[2024-01-25 19:09:05,379] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:09:05,380] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:09:05,380] [INFO] DQC Reference Directory: /var/lib/cwl/stg45d3b5dd-c1b2-4303-b871-ed1169022098/dqc_reference
[2024-01-25 19:09:06,491] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:09:06,492] [INFO] Task started: Prodigal
[2024-01-25 19:09:06,492] [INFO] Running command: gunzip -c /var/lib/cwl/stg6799db7c-6415-4b52-9549-7dbba7de8c6e/GCF_025564085.1_ASM2556408v1_genomic.fna.gz | prodigal -d GCF_025564085.1_ASM2556408v1_genomic.fna/cds.fna -a GCF_025564085.1_ASM2556408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:18,304] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:18,305] [INFO] Task started: HMMsearch
[2024-01-25 19:09:18,305] [INFO] Running command: hmmsearch --tblout GCF_025564085.1_ASM2556408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45d3b5dd-c1b2-4303-b871-ed1169022098/dqc_reference/reference_markers.hmm GCF_025564085.1_ASM2556408v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:18,556] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:18,557] [INFO] Found 6/6 markers.
[2024-01-25 19:09:18,596] [INFO] Query marker FASTA was written to GCF_025564085.1_ASM2556408v1_genomic.fna/markers.fasta
[2024-01-25 19:09:18,596] [INFO] Task started: Blastn
[2024-01-25 19:09:18,596] [INFO] Running command: blastn -query GCF_025564085.1_ASM2556408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45d3b5dd-c1b2-4303-b871-ed1169022098/dqc_reference/reference_markers.fasta -out GCF_025564085.1_ASM2556408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:19,491] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:19,494] [INFO] Selected 19 target genomes.
[2024-01-25 19:09:19,495] [INFO] Target genome list was writen to GCF_025564085.1_ASM2556408v1_genomic.fna/target_genomes.txt
[2024-01-25 19:09:19,506] [INFO] Task started: fastANI
[2024-01-25 19:09:19,506] [INFO] Running command: fastANI --query /var/lib/cwl/stg6799db7c-6415-4b52-9549-7dbba7de8c6e/GCF_025564085.1_ASM2556408v1_genomic.fna.gz --refList GCF_025564085.1_ASM2556408v1_genomic.fna/target_genomes.txt --output GCF_025564085.1_ASM2556408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:09:39,765] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:39,765] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45d3b5dd-c1b2-4303-b871-ed1169022098/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:09:39,766] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45d3b5dd-c1b2-4303-b871-ed1169022098/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:09:39,777] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:09:39,777] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:09:39,777] [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
Leclercia adecarboxylata	strain=NBRC 102595	GCA_001515505.1	83655	83655	suspected-type	True	86.7731	1243	1607	95	below_threshold
Leclercia adecarboxylata	strain=ATCC 23216	GCA_000735515.1	83655	83655	suspected-type	True	86.7515	1231	1607	95	below_threshold
Leclercia adecarboxylata	strain=FDAARGOS_1505	GCA_020097395.1	83655	83655	suspected-type	True	86.7506	1271	1607	95	below_threshold
Lelliottia nimipressuralis	strain=CCUG 25894	GCA_004115925.1	69220	69220	type	True	84.1489	1059	1607	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	84.0676	1095	1607	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_018987305.1	2815358	2815358	type	True	83.9017	1088	1607	95	below_threshold
Enterobacter roggenkampii	strain=DSM 16690	GCA_024390995.1	1812935	1812935	type	True	83.8555	1039	1607	95	below_threshold
Lelliottia aquatilis	strain=6331-17	GCA_002923025.1	2080838	2080838	type	True	83.8042	1090	1607	95	below_threshold
Enterobacter hormaechei subsp. oharae	strain=FDAARGOS_1533	GCA_020097195.1	301102	158836	type	True	83.7879	1085	1607	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	83.7791	1037	1607	95	below_threshold
Leclercia pneumoniae	strain=49125	GCA_017348915.1	2815358	2815358	type	True	83.7625	1118	1607	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_002939185.1	2071710	2071710	type	True	83.7486	1019	1607	95	below_threshold
Enterobacter mori	strain=LMG 25706	GCA_000211415.1	539813	539813	type	True	83.7203	1049	1607	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	83.708	1065	1607	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	83.542	1088	1607	95	below_threshold
Lelliottia amnigena	strain=NBRC 105700	GCA_001514515.1	61646	61646	type	True	83.2107	1017	1607	95	below_threshold
Lelliottia amnigena	strain=FDAARGOS 1444	GCA_019047465.1	61646	61646	type	True	83.208	1032	1607	95	below_threshold
