[2023-06-13 18:27:16,841] [INFO] DFAST_QC pipeline started.
[2023-06-13 18:27:16,842] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 18:27:16,842] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c3f44dd-83c1-44f7-a76e-7301dde812e3/dqc_reference
[2023-06-13 18:27:17,970] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 18:27:17,971] [INFO] Task started: Prodigal
[2023-06-13 18:27:17,971] [INFO] Running command: gunzip -c /var/lib/cwl/stg290bda4c-bc2c-408e-9679-6e956e0ef991/GCA_022486935.1_ASM2248693v1_genomic.fna.gz | prodigal -d GCA_022486935.1_ASM2248693v1_genomic.fna/cds.fna -a GCA_022486935.1_ASM2248693v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 18:27:21,845] [INFO] Task succeeded: Prodigal
[2023-06-13 18:27:21,845] [INFO] Task started: HMMsearch
[2023-06-13 18:27:21,845] [INFO] Running command: hmmsearch --tblout GCA_022486935.1_ASM2248693v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c3f44dd-83c1-44f7-a76e-7301dde812e3/dqc_reference/reference_markers.hmm GCA_022486935.1_ASM2248693v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 18:27:22,000] [INFO] Task succeeded: HMMsearch
[2023-06-13 18:27:22,001] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg290bda4c-bc2c-408e-9679-6e956e0ef991/GCA_022486935.1_ASM2248693v1_genomic.fna.gz]
[2023-06-13 18:27:22,020] [INFO] Query marker FASTA was written to GCA_022486935.1_ASM2248693v1_genomic.fna/markers.fasta
[2023-06-13 18:27:22,020] [INFO] Task started: Blastn
[2023-06-13 18:27:22,020] [INFO] Running command: blastn -query GCA_022486935.1_ASM2248693v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c3f44dd-83c1-44f7-a76e-7301dde812e3/dqc_reference/reference_markers.fasta -out GCA_022486935.1_ASM2248693v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:27:22,583] [INFO] Task succeeded: Blastn
[2023-06-13 18:27:22,586] [INFO] Selected 19 target genomes.
[2023-06-13 18:27:22,587] [INFO] Target genome list was writen to GCA_022486935.1_ASM2248693v1_genomic.fna/target_genomes.txt
[2023-06-13 18:27:22,590] [INFO] Task started: fastANI
[2023-06-13 18:27:22,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg290bda4c-bc2c-408e-9679-6e956e0ef991/GCA_022486935.1_ASM2248693v1_genomic.fna.gz --refList GCA_022486935.1_ASM2248693v1_genomic.fna/target_genomes.txt --output GCA_022486935.1_ASM2248693v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 18:27:34,302] [INFO] Task succeeded: fastANI
[2023-06-13 18:27:34,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c3f44dd-83c1-44f7-a76e-7301dde812e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 18:27:34,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c3f44dd-83c1-44f7-a76e-7301dde812e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 18:27:34,307] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 18:27:34,307] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 18:27:34,307] [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
Lactimicrobium massiliense	strain=Marseille-P4301	GCA_900343155.1	2161814	2161814	type	True	77.0873	67	542	95	below_threshold
Galactobacillus timonensis	strain=Marseille-P4641	GCA_900240265.1	2041840	2041840	type	True	76.7979	58	542	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 18:27:34,309] [INFO] DFAST Taxonomy check result was written to GCA_022486935.1_ASM2248693v1_genomic.fna/tc_result.tsv
[2023-06-13 18:27:34,309] [INFO] ===== Taxonomy check completed =====
[2023-06-13 18:27:34,309] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 18:27:34,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c3f44dd-83c1-44f7-a76e-7301dde812e3/dqc_reference/checkm_data
[2023-06-13 18:27:34,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 18:27:34,330] [INFO] Task started: CheckM
[2023-06-13 18:27:34,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022486935.1_ASM2248693v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022486935.1_ASM2248693v1_genomic.fna/checkm_input GCA_022486935.1_ASM2248693v1_genomic.fna/checkm_result
[2023-06-13 18:27:52,329] [INFO] Task succeeded: CheckM
[2023-06-13 18:27:52,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.65%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 18:27:52,349] [INFO] ===== Completeness check finished =====
[2023-06-13 18:27:52,350] [INFO] ===== Start GTDB Search =====
[2023-06-13 18:27:52,351] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022486935.1_ASM2248693v1_genomic.fna/markers.fasta)
[2023-06-13 18:27:52,351] [INFO] Task started: Blastn
[2023-06-13 18:27:52,351] [INFO] Running command: blastn -query GCA_022486935.1_ASM2248693v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c3f44dd-83c1-44f7-a76e-7301dde812e3/dqc_reference/reference_markers_gtdb.fasta -out GCA_022486935.1_ASM2248693v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:27:53,258] [INFO] Task succeeded: Blastn
[2023-06-13 18:27:53,263] [INFO] Selected 21 target genomes.
[2023-06-13 18:27:53,263] [INFO] Target genome list was writen to GCA_022486935.1_ASM2248693v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 18:27:53,268] [INFO] Task started: fastANI
[2023-06-13 18:27:53,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg290bda4c-bc2c-408e-9679-6e956e0ef991/GCA_022486935.1_ASM2248693v1_genomic.fna.gz --refList GCA_022486935.1_ASM2248693v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022486935.1_ASM2248693v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 18:28:01,013] [INFO] Task succeeded: fastANI
[2023-06-13 18:28:01,022] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 18:28:01,022] [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_009929095.1	s__Bulleidia sp009929095	78.5881	116	542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009696165.1	s__Bulleidia intestinalis	77.912	82	542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	97.55	97.14	0.90	0.85	19	-
GCA_900314345.1	s__Bulleidia sp900314345	77.6471	61	542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	100.00	100.00	0.98	0.98	2	-
GCA_900314905.1	s__Bulleidia sp900314905	77.0929	78	542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	99.98	99.98	0.96	0.96	2	-
GCF_900343155.1	s__Bulleidia massiliensis	77.0873	67	542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.00	97.48	0.85	0.81	18	-
GCA_017543005.1	s__Bulleidia sp017543005	77.0691	59	542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.24	98.24	0.79	0.79	2	-
GCA_017459725.1	s__Bulleidia sp017459725	76.9169	60	542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432325.1	s__Bulleidia sp017432325	76.7959	63	542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017469885.1	s__Bulleidia sp017469885	76.7927	64	542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017420585.1	s__Bulleidia sp017420585	76.7553	60	542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.75	98.73	0.84	0.83	3	-
GCA_015058875.1	s__Bulleidia sp015058875	76.672	69	542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	97.73	97.73	0.82	0.82	2	-
GCA_017433125.1	s__Bulleidia sp017433125	76.6147	64	542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.54	98.45	0.90	0.88	3	-
GCA_902778375.1	s__Bulleidia sp902778375	76.5613	53	542	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	97.02	97.02	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-13 18:28:01,024] [INFO] GTDB search result was written to GCA_022486935.1_ASM2248693v1_genomic.fna/result_gtdb.tsv
[2023-06-13 18:28:01,025] [INFO] ===== GTDB Search completed =====
[2023-06-13 18:28:01,027] [INFO] DFAST_QC result json was written to GCA_022486935.1_ASM2248693v1_genomic.fna/dqc_result.json
[2023-06-13 18:28:01,028] [INFO] DFAST_QC completed!
[2023-06-13 18:28:01,028] [INFO] Total running time: 0h0m44s