[2024-01-24 13:36:45,624] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,626] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,627] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b51113d-6472-4b5f-96a3-7878e688d62b/dqc_reference
[2024-01-24 13:36:46,951] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,952] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,952] [INFO] Running command: gunzip -c /var/lib/cwl/stg734d98ec-44d1-491f-910d-5b3ff69e8739/GCF_009660455.1_ASM966045v1_genomic.fna.gz | prodigal -d GCF_009660455.1_ASM966045v1_genomic.fna/cds.fna -a GCF_009660455.1_ASM966045v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:00,722] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:00,722] [INFO] Task started: HMMsearch
[2024-01-24 13:37:00,722] [INFO] Running command: hmmsearch --tblout GCF_009660455.1_ASM966045v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b51113d-6472-4b5f-96a3-7878e688d62b/dqc_reference/reference_markers.hmm GCF_009660455.1_ASM966045v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:01,006] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:01,007] [INFO] Found 6/6 markers.
[2024-01-24 13:37:01,054] [INFO] Query marker FASTA was written to GCF_009660455.1_ASM966045v1_genomic.fna/markers.fasta
[2024-01-24 13:37:01,054] [INFO] Task started: Blastn
[2024-01-24 13:37:01,054] [INFO] Running command: blastn -query GCF_009660455.1_ASM966045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b51113d-6472-4b5f-96a3-7878e688d62b/dqc_reference/reference_markers.fasta -out GCF_009660455.1_ASM966045v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:01,966] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:01,969] [INFO] Selected 10 target genomes.
[2024-01-24 13:37:01,969] [INFO] Target genome list was writen to GCF_009660455.1_ASM966045v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:01,973] [INFO] Task started: fastANI
[2024-01-24 13:37:01,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg734d98ec-44d1-491f-910d-5b3ff69e8739/GCF_009660455.1_ASM966045v1_genomic.fna.gz --refList GCF_009660455.1_ASM966045v1_genomic.fna/target_genomes.txt --output GCF_009660455.1_ASM966045v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:14,132] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:14,133] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b51113d-6472-4b5f-96a3-7878e688d62b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:14,133] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b51113d-6472-4b5f-96a3-7878e688d62b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:14,143] [INFO] Found 10 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 13:37:14,143] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:14,143] [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 cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	95.3329	1456	1598	95	conclusive
Enterobacter cloacae	strain=ATCC 13047	GCA_001997105.1	550	550	type	True	95.324	1454	1598	95	conclusive
Enterobacter cloacae	strain=ATCC 13047	GCA_000755525.1	550	550	type	True	95.3161	1470	1598	95	conclusive
Enterobacter cloacae subsp. cloacae	strain=ATCC 13047	GCA_000025565.1	336306	550	type	True	95.3008	1481	1598	95	conclusive
Enterobacter cloacae	strain=FDAARGOS 1431	GCA_019047105.1	550	550	type	True	95.2759	1476	1598	95	conclusive
Enterobacter cloacae	strain=DSM 30054	GCA_013376815.1	550	550	type	True	95.2716	1481	1598	95	conclusive
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	89.4939	1329	1598	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	89.1211	1257	1598	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	87.9452	1278	1598	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	87.3927	1255	1598	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:14,145] [INFO] DFAST Taxonomy check result was written to GCF_009660455.1_ASM966045v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:14,146] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:14,146] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:14,146] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b51113d-6472-4b5f-96a3-7878e688d62b/dqc_reference/checkm_data
[2024-01-24 13:37:14,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:14,226] [INFO] Task started: CheckM
[2024-01-24 13:37:14,226] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009660455.1_ASM966045v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009660455.1_ASM966045v1_genomic.fna/checkm_input GCF_009660455.1_ASM966045v1_genomic.fna/checkm_result
[2024-01-24 13:37:58,444] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:58,445] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:58,463] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:58,464] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:58,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009660455.1_ASM966045v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:58,464] [INFO] Task started: Blastn
[2024-01-24 13:37:58,465] [INFO] Running command: blastn -query GCF_009660455.1_ASM966045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b51113d-6472-4b5f-96a3-7878e688d62b/dqc_reference/reference_markers_gtdb.fasta -out GCF_009660455.1_ASM966045v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:59,947] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:59,951] [INFO] Selected 20 target genomes.
[2024-01-24 13:37:59,951] [INFO] Target genome list was writen to GCF_009660455.1_ASM966045v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:59,979] [INFO] Task started: fastANI
[2024-01-24 13:37:59,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg734d98ec-44d1-491f-910d-5b3ff69e8739/GCF_009660455.1_ASM966045v1_genomic.fna.gz --refList GCF_009660455.1_ASM966045v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009660455.1_ASM966045v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:23,512] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:23,528] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:23,529] [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_000025565.1	s__Enterobacter cloacae	95.2834	1483	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.05	95.14	0.91	0.80	129	conclusive
GCF_002939185.1	s__Enterobacter sichuanensis	89.4182	1313	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	97.99	0.90	0.85	19	-
GCF_003634515.1	s__Enterobacter asburiae_A	89.1275	1353	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.0274	97.62	96.46	0.91	0.85	7	-
GCF_007035645.1	s__Enterobacter asburiae_B	89.1145	1318	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.8818	98.31	97.34	0.92	0.85	70	-
GCF_001729805.1	s__Enterobacter roggenkampii	89.0716	1331	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.21	95.50	0.89	0.83	197	-
GCF_009755685.1	s__Enterobacter sp000568095	89.0538	1335	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0476	98.37	98.04	0.95	0.92	11	-
GCF_000493015.1	s__Enterobacter sp000493015	89.0376	1339	1598	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	88.9805	1305	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	96.5795	99.13	97.97	0.97	0.95	7	-
GCF_011754535.1	s__Enterobacter cloacae_N	88.9521	1339	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.03	98.99	0.93	0.91	4	-
GCF_008080435.1	s__Enterobacter asburiae_C	88.8447	1355	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.5575	N/A	N/A	N/A	N/A	1	-
GCF_900324475.1	s__Enterobacter bugandensis	88.8364	1311	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.49	95.52	0.94	0.88	115	-
GCF_001984825.2	s__Enterobacter chengduensis	88.6991	1322	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.11	95.58	0.88	0.79	24	-
GCF_001729765.1	s__Enterobacter kobei	88.4686	1284	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.81	98.45	0.89	0.85	141	-
GCF_003046225.1	s__Enterobacter cloacae_I	88.3866	1272	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.61	95.47	0.89	0.86	14	-
GCF_001750725.1	s__Enterobacter ludwigii	88.2655	1369	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.79	98.47	0.93	0.83	88	-
GCF_003594935.1	s__Enterobacter huaxiensis	87.7886	1276	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.98	98.98	0.94	0.94	2	-
GCF_014169315.1	s__Enterobacter cloacae_P	87.7377	1177	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.13	99.10	0.85	0.85	3	-
GCF_001729745.1	s__Enterobacter hormaechei_A	87.4358	1280	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	96.63	95.22	0.89	0.83	1867	-
GCF_900322725.1	s__Enterobacter quasihormaechei	87.3858	1251	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	97.61	0.96	0.89	41	-
GCF_019047785.1	s__Enterobacter cancerogenus	86.7564	1214	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.78	98.42	0.93	0.90	16	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:23,535] [INFO] GTDB search result was written to GCF_009660455.1_ASM966045v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:23,535] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:23,540] [INFO] DFAST_QC result json was written to GCF_009660455.1_ASM966045v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:23,540] [INFO] DFAST_QC completed!
[2024-01-24 13:38:23,541] [INFO] Total running time: 0h1m38s