[2024-01-24 12:06:14,583] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,586] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,586] [INFO] DQC Reference Directory: /var/lib/cwl/stg81f6c0a8-a7bc-4785-8edf-43b2d7ccfb94/dqc_reference
[2024-01-24 12:06:16,129] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:16,130] [INFO] Task started: Prodigal
[2024-01-24 12:06:16,130] [INFO] Running command: gunzip -c /var/lib/cwl/stga9983b6e-7ad4-4065-99be-0332f5ff6730/GCF_019047785.1_ASM1904778v1_genomic.fna.gz | prodigal -d GCF_019047785.1_ASM1904778v1_genomic.fna/cds.fna -a GCF_019047785.1_ASM1904778v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:30,076] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:30,077] [INFO] Task started: HMMsearch
[2024-01-24 12:06:30,077] [INFO] Running command: hmmsearch --tblout GCF_019047785.1_ASM1904778v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81f6c0a8-a7bc-4785-8edf-43b2d7ccfb94/dqc_reference/reference_markers.hmm GCF_019047785.1_ASM1904778v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:30,435] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:30,437] [INFO] Found 6/6 markers.
[2024-01-24 12:06:30,487] [INFO] Query marker FASTA was written to GCF_019047785.1_ASM1904778v1_genomic.fna/markers.fasta
[2024-01-24 12:06:30,488] [INFO] Task started: Blastn
[2024-01-24 12:06:30,488] [INFO] Running command: blastn -query GCF_019047785.1_ASM1904778v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81f6c0a8-a7bc-4785-8edf-43b2d7ccfb94/dqc_reference/reference_markers.fasta -out GCF_019047785.1_ASM1904778v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:31,491] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:31,494] [INFO] Selected 18 target genomes.
[2024-01-24 12:06:31,495] [INFO] Target genome list was writen to GCF_019047785.1_ASM1904778v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:31,502] [INFO] Task started: fastANI
[2024-01-24 12:06:31,502] [INFO] Running command: fastANI --query /var/lib/cwl/stga9983b6e-7ad4-4065-99be-0332f5ff6730/GCF_019047785.1_ASM1904778v1_genomic.fna.gz --refList GCF_019047785.1_ASM1904778v1_genomic.fna/target_genomes.txt --output GCF_019047785.1_ASM1904778v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:52,670] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:52,670] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81f6c0a8-a7bc-4785-8edf-43b2d7ccfb94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:52,670] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81f6c0a8-a7bc-4785-8edf-43b2d7ccfb94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:52,687] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:06:52,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:52,688] [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 cancerogenus	strain=FDAARGOS 1428	GCA_019047785.1	69218	69218	type	True	100.0	1607	1607	95	conclusive
Enterobacter cancerogenus		GCA_900185905.1	69218	69218	type	True	99.9851	1584	1607	95	conclusive
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	87.5803	1270	1607	95	below_threshold
Enterobacter quasimori	strain=090044	GCA_003964905.1	2838947	2838947	type	True	87.4994	1233	1607	95	below_threshold
Enterobacter oligotrophicus	strain=CCA6	GCA_009176645.1	2478464	2478464	type	True	87.4619	1268	1607	95	below_threshold
Enterobacter bugandensis	strain=FDAARGOS 1427	GCA_019046905.1	881260	881260	type	True	87.4153	1246	1607	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	87.3818	1170	1607	95	below_threshold
Enterobacter chengduensis	strain=WCHECl-C4 = WCHECh050004	GCA_001984825.2	2494701	2494701	type	True	87.3785	1200	1607	95	below_threshold
Enterobacter bugandensis		GCA_900324475.1	881260	881260	type	True	87.3659	1239	1607	95	below_threshold
Enterobacter hormaechei subsp. oharae	strain=DSM 16687	GCA_001729705.1	301102	158836	type	True	87.3467	1253	1607	95	below_threshold
Enterobacter hormaechei subsp. oharae	strain=FDAARGOS_1533	GCA_020097195.1	301102	158836	type	True	87.3327	1254	1607	95	below_threshold
Enterobacter mori	strain=LMG 25706	GCA_000211415.1	539813	539813	type	True	87.2833	1191	1607	95	below_threshold
Enterobacter hormaechei subsp. xiangfangensis	strain=LMG27195	GCA_001729785.1	1296536	158836	type	True	87.1934	1242	1607	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	87.1871	1244	1607	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	86.8348	1170	1607	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	86.818	1223	1607	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	84.6672	1072	1607	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	84.5866	1070	1607	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:52,691] [INFO] DFAST Taxonomy check result was written to GCF_019047785.1_ASM1904778v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:52,692] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:52,692] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:52,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81f6c0a8-a7bc-4785-8edf-43b2d7ccfb94/dqc_reference/checkm_data
