[2023-06-13 09:48:25,068] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:48:25,076] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:48:25,076] [INFO] DQC Reference Directory: /var/lib/cwl/stg81e5a8ae-5075-466a-81e6-db07342b2df8/dqc_reference
[2023-06-13 09:48:26,444] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:48:26,445] [INFO] Task started: Prodigal
[2023-06-13 09:48:26,445] [INFO] Running command: gunzip -c /var/lib/cwl/stge3d7412f-d340-49fc-a5b8-0bd6c5139982/GCA_022482285.1_ASM2248228v1_genomic.fna.gz | prodigal -d GCA_022482285.1_ASM2248228v1_genomic.fna/cds.fna -a GCA_022482285.1_ASM2248228v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:48:31,551] [INFO] Task succeeded: Prodigal
[2023-06-13 09:48:31,552] [INFO] Task started: HMMsearch
[2023-06-13 09:48:31,552] [INFO] Running command: hmmsearch --tblout GCA_022482285.1_ASM2248228v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81e5a8ae-5075-466a-81e6-db07342b2df8/dqc_reference/reference_markers.hmm GCA_022482285.1_ASM2248228v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:48:31,745] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:48:31,746] [INFO] Found 6/6 markers.
[2023-06-13 09:48:31,769] [INFO] Query marker FASTA was written to GCA_022482285.1_ASM2248228v1_genomic.fna/markers.fasta
[2023-06-13 09:48:31,769] [INFO] Task started: Blastn
[2023-06-13 09:48:31,769] [INFO] Running command: blastn -query GCA_022482285.1_ASM2248228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81e5a8ae-5075-466a-81e6-db07342b2df8/dqc_reference/reference_markers.fasta -out GCA_022482285.1_ASM2248228v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:48:32,334] [INFO] Task succeeded: Blastn
[2023-06-13 09:48:32,340] [INFO] Selected 14 target genomes.
[2023-06-13 09:48:32,340] [INFO] Target genome list was writen to GCA_022482285.1_ASM2248228v1_genomic.fna/target_genomes.txt
[2023-06-13 09:48:32,342] [INFO] Task started: fastANI
[2023-06-13 09:48:32,342] [INFO] Running command: fastANI --query /var/lib/cwl/stge3d7412f-d340-49fc-a5b8-0bd6c5139982/GCA_022482285.1_ASM2248228v1_genomic.fna.gz --refList GCA_022482285.1_ASM2248228v1_genomic.fna/target_genomes.txt --output GCA_022482285.1_ASM2248228v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 09:48:37,610] [INFO] Task succeeded: fastANI
[2023-06-13 09:48:37,610] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81e5a8ae-5075-466a-81e6-db07342b2df8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 09:48:37,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81e5a8ae-5075-466a-81e6-db07342b2df8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 09:48:37,619] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 09:48:37,619] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 09:48:37,620] [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
Limosilactobacillus oris	strain=DSM 4864	GCA_001434465.1	1632	1632	type	True	95.7294	536	681	95	conclusive
Limosilactobacillus antri	strain=DSM 16041	GCA_000160835.1	227943	227943	type	True	85.9359	509	681	95	below_threshold
Limosilactobacillus antri	strain=DSM 16041	GCA_001435475.1	227943	227943	type	True	85.8508	504	681	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001027985.1	47493	47493	type	True	80.2684	276	681	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001435935.1	47493	47493	type	True	80.2219	269	681	95	below_threshold
Limosilactobacillus pontis	strain=DSM 8475	GCA_001435345.1	35787	35787	type	True	79.8908	190	681	95	below_threshold
Limosilactobacillus urinaemulieris	strain=c9Ua_26_M	GCA_014838745.1	2742600	2742600	type	True	79.6974	107	681	95	below_threshold
Limosilactobacillus secaliphilus	strain=DSM 17896	GCA_001437055.1	396268	396268	type	True	78.4456	102	681	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 09:48:37,621] [INFO] DFAST Taxonomy check result was written to GCA_022482285.1_ASM2248228v1_genomic.fna/tc_result.tsv
[2023-06-13 09:48:37,622] [INFO] ===== Taxonomy check completed =====
