[2024-01-25 17:52:20,512] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:52:20,514] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:52:20,514] [INFO] DQC Reference Directory: /var/lib/cwl/stg0724cb10-0252-4d89-a4eb-67d257a642e2/dqc_reference
[2024-01-25 17:52:21,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:52:21,643] [INFO] Task started: Prodigal
[2024-01-25 17:52:21,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ad4794b-a111-46be-8125-435d6caac5d2/GCF_000735375.1_GHAL_DRAFTv1_genomic.fna.gz | prodigal -d GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/cds.fna -a GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:52:32,187] [INFO] Task succeeded: Prodigal
[2024-01-25 17:52:32,188] [INFO] Task started: HMMsearch
[2024-01-25 17:52:32,188] [INFO] Running command: hmmsearch --tblout GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0724cb10-0252-4d89-a4eb-67d257a642e2/dqc_reference/reference_markers.hmm GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:52:32,443] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:52:32,444] [INFO] Found 6/6 markers.
[2024-01-25 17:52:32,484] [INFO] Query marker FASTA was written to GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/markers.fasta
[2024-01-25 17:52:32,484] [INFO] Task started: Blastn
[2024-01-25 17:52:32,484] [INFO] Running command: blastn -query GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0724cb10-0252-4d89-a4eb-67d257a642e2/dqc_reference/reference_markers.fasta -out GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:33,252] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:33,255] [INFO] Selected 15 target genomes.
[2024-01-25 17:52:33,256] [INFO] Target genome list was writen to GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/target_genomes.txt
[2024-01-25 17:52:33,266] [INFO] Task started: fastANI
[2024-01-25 17:52:33,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ad4794b-a111-46be-8125-435d6caac5d2/GCF_000735375.1_GHAL_DRAFTv1_genomic.fna.gz --refList GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/target_genomes.txt --output GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:45,235] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:45,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0724cb10-0252-4d89-a4eb-67d257a642e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:45,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0724cb10-0252-4d89-a4eb-67d257a642e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:45,243] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:52:45,244] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:52:45,244] [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
Hafnia alvei	strain=ATCC 13337	GCA_000735375.1	569	569	type	True	100.0	1542	1551	95	conclusive
Hafnia alvei	strain=ATCC 13337	GCA_003668715.1	569	569	type	True	99.994	1543	1551	95	conclusive
Obesumbacterium proteus	strain=DSM 2777	GCA_001586165.1	82983	82983	type	True	94.3159	1315	1551	95	below_threshold
Obesumbacterium proteus	strain=ATCC 12841	GCA_001655035.1	82983	82983	type	True	94.2187	1299	1551	95	below_threshold
Hafnia paralvei	strain=ATCC 29927	GCA_001655005.1	546367	546367	type	True	84.2981	1077	1551	95	below_threshold
Hafnia paralvei	strain=ATCC 29927	GCA_023698525.1	546367	546367	type	True	84.1364	1086	1551	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.8091	338	1551	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.6069	357	1551	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	78.5804	304	1551	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.5629	341	1551	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:52:45,245] [INFO] DFAST Taxonomy check result was written to GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/tc_result.tsv
[2024-01-25 17:52:45,246] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:45,246] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:45,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0724cb10-0252-4d89-a4eb-67d257a642e2/dqc_reference/checkm_data
[2024-01-25 17:52:45,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:45,302] [INFO] Task started: CheckM
[2024-01-25 17:52:45,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/checkm_input GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/checkm_result
[2024-01-25 17:53:19,786] [INFO] Task succeeded: CheckM
[2024-01-25 17:53:19,787] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:53:19,807] [INFO] ===== Completeness check finished =====
[2024-01-25 17:53:19,807] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:53:19,808] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/markers.fasta)
[2024-01-25 17:53:19,809] [INFO] Task started: Blastn
[2024-01-25 17:53:19,809] [INFO] Running command: blastn -query GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0724cb10-0252-4d89-a4eb-67d257a642e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:20,904] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:20,907] [INFO] Selected 15 target genomes.
[2024-01-25 17:53:20,907] [INFO] Target genome list was writen to GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:53:20,920] [INFO] Task started: fastANI
[2024-01-25 17:53:20,920] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ad4794b-a111-46be-8125-435d6caac5d2/GCF_000735375.1_GHAL_DRAFTv1_genomic.fna.gz --refList GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/target_genomes_gtdb.txt --output GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:53:34,746] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:34,754] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:53:34,754] [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_000735375.1	s__Hafnia alvei	100.0	1542	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	97.59	95.60	0.91	0.87	31	conclusive
GCF_001586165.1	s__Hafnia proteus	94.3159	1315	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	98.09	96.49	0.93	0.89	5	-
GCF_900095695.1	s__Hafnia alvei_B	92.9723	1305	1551	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	84.3033	1076	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Hafnia	95.0	98.49	95.65	0.88	0.84	34	-
GCF_015644585.1	s__Rahnella laticis	78.9053	344	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	96.65	95.20	0.90	0.83	8	-
GCF_000341505.1	s__Edwardsiella tarda	78.7033	288	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.01	97.25	0.94	0.84	19	-
GCF_000633355.1	s__Serratia_A sp000633355	78.653	388	1551	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_014189855.1	s__Buttiauxella sp014189855	78.5688	341	1551	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	78.5682	427	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900094795.1	s__Kosakonia oryziphila	78.4915	251	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000951135.1	s__Rouxiella chamberiensis	78.327	262	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rouxiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001267535.1	s__Erwinia iniecta	78.1588	283	1551	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	99.95	99.95	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:53:34,756] [INFO] GTDB search result was written to GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:53:34,757] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:53:34,759] [INFO] DFAST_QC result json was written to GCF_000735375.1_GHAL_DRAFTv1_genomic.fna/dqc_result.json
[2024-01-25 17:53:34,759] [INFO] DFAST_QC completed!
[2024-01-25 17:53:34,759] [INFO] Total running time: 0h1m14s