[2024-01-25 17:52:35,528] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:52:35,531] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:52:35,532] [INFO] DQC Reference Directory: /var/lib/cwl/stg963c82e0-3c19-4932-948e-6beedfa5c379/dqc_reference
[2024-01-25 17:52:36,711] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:52:36,711] [INFO] Task started: Prodigal
[2024-01-25 17:52:36,712] [INFO] Running command: gunzip -c /var/lib/cwl/stg32db7d52-77b9-4cd7-aaec-860b7c68d9b1/GCF_025527015.1_ASM2552701v1_genomic.fna.gz | prodigal -d GCF_025527015.1_ASM2552701v1_genomic.fna/cds.fna -a GCF_025527015.1_ASM2552701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:52:48,896] [INFO] Task succeeded: Prodigal
[2024-01-25 17:52:48,897] [INFO] Task started: HMMsearch
[2024-01-25 17:52:48,897] [INFO] Running command: hmmsearch --tblout GCF_025527015.1_ASM2552701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg963c82e0-3c19-4932-948e-6beedfa5c379/dqc_reference/reference_markers.hmm GCF_025527015.1_ASM2552701v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:52:49,143] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:52:49,144] [INFO] Found 6/6 markers.
[2024-01-25 17:52:49,185] [INFO] Query marker FASTA was written to GCF_025527015.1_ASM2552701v1_genomic.fna/markers.fasta
[2024-01-25 17:52:49,185] [INFO] Task started: Blastn
[2024-01-25 17:52:49,185] [INFO] Running command: blastn -query GCF_025527015.1_ASM2552701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg963c82e0-3c19-4932-948e-6beedfa5c379/dqc_reference/reference_markers.fasta -out GCF_025527015.1_ASM2552701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:50,045] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:50,047] [INFO] Selected 18 target genomes.
[2024-01-25 17:52:50,047] [INFO] Target genome list was writen to GCF_025527015.1_ASM2552701v1_genomic.fna/target_genomes.txt
[2024-01-25 17:52:50,061] [INFO] Task started: fastANI
[2024-01-25 17:52:50,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg32db7d52-77b9-4cd7-aaec-860b7c68d9b1/GCF_025527015.1_ASM2552701v1_genomic.fna.gz --refList GCF_025527015.1_ASM2552701v1_genomic.fna/target_genomes.txt --output GCF_025527015.1_ASM2552701v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:53:05,880] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:05,880] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg963c82e0-3c19-4932-948e-6beedfa5c379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:53:05,881] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg963c82e0-3c19-4932-948e-6beedfa5c379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:53:05,891] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:53:05,891] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:53:05,892] [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
Erwinia iniecta	strain=B120	GCA_001267535.1	1560201	1560201	type	True	83.8542	1084	1740	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	80.5108	849	1740	95	below_threshold
Erwinia aphidicola	strain=JCM 21238	GCA_014773485.1	68334	68334	type	True	80.4892	843	1740	95	below_threshold
[Pantoea] beijingensis	strain=JZB2120001	GCA_022647505.1	1324864	1324864	type	True	80.3099	642	1740	95	below_threshold
Mixta gaviniae	strain=DSM 22758	GCA_002953195.1	665914	665914	type	True	80.2632	793	1740	95	below_threshold
[Pantoea] beijingensis	strain=LMG 27579	GCA_004022165.1	1324864	1324864	type	True	80.2298	640	1740	95	below_threshold
Mixta tenebrionis	strain=BIT-26	GCA_006517625.1	2562439	2562439	type	True	80.0131	721	1740	95	below_threshold
Erwinia persicina	strain=NBRC 102418	GCA_001571305.1	55211	55211	type	True	79.8554	726	1740	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	79.8083	713	1740	95	below_threshold
Erwinia tasmaniensis	strain=Et1/99	GCA_000026185.1	338565	338565	type	True	79.7713	586	1740	95	below_threshold
Pantoea deleyi	strain=LMG24200	GCA_022647325.1	470932	470932	type	True	79.7448	737	1740	95	below_threshold
Serratia rhizosphaerae	strain=KUDC3025	GCA_009817885.1	2597702	2597702	type	True	79.0061	581	1740	95	below_threshold
Serratia rubidaea	strain=FDAARGOS_926	GCA_016026735.1	61652	61652	type	True	78.7545	615	1740	95	below_threshold
Serratia rubidaea	strain=NBRC 103169	GCA_001598675.1	61652	61652	type	True	78.6919	605	1740	95	below_threshold
Serratia rubidaea	strain=CIP 103234	GCA_001304675.1	61652	61652	type	True	78.6629	573	1740	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	78.5989	457	1740	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	78.5851	469	1740	95	below_threshold
Klebsiella aerogenes	strain=KCTC 2190	GCA_000215745.1	548	548	type	True	78.4692	522	1740	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:53:05,893] [INFO] DFAST Taxonomy check result was written to GCF_025527015.1_ASM2552701v1_genomic.fna/tc_result.tsv
