[2024-01-24 13:22:02,586] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:02,589] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:02,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg7fb16c3c-2b1e-4bc0-b7f8-c62f2154e0ea/dqc_reference
[2024-01-24 13:22:03,906] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,907] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,907] [INFO] Running command: gunzip -c /var/lib/cwl/stg3378ed60-b7c4-455e-a4bf-44473a974239/GCF_026420145.1_ASM2642014v1_genomic.fna.gz | prodigal -d GCF_026420145.1_ASM2642014v1_genomic.fna/cds.fna -a GCF_026420145.1_ASM2642014v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:17,246] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:17,247] [INFO] Task started: HMMsearch
[2024-01-24 13:22:17,247] [INFO] Running command: hmmsearch --tblout GCF_026420145.1_ASM2642014v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7fb16c3c-2b1e-4bc0-b7f8-c62f2154e0ea/dqc_reference/reference_markers.hmm GCF_026420145.1_ASM2642014v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:17,571] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:17,572] [INFO] Found 6/6 markers.
[2024-01-24 13:22:17,614] [INFO] Query marker FASTA was written to GCF_026420145.1_ASM2642014v1_genomic.fna/markers.fasta
[2024-01-24 13:22:17,614] [INFO] Task started: Blastn
[2024-01-24 13:22:17,614] [INFO] Running command: blastn -query GCF_026420145.1_ASM2642014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7fb16c3c-2b1e-4bc0-b7f8-c62f2154e0ea/dqc_reference/reference_markers.fasta -out GCF_026420145.1_ASM2642014v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:18,618] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:18,621] [INFO] Selected 13 target genomes.
[2024-01-24 13:22:18,622] [INFO] Target genome list was writen to GCF_026420145.1_ASM2642014v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:18,628] [INFO] Task started: fastANI
[2024-01-24 13:22:18,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg3378ed60-b7c4-455e-a4bf-44473a974239/GCF_026420145.1_ASM2642014v1_genomic.fna.gz --refList GCF_026420145.1_ASM2642014v1_genomic.fna/target_genomes.txt --output GCF_026420145.1_ASM2642014v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:34,717] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:34,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7fb16c3c-2b1e-4bc0-b7f8-c62f2154e0ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:34,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7fb16c3c-2b1e-4bc0-b7f8-c62f2154e0ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:34,729] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:34,729] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:22:34,729] [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
Enterobacter asburiae	strain=FDAARGOS_892	GCA_016027695.1	61645	61645	type	True	94.6498	1327	1614	95	below_threshold
Enterobacter asburiae	strain=ATCC 35953	GCA_001521715.1	61645	61645	type	True	94.6049	1336	1614	95	below_threshold
Enterobacter vonholyi	strain=E13	GCA_008364555.1	2797505	2797505	type	True	94.3098	1369	1614	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_001729805.1	1812935	1812935	type	True	94.2957	1380	1614	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	94.2953	1305	1614	95	below_threshold
Enterobacter roggenkampii	strain=FDAARGOS 1430	GCA_019047025.1	1812935	1812935	type	True	94.2592	1378	1614	95	below_threshold
Enterobacter chengduensis	strain=WCHECl-C4 = WCHECh050004	GCA_001984825.2	2494701	2494701	type	True	93.1724	1344	1614	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	91.7944	1377	1614	95	below_threshold
Enterobacter quasimori	strain=090044	GCA_003964905.1	2838947	2838947	type	True	91.472	1298	1614	95	below_threshold
Enterobacter kobei	strain=DSM 13645	GCA_001729765.1	208224	208224	type	True	90.6835	1317	1614	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	89.3133	1270	1614	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	89.0256	1297	1614	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	88.1651	1230	1614	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:34,731] [INFO] DFAST Taxonomy check result was written to GCF_026420145.1_ASM2642014v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:34,732] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:34,732] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:34,732] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7fb16c3c-2b1e-4bc0-b7f8-c62f2154e0ea/dqc_reference/checkm_data
[2024-01-24 13:22:34,734] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:34,782] [INFO] Task started: CheckM
[2024-01-24 13:22:34,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026420145.1_ASM2642014v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026420145.1_ASM2642014v1_genomic.fna/checkm_input GCF_026420145.1_ASM2642014v1_genomic.fna/checkm_result
[2024-01-24 13:23:17,653] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:17,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:17,672] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:17,673] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:17,673] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026420145.1_ASM2642014v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:17,674] [INFO] Task started: Blastn
[2024-01-24 13:23:17,674] [INFO] Running command: blastn -query GCF_026420145.1_ASM2642014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7fb16c3c-2b1e-4bc0-b7f8-c62f2154e0ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_026420145.1_ASM2642014v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:19,132] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:19,135] [INFO] Selected 10 target genomes.
[2024-01-24 13:23:19,135] [INFO] Target genome list was writen to GCF_026420145.1_ASM2642014v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:19,180] [INFO] Task started: fastANI
[2024-01-24 13:23:19,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg3378ed60-b7c4-455e-a4bf-44473a974239/GCF_026420145.1_ASM2642014v1_genomic.fna.gz --refList GCF_026420145.1_ASM2642014v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026420145.1_ASM2642014v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:30,840] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:30,849] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:30,849] [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_009755685.1	s__Enterobacter sp000568095	98.3701	1492	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0476	98.37	98.04	0.95	0.92	11	conclusive
GCF_003634515.1	s__Enterobacter asburiae_A	94.9708	1429	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.0274	97.62	96.46	0.91	0.85	7	-
GCF_008080435.1	s__Enterobacter asburiae_C	94.6324	1406	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.5575	N/A	N/A	N/A	N/A	1	-
GCF_001521715.1	s__Enterobacter asburiae	94.6049	1336	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.42	96.92	0.89	0.84	32	-
GCF_007035645.1	s__Enterobacter asburiae_B	94.5571	1381	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.31	97.34	0.92	0.85	70	-
GCF_000493015.1	s__Enterobacter sp000493015	94.4247	1398	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.7595	98.68	98.68	0.92	0.92	2	-
GCF_008364625.1	s__Enterobacter dykesii	94.3409	1371	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.5795	99.13	97.97	0.97	0.95	7	-
GCF_008364555.1	s__Enterobacter vonholyi	94.3098	1369	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.34	98.09	0.94	0.93	8	-
GCF_001729805.1	s__Enterobacter roggenkampii	94.2957	1380	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.21	95.50	0.89	0.83	197	-
GCF_002208095.1	s__Enterobacter cloacae_M	94.2759	1395	1614	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.7528	98.28	96.89	0.91	0.85	84	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:30,850] [INFO] GTDB search result was written to GCF_026420145.1_ASM2642014v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:30,851] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:30,855] [INFO] DFAST_QC result json was written to GCF_026420145.1_ASM2642014v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:30,855] [INFO] DFAST_QC completed!
[2024-01-24 13:23:30,855] [INFO] Total running time: 0h1m28s