[2023-06-13 09:48:37,622] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:48:37,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81e5a8ae-5075-466a-81e6-db07342b2df8/dqc_reference/checkm_data
[2023-06-13 09:48:37,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:48:37,645] [INFO] Task started: CheckM
[2023-06-13 09:48:37,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022482285.1_ASM2248228v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022482285.1_ASM2248228v1_genomic.fna/checkm_input GCA_022482285.1_ASM2248228v1_genomic.fna/checkm_result
[2023-06-13 09:48:59,067] [INFO] Task succeeded: CheckM
[2023-06-13 09:48:59,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 09:48:59,086] [INFO] ===== Completeness check finished =====
[2023-06-13 09:48:59,087] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:48:59,087] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022482285.1_ASM2248228v1_genomic.fna/markers.fasta)
[2023-06-13 09:48:59,087] [INFO] Task started: Blastn
[2023-06-13 09:48:59,088] [INFO] Running command: blastn -query GCA_022482285.1_ASM2248228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81e5a8ae-5075-466a-81e6-db07342b2df8/dqc_reference/reference_markers_gtdb.fasta -out GCA_022482285.1_ASM2248228v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:48:59,837] [INFO] Task succeeded: Blastn
[2023-06-13 09:48:59,841] [INFO] Selected 13 target genomes.
[2023-06-13 09:48:59,842] [INFO] Target genome list was writen to GCA_022482285.1_ASM2248228v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:48:59,844] [INFO] Task started: fastANI
[2023-06-13 09:48:59,844] [INFO] Running command: fastANI --query /var/lib/cwl/stge3d7412f-d340-49fc-a5b8-0bd6c5139982/GCA_022482285.1_ASM2248228v1_genomic.fna.gz --refList GCA_022482285.1_ASM2248228v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022482285.1_ASM2248228v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:49:04,160] [INFO] Task succeeded: fastANI
[2023-06-13 09:49:04,171] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 09:49:04,171] [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_001434465.1	s__Limosilactobacillus oris	95.7294	536	681	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.39	95.80	0.88	0.80	8	conclusive
GCF_000160835.1	s__Limosilactobacillus antri	85.9479	508	681	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.98	99.98	0.99	0.99	3	-
GCA_019117185.1	s__Limosilactobacillus intestinipullorum	80.9082	273	681	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.21	99.14	0.84	0.80	3	-
GCA_902834055.1	s__Limosilactobacillus sp902834055	80.4772	128	681	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214235.1	s__Limosilactobacillus sp905214235	80.3717	277	681	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435935.1	s__Limosilactobacillus panis	80.1958	272	681	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.95	99.95	0.95	0.95	2	-
GCA_019117285.1	s__Limosilactobacillus intestinigallinarum	80.1211	140	681	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.99	99.99	0.94	0.94	2	-
GCF_002940945.1	s__Limosilactobacillus pontis_A	79.8372	170	681	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118405.1	s__Limosilactobacillus gallistercoris	79.225	145	681	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.70	98.67	0.88	0.83	3	-
GCA_002299975.1	s__Limosilactobacillus sp002299975	78.6932	133	681	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.38	99.38	0.84	0.84	2	-
GCF_001437055.1	s__Limosilactobacillus secaliphilus	78.4456	102	681	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 09:49:04,174] [INFO] GTDB search result was written to GCA_022482285.1_ASM2248228v1_genomic.fna/result_gtdb.tsv
[2023-06-13 09:49:04,182] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:49:04,186] [INFO] DFAST_QC result json was written to GCA_022482285.1_ASM2248228v1_genomic.fna/dqc_result.json
[2023-06-13 09:49:04,187] [INFO] DFAST_QC completed!
[2023-06-13 09:49:04,187] [INFO] Total running time: 0h0m39s