[2024-01-25 17:53:05,893] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:53:05,893] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:53:05,894] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg963c82e0-3c19-4932-948e-6beedfa5c379/dqc_reference/checkm_data
[2024-01-25 17:53:05,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:53:05,944] [INFO] Task started: CheckM
[2024-01-25 17:53:05,945] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025527015.1_ASM2552701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025527015.1_ASM2552701v1_genomic.fna/checkm_input GCF_025527015.1_ASM2552701v1_genomic.fna/checkm_result
[2024-01-25 17:53:42,869] [INFO] Task succeeded: CheckM
[2024-01-25 17:53:42,869] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:53:42,887] [INFO] ===== Completeness check finished =====
[2024-01-25 17:53:42,887] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:53:42,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025527015.1_ASM2552701v1_genomic.fna/markers.fasta)
[2024-01-25 17:53:42,888] [INFO] Task started: Blastn
[2024-01-25 17:53:42,888] [INFO] Running command: blastn -query GCF_025527015.1_ASM2552701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg963c82e0-3c19-4932-948e-6beedfa5c379/dqc_reference/reference_markers_gtdb.fasta -out GCF_025527015.1_ASM2552701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:44,278] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:44,283] [INFO] Selected 18 target genomes.
[2024-01-25 17:53:44,283] [INFO] Target genome list was writen to GCF_025527015.1_ASM2552701v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:53:44,300] [INFO] Task started: fastANI
[2024-01-25 17:53:44,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg32db7d52-77b9-4cd7-aaec-860b7c68d9b1/GCF_025527015.1_ASM2552701v1_genomic.fna.gz --refList GCF_025527015.1_ASM2552701v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025527015.1_ASM2552701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:54:04,587] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:04,598] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:54:04,599] [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_017875465.1	s__Erwinia toletana	91.7213	1514	1740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.93	99.93	0.98	0.98	2	-
GCF_001267535.1	s__Erwinia iniecta	83.8377	1086	1740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.95	99.95	0.99	0.99	2	-
GCF_000196615.1	s__Erwinia billingiae	80.585	856	1740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	97.77	97.43	0.91	0.82	7	-
GCF_014773485.1	s__Erwinia aphidicola	80.5131	839	1740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.08	98.09	0.88	0.85	7	-
GCF_009765445.1	s__Erwinia sp009765445	80.3177	784	1740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751505.1	s__Erwinia sp003751505	80.2822	786	1740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002953195.1	s__Mixta gaviniae	80.2567	793	1740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	99.91	99.91	0.99	0.99	2	-
GCF_004022165.1	s__Erwinia beijingensis	80.2299	640	1740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.78	99.57	0.98	0.97	3	-
GCF_016909495.1	s__Erwinia coffeiphila	80.1357	762	1740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	96.75	96.67	0.88	0.87	4	-
GCF_009738185.1	s__Erwinia sp009738185	79.9917	762	1740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.50	99.50	0.98	0.98	2	-
GCF_003937915.1	s__Erwinia sp003937915	79.9584	714	1740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101395.1	s__Mixta alhagi	79.9169	727	1740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Mixta	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012271765.1	s__Erwinia rhapontici	79.9065	783	1740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	98.76	96.56	0.93	0.92	9	-
GCF_001571305.1	s__Erwinia persicina	79.8843	722	1740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.41	99.25	0.96	0.94	13	-
GCF_014838825.1	s__Erwinia persicina_A	79.8605	739	1740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.46	99.46	0.97	0.97	2	-
GCF_004792415.1	s__Pantoea vagans	79.7936	742	1740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pantoea	95.0	97.00	95.86	0.91	0.88	14	-
GCF_009817885.1	s__Serratia_B rhizosphaerae	79.0212	579	1740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_B	95.0	97.16	97.09	0.90	0.89	7	-
GCA_901472405.1	s__Serratia_B rubidaea	78.6809	613	1740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_B	95.0	98.79	97.55	0.96	0.91	11	-
--------------------------------------------------------------------------------
[2024-01-25 17:54:04,600] [INFO] GTDB search result was written to GCF_025527015.1_ASM2552701v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:54:04,600] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:54:04,604] [INFO] DFAST_QC result json was written to GCF_025527015.1_ASM2552701v1_genomic.fna/dqc_result.json
[2024-01-25 17:54:04,605] [INFO] DFAST_QC completed!
[2024-01-25 17:54:04,605] [INFO] Total running time: 0h1m29s