[2023-06-08 19:34:26,671] [INFO] DFAST_QC pipeline started.
[2023-06-08 19:34:26,674] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 19:34:26,675] [INFO] DQC Reference Directory: /var/lib/cwl/stg00215fd7-b9b8-4bdf-8f29-e9cbf3928401/dqc_reference
[2023-06-08 19:34:27,958] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 19:34:27,959] [INFO] Task started: Prodigal
[2023-06-08 19:34:27,959] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b4a1552-7616-45d2-874f-36b1d4efbc76/GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 19:34:37,662] [INFO] Task succeeded: Prodigal
[2023-06-08 19:34:37,663] [INFO] Task started: HMMsearch
[2023-06-08 19:34:37,663] [INFO] Running command: hmmsearch --tblout GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00215fd7-b9b8-4bdf-8f29-e9cbf3928401/dqc_reference/reference_markers.hmm GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 19:34:37,934] [INFO] Task succeeded: HMMsearch
[2023-06-08 19:34:37,936] [INFO] Found 6/6 markers.
[2023-06-08 19:34:37,975] [INFO] Query marker FASTA was written to GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 19:34:37,976] [INFO] Task started: Blastn
[2023-06-08 19:34:37,976] [INFO] Running command: blastn -query GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg00215fd7-b9b8-4bdf-8f29-e9cbf3928401/dqc_reference/reference_markers.fasta -out GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:34:38,815] [INFO] Task succeeded: Blastn
[2023-06-08 19:34:38,820] [INFO] Selected 10 target genomes.
[2023-06-08 19:34:38,820] [INFO] Target genome list was writen to GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 19:34:38,824] [INFO] Task started: fastANI
[2023-06-08 19:34:38,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b4a1552-7616-45d2-874f-36b1d4efbc76/GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 19:34:48,401] [INFO] Task succeeded: fastANI
[2023-06-08 19:34:48,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00215fd7-b9b8-4bdf-8f29-e9cbf3928401/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 19:34:48,403] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00215fd7-b9b8-4bdf-8f29-e9cbf3928401/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 19:34:48,416] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2023-06-08 19:34:48,416] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 19:34:48,416] [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
Obesumbacterium proteus	strain=DSM 2777	GCA_001586165.1	82983	82983	type	True	97.9427	1229	1303	95	conclusive
Obesumbacterium proteus	strain=ATCC 12841	GCA_001655035.1	82983	82983	type	True	97.9021	1227	1303	95	conclusive
Hafnia alvei	strain=ATCC 13337	GCA_003668715.1	569	569	type	True	94.5244	1157	1303	95	below_threshold
Hafnia alvei	strain=ATCC 13337	GCA_000735375.1	569	569	type	True	94.5173	1145	1303	95	below_threshold
Hafnia paralvei	strain=ATCC 29927	GCA_001655005.1	546367	546367	type	True	84.2239	952	1303	95	below_threshold
Hafnia paralvei	strain=ATCC 29927	GCA_023698525.1	546367	546367	type	True	84.1832	950	1303	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.4921	303	1303	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	78.3437	309	1303	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.32	317	1303	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.3092	308	1303	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 19:34:48,418] [INFO] DFAST Taxonomy check result was written to GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 19:34:48,419] [INFO] ===== Taxonomy check completed =====
[2023-06-08 19:34:48,419] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 19:34:48,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00215fd7-b9b8-4bdf-8f29-e9cbf3928401/dqc_reference/checkm_data
[2023-06-08 19:34:48,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 19:34:48,468] [INFO] Task started: CheckM
[2023-06-08 19:34:48,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 19:35:22,683] [INFO] Task succeeded: CheckM
[2023-06-08 19:35:22,684] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 19:35:22,707] [INFO] ===== Completeness check finished =====
[2023-06-08 19:35:22,707] [INFO] ===== Start GTDB Search =====
[2023-06-08 19:35:22,707] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 19:35:22,708] [INFO] Task started: Blastn
[2023-06-08 19:35:22,708] [INFO] Running command: blastn -query GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg00215fd7-b9b8-4bdf-8f29-e9cbf3928401/dqc_reference/reference_markers_gtdb.fasta -out GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:35:23,997] [INFO] Task succeeded: Blastn
[2023-06-08 19:35:24,002] [INFO] Selected 11 target genomes.
[2023-06-08 19:35:24,002] [INFO] Target genome list was writen to GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 19:35:24,113] [INFO] Task started: fastANI
[2023-06-08 19:35:24,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b4a1552-7616-45d2-874f-36b1d4efbc76/GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 19:35:34,295] [INFO] Task succeeded: fastANI
[2023-06-08 19:35:34,308] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 19:35:34,308] [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_001586165.1	s__Hafnia proteus	97.9427	1229	1303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	98.09	96.49	0.93	0.89	5	conclusive
GCF_000735375.1	s__Hafnia alvei	94.5173	1145	1303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	97.59	95.60	0.91	0.87	31	-
GCF_900095695.1	s__Hafnia alvei_B	92.954	1170	1303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001655005.1	s__Hafnia paralvei	84.23	951	1303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	98.49	95.65	0.88	0.84	34	-
GCF_001976145.1	s__Chania oryzae	78.3531	343	1303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania	95.0	98.90	98.79	0.94	0.94	3	-
GCF_014189855.1	s__Buttiauxella sp014189855	78.329	280	1303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Buttiauxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003363015.1	s__Enterobacillus tribolii	78.2853	400	1303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633355.1	s__Serratia_A sp000633355	78.183	362	1303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000496755.2	s__Serratia_A sp000496755	78.1223	184	1303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001267535.1	s__Erwinia iniecta	77.832	256	1303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.95	99.95	0.99	0.99	2	-
GCF_013394855.1	s__Limnobaculum xujianqingii	77.3222	165	1303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Limnobaculum	95.0	98.42	97.65	0.92	0.89	4	-
--------------------------------------------------------------------------------
[2023-06-08 19:35:34,310] [INFO] GTDB search result was written to GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 19:35:34,311] [INFO] ===== GTDB Search completed =====
[2023-06-08 19:35:34,314] [INFO] DFAST_QC result json was written to GCA_947072425.1_ERR5094894_bin.3_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 19:35:34,315] [INFO] DFAST_QC completed!
[2023-06-08 19:35:34,315] [INFO] Total running time: 0h1m8s