[2023-06-13 01:53:52,963] [INFO] DFAST_QC pipeline started.
[2023-06-13 01:53:52,970] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 01:53:52,971] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d0bd63e-57cf-4966-9998-ac57dd1f77e6/dqc_reference
[2023-06-13 01:53:54,346] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 01:53:54,347] [INFO] Task started: Prodigal
[2023-06-13 01:53:54,347] [INFO] Running command: gunzip -c /var/lib/cwl/stg8294aaf6-fe89-4a2e-909d-168f7d9a959c/GCA_022483045.1_ASM2248304v1_genomic.fna.gz | prodigal -d GCA_022483045.1_ASM2248304v1_genomic.fna/cds.fna -a GCA_022483045.1_ASM2248304v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 01:54:01,476] [INFO] Task succeeded: Prodigal
[2023-06-13 01:54:01,477] [INFO] Task started: HMMsearch
[2023-06-13 01:54:01,477] [INFO] Running command: hmmsearch --tblout GCA_022483045.1_ASM2248304v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d0bd63e-57cf-4966-9998-ac57dd1f77e6/dqc_reference/reference_markers.hmm GCA_022483045.1_ASM2248304v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 01:54:01,758] [INFO] Task succeeded: HMMsearch
[2023-06-13 01:54:01,759] [INFO] Found 6/6 markers.
[2023-06-13 01:54:01,794] [INFO] Query marker FASTA was written to GCA_022483045.1_ASM2248304v1_genomic.fna/markers.fasta
[2023-06-13 01:54:01,794] [INFO] Task started: Blastn
[2023-06-13 01:54:01,794] [INFO] Running command: blastn -query GCA_022483045.1_ASM2248304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d0bd63e-57cf-4966-9998-ac57dd1f77e6/dqc_reference/reference_markers.fasta -out GCA_022483045.1_ASM2248304v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:54:02,489] [INFO] Task succeeded: Blastn
[2023-06-13 01:54:02,493] [INFO] Selected 16 target genomes.
[2023-06-13 01:54:02,493] [INFO] Target genome list was writen to GCA_022483045.1_ASM2248304v1_genomic.fna/target_genomes.txt
[2023-06-13 01:54:02,496] [INFO] Task started: fastANI
[2023-06-13 01:54:02,496] [INFO] Running command: fastANI --query /var/lib/cwl/stg8294aaf6-fe89-4a2e-909d-168f7d9a959c/GCA_022483045.1_ASM2248304v1_genomic.fna.gz --refList GCA_022483045.1_ASM2248304v1_genomic.fna/target_genomes.txt --output GCA_022483045.1_ASM2248304v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 01:54:14,052] [INFO] Task succeeded: fastANI
[2023-06-13 01:54:14,052] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d0bd63e-57cf-4966-9998-ac57dd1f77e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 01:54:14,053] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d0bd63e-57cf-4966-9998-ac57dd1f77e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 01:54:14,060] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 01:54:14,060] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 01:54:14,061] [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
Caproicibacterium lactatifermentans	strain=LBM19010	GCA_013315815.1	2666138	2666138	type	True	79.6542	295	821	95	below_threshold
Caproicibacter fermentans	strain=EA1	GCA_009746625.1	2576756	2576756	type	True	78.8052	62	821	95	below_threshold
Caproicibacterium amylolyticum	strain=LBM18003	GCA_014467055.1	2766537	2766537	type	True	78.8016	237	821	95	below_threshold
Anaeromassilibacillus senegalensis	strain=mt9	GCA_001261775.1	1673717	1673717	type	True	77.0239	57	821	95	below_threshold
Clostridium jeddahense	strain=JCD	GCA_000577335.1	1414721	1414721	type	True	76.2028	52	821	95	below_threshold
Hydrogeniiclostridium mannosilyticum	strain=ASD2818	GCA_003268275.1	2764322	2764322	type	True	76.1568	51	821	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 01:54:14,070] [INFO] DFAST Taxonomy check result was written to GCA_022483045.1_ASM2248304v1_genomic.fna/tc_result.tsv
[2023-06-13 01:54:14,071] [INFO] ===== Taxonomy check completed =====