Lelliottia amnigena	strain=LMG 2784	GCA_002553545.1	61646	61646	type	True	83.178	1016	1607	95	below_threshold
Raoultella planticola	strain=ATCC 33531	GCA_000735435.1	575	575	type	True	81.0599	901	1607	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:09:39,779] [INFO] DFAST Taxonomy check result was written to GCF_025564085.1_ASM2556408v1_genomic.fna/tc_result.tsv
[2024-01-25 19:09:39,779] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:09:39,780] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:09:39,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45d3b5dd-c1b2-4303-b871-ed1169022098/dqc_reference/checkm_data
[2024-01-25 19:09:39,780] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:09:39,826] [INFO] Task started: CheckM
[2024-01-25 19:09:39,826] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025564085.1_ASM2556408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025564085.1_ASM2556408v1_genomic.fna/checkm_input GCF_025564085.1_ASM2556408v1_genomic.fna/checkm_result
[2024-01-25 19:10:15,876] [INFO] Task succeeded: CheckM
[2024-01-25 19:10:15,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:10:15,897] [INFO] ===== Completeness check finished =====
[2024-01-25 19:10:15,897] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:10:15,898] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025564085.1_ASM2556408v1_genomic.fna/markers.fasta)
[2024-01-25 19:10:15,898] [INFO] Task started: Blastn
[2024-01-25 19:10:15,898] [INFO] Running command: blastn -query GCF_025564085.1_ASM2556408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45d3b5dd-c1b2-4303-b871-ed1169022098/dqc_reference/reference_markers_gtdb.fasta -out GCF_025564085.1_ASM2556408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:17,372] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:17,375] [INFO] Selected 13 target genomes.
[2024-01-25 19:10:17,375] [INFO] Target genome list was writen to GCF_025564085.1_ASM2556408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:17,386] [INFO] Task started: fastANI
[2024-01-25 19:10:17,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg6799db7c-6415-4b52-9549-7dbba7de8c6e/GCF_025564085.1_ASM2556408v1_genomic.fna.gz --refList GCF_025564085.1_ASM2556408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025564085.1_ASM2556408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:31,849] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:31,857] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:10:31,858] [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_006874705.1	s__Leclercia adecarboxylata_C	87.3526	1298	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	98.71	98.25	0.93	0.90	13	-
GCF_011290365.1	s__Leclercia sp003024485	87.3498	1267	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	98.06	98.06	0.90	0.90	2	-
GCA_002360945.1	s__Leclercia adecarboxylata_B	87.2839	1273	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	99.97	99.97	0.98	0.98	2	-
GCF_006171285.1	s__Leclercia adecarboxylata_A	86.9864	1303	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	97.80	96.55	0.92	0.89	4	-
GCA_901472455.1	s__Leclercia adecarboxylata	86.5952	1263	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	98.53	98.09	0.95	0.87	86	-
GCF_002902985.1	s__Leclercia sp002902985	86.5153	1253	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Leclercia	95.0	98.13	96.37	0.93	0.86	16	-
GCF_004115925.1	s__Lelliottia nimipressuralis	84.1489	1059	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	98.29	98.00	0.93	0.92	11	-
GCF_003594935.1	s__Enterobacter huaxiensis	83.9909	1095	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	98.98	98.98	0.94	0.94	2	-
GCA_002271215.1	s__Lelliottia jeotgali	83.8269	1092	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	98.81	98.80	0.92	0.92	9	-
GCA_009668015.1	s__Lelliottia sp009668015	83.4905	1036	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016325.1	s__Lelliottia sp000016325	83.3594	1044	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	95.60	95.60	0.93	0.93	2	-
GCA_900635465.1	s__Lelliottia amnigena	83.1812	1027	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lelliottia	95.0	98.81	98.20	0.95	0.91	15	-
GCA_002386445.1	s__Pseudomonas_E sp002386445	77.3158	76	1607	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:10:31,859] [INFO] GTDB search result was written to GCF_025564085.1_ASM2556408v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:31,859] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:31,863] [INFO] DFAST_QC result json was written to GCF_025564085.1_ASM2556408v1_genomic.fna/dqc_result.json
[2024-01-25 19:10:31,863] [INFO] DFAST_QC completed!
[2024-01-25 19:10:31,863] [INFO] Total running time: 0h1m26s