622	type	True	85.79	1335	1804	95	below_threshold
Rahnella contaminans	strain=Lac-M11	GCA_011065485.1	2703882	2703882	type	True	85.7618	1304	1804	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	85.4695	1125	1804	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.2015	650	1804	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:33,567] [INFO] DFAST Taxonomy check result was written to GCF_019049655.1_ASM1904965v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:33,568] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:33,568] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:33,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacec509e-12d0-4be4-9792-2d40c33f137c/dqc_reference/checkm_data
[2024-01-24 13:09:33,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:33,620] [INFO] Task started: CheckM
[2024-01-24 13:09:33,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019049655.1_ASM1904965v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019049655.1_ASM1904965v1_genomic.fna/checkm_input GCF_019049655.1_ASM1904965v1_genomic.fna/checkm_result
[2024-01-24 13:10:22,706] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:22,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:22,730] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:22,731] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:22,731] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019049655.1_ASM1904965v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:22,732] [INFO] Task started: Blastn
[2024-01-24 13:10:22,732] [INFO] Running command: blastn -query GCF_019049655.1_ASM1904965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacec509e-12d0-4be4-9792-2d40c33f137c/dqc_reference/reference_markers_gtdb.fasta -out GCF_019049655.1_ASM1904965v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:23,932] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:23,935] [INFO] Selected 15 target genomes.
[2024-01-24 13:10:23,935] [INFO] Target genome list was writen to GCF_019049655.1_ASM1904965v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:23,958] [INFO] Task started: fastANI
[2024-01-24 13:10:23,958] [INFO] Running command: fastANI --query /var/lib/cwl/stgd59ebe71-4dde-40b7-8771-a5f9ba930e5a/GCF_019049655.1_ASM1904965v1_genomic.fna.gz --refList GCF_019049655.1_ASM1904965v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019049655.1_ASM1904965v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:41,976] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:41,989] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:41,989] [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_001422575.1	s__Rahnella sp001422575	98.135	1634	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	98.18	98.11	0.91	0.87	5	conclusive
GCF_003263515.1	s__Rahnella inusitata	87.9273	1386	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	99.32	98.94	0.97	0.94	4	-
GCA_013457415.1	s__Rahnella sp013457415	87.459	1394	1804	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	86.4524	1323	1804	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	86.3313	1350	1804	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	86.2889	1324	1804	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	86.2285	1274	1804	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	86.1735	1332	1804	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	86.0794	1306	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015644585.1	s__Rahnella laticis	85.8063	1332	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	96.65	95.20	0.90	0.83	8	-
GCF_002951615.1	s__Rahnella sp002951615	85.6987	1301	1804	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	85.1344	1310	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001047675.1	s__Yersinia aleksiciae	78.9337	360	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.22	98.37	0.87	0.82	10	-
GCF_001155565.1	s__Yersinia frederiksenii_A	78.6658	348	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.53	99.44	0.95	0.92	10	-
GCF_015548865.1	s__Symbiopectobacterium marcescens_A	77.8928	283	1804	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Symbiopectobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:41,991] [INFO] GTDB search result was written to GCF_019049655.1_ASM1904965v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:41,991] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:41,996] [INFO] DFAST_QC result json was written to GCF_019049655.1_ASM1904965v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:41,997] [INFO] DFAST_QC completed!
[2024-01-24 13:10:41,997] [INFO] Total running time: 0h1m44s