[2024-01-24 12:06:52,694] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:52,747] [INFO] Task started: CheckM
[2024-01-24 12:06:52,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019047785.1_ASM1904778v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019047785.1_ASM1904778v1_genomic.fna/checkm_input GCF_019047785.1_ASM1904778v1_genomic.fna/checkm_result
[2024-01-24 12:07:36,506] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:36,508] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:36,542] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:36,543] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:36,543] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019047785.1_ASM1904778v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:36,544] [INFO] Task started: Blastn
[2024-01-24 12:07:36,544] [INFO] Running command: blastn -query GCF_019047785.1_ASM1904778v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81f6c0a8-a7bc-4785-8edf-43b2d7ccfb94/dqc_reference/reference_markers_gtdb.fasta -out GCF_019047785.1_ASM1904778v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:38,003] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:38,007] [INFO] Selected 17 target genomes.
[2024-01-24 12:07:38,007] [INFO] Target genome list was writen to GCF_019047785.1_ASM1904778v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:38,024] [INFO] Task started: fastANI
[2024-01-24 12:07:38,024] [INFO] Running command: fastANI --query /var/lib/cwl/stga9983b6e-7ad4-4065-99be-0332f5ff6730/GCF_019047785.1_ASM1904778v1_genomic.fna.gz --refList GCF_019047785.1_ASM1904778v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019047785.1_ASM1904778v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:56,866] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:56,888] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:56,888] [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_019047785.1	s__Enterobacter cancerogenus	100.0	1607	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.78	98.42	0.93	0.90	16	conclusive
GCF_004331265.1	s__Enterobacter wuhouensis	87.5803	1270	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003594935.1	s__Enterobacter huaxiensis	87.4865	1290	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.98	98.98	0.94	0.94	2	-
GCF_009176645.1	s__Enterobacter oligotrophicus	87.4721	1267	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.55	99.09	0.97	0.94	3	-
GCF_000493015.1	s__Enterobacter sp000493015	87.4293	1240	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.7595	98.68	98.68	0.92	0.92	2	-
GCF_001984825.2	s__Enterobacter chengduensis	87.3703	1199	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.11	95.58	0.88	0.79	24	-
GCF_900324475.1	s__Enterobacter bugandensis	87.3511	1237	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.49	95.52	0.94	0.88	115	-
GCF_000211415.1	s__Enterobacter mori	87.2806	1192	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.59	96.13	0.88	0.85	23	-
GCF_011754535.1	s__Enterobacter cloacae_N	87.2576	1259	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.03	98.99	0.93	0.91	4	-
GCF_003057745.1	s__Enterobacter sp003057745	87.2484	1206	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755685.1	s__Enterobacter sp000568095	87.2483	1230	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0476	98.37	98.04	0.95	0.92	11	-
GCF_003594915.1	s__Enterobacter chuandaensis	87.1944	1215	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.38	98.32	0.92	0.92	3	-
GCF_013375935.1	s__Enterobacter cloacae_O	87.1318	1261	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.68	98.59	0.94	0.92	6	-
GCF_001729745.1	s__Enterobacter hormaechei_A	87.1195	1281	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	96.63	95.22	0.89	0.83	1867	-
GCF_001875655.1	s__Enterobacter hormaechei	87.116	1252	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	99.46	98.52	0.92	0.86	32	-
GCF_011078175.1	s__Enterobacter cloacae_Q	86.8018	1221	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017348915.1	s__UBA7405 sp000755535	84.6513	1071	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__UBA7405	95.0	98.56	97.85	0.93	0.89	10	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:56,890] [INFO] GTDB search result was written to GCF_019047785.1_ASM1904778v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:56,891] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:56,895] [INFO] DFAST_QC result json was written to GCF_019047785.1_ASM1904778v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:56,895] [INFO] DFAST_QC completed!
[2024-01-24 12:07:56,896] [INFO] Total running time: 0h1m42s