[2023-06-13 01:54:14,072] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 01:54:14,072] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d0bd63e-57cf-4966-9998-ac57dd1f77e6/dqc_reference/checkm_data
[2023-06-13 01:54:14,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 01:54:14,145] [INFO] Task started: CheckM
[2023-06-13 01:54:14,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022483045.1_ASM2248304v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022483045.1_ASM2248304v1_genomic.fna/checkm_input GCA_022483045.1_ASM2248304v1_genomic.fna/checkm_result
[2023-06-13 01:54:41,954] [INFO] Task succeeded: CheckM
[2023-06-13 01:54:41,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 01:54:41,980] [INFO] ===== Completeness check finished =====
[2023-06-13 01:54:41,980] [INFO] ===== Start GTDB Search =====
[2023-06-13 01:54:41,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022483045.1_ASM2248304v1_genomic.fna/markers.fasta)
[2023-06-13 01:54:41,980] [INFO] Task started: Blastn
[2023-06-13 01:54:41,981] [INFO] Running command: blastn -query GCA_022483045.1_ASM2248304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d0bd63e-57cf-4966-9998-ac57dd1f77e6/dqc_reference/reference_markers_gtdb.fasta -out GCA_022483045.1_ASM2248304v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:54:43,070] [INFO] Task succeeded: Blastn
[2023-06-13 01:54:43,074] [INFO] Selected 22 target genomes.
[2023-06-13 01:54:43,074] [INFO] Target genome list was writen to GCA_022483045.1_ASM2248304v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 01:54:43,086] [INFO] Task started: fastANI
[2023-06-13 01:54:43,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg8294aaf6-fe89-4a2e-909d-168f7d9a959c/GCA_022483045.1_ASM2248304v1_genomic.fna.gz --refList GCA_022483045.1_ASM2248304v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022483045.1_ASM2248304v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 01:54:51,658] [INFO] Task succeeded: fastANI
[2023-06-13 01:54:51,678] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 01:54:51,678] [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
GCA_002119605.1	s__Caproicibacterium sp002119605	79.3838	293	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacterium	95.0	99.88	99.69	0.99	0.94	26	-
GCF_014467055.1	s__Caproicibacterium amylolyticum	78.6789	236	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacterium	95.0	98.85	98.85	0.89	0.89	2	-
GCA_900184925.1	s__Caproicibacter sp900184925	78.4885	63	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000752215.1	s__Caproiciproducens sp000752215	78.3112	70	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	98.70	97.09	0.94	0.88	5	-
GCA_002399445.1	s__Caproicibacterium sp002399445	77.5094	131	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacterium	95.0	99.23	98.41	0.93	0.89	8	-
GCA_900554535.1	s__Caproicibacterium sp900554535	76.9468	77	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacterium	95.0	99.83	99.83	0.87	0.87	2	-
GCF_000577335.1	s__Clostridium_E jeddahense	76.2028	52	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Clostridium_E	95.0	97.87	96.05	0.91	0.86	8	-
GCF_003268275.1	s__Hydrogeniiclostridium mannosilyticum	76.1568	51	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Hydrogeniiclostridium	95.0	99.29	98.81	0.93	0.88	5	-
GCA_012839345.1	s__Caproiciproducens sp012839345	76.0308	54	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	99.55	99.55	0.92	0.92	2	-
GCA_900546895.1	s__Caproiciproducens sp900546895	75.9764	52	821	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 01:54:51,681] [INFO] GTDB search result was written to GCA_022483045.1_ASM2248304v1_genomic.fna/result_gtdb.tsv
[2023-06-13 01:54:51,683] [INFO] ===== GTDB Search completed =====
[2023-06-13 01:54:51,686] [INFO] DFAST_QC result json was written to GCA_022483045.1_ASM2248304v1_genomic.fna/dqc_result.json
[2023-06-13 01:54:51,686] [INFO] DFAST_QC completed!
[2023-06-13 01:54:51,686] [INFO] Total running time: 0h0m59s