[2023-06-08 03:59:55,237] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:59:55,258] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:59:55,258] [INFO] DQC Reference Directory: /var/lib/cwl/stged6c9aef-3099-4942-b2aa-6f2595a5e9cd/dqc_reference
[2023-06-08 03:59:56,673] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:59:56,674] [INFO] Task started: Prodigal
[2023-06-08 03:59:56,674] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e339358-e947-4550-bc79-3f9c7a9d2a7d/GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:59:59,693] [INFO] Task succeeded: Prodigal
[2023-06-08 03:59:59,694] [INFO] Task started: HMMsearch
[2023-06-08 03:59:59,694] [INFO] Running command: hmmsearch --tblout GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged6c9aef-3099-4942-b2aa-6f2595a5e9cd/dqc_reference/reference_markers.hmm GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:59:59,963] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:59:59,964] [INFO] Found 6/6 markers.
[2023-06-08 04:00:00,047] [INFO] Query marker FASTA was written to GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 04:00:00,047] [INFO] Task started: Blastn
[2023-06-08 04:00:00,047] [INFO] Running command: blastn -query GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stged6c9aef-3099-4942-b2aa-6f2595a5e9cd/dqc_reference/reference_markers.fasta -out GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:00:00,724] [INFO] Task succeeded: Blastn
[2023-06-08 04:00:00,728] [INFO] Selected 13 target genomes.
[2023-06-08 04:00:00,728] [INFO] Target genome list was writen to GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 04:00:00,729] [INFO] Task started: fastANI
[2023-06-08 04:00:00,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e339358-e947-4550-bc79-3f9c7a9d2a7d/GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 04:00:05,283] [INFO] Task succeeded: fastANI
[2023-06-08 04:00:05,284] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged6c9aef-3099-4942-b2aa-6f2595a5e9cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 04:00:05,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged6c9aef-3099-4942-b2aa-6f2595a5e9cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 04:00:05,294] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2023-06-08 04:00:05,294] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 04:00:05,294] [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
Lactobacillus johnsonii	strain=ATCC 33200	GCA_001433975.1	33959	33959	type	True	96.3162	422	522	95	conclusive
Lactobacillus johnsonii	strain=ATCC 33200	GCA_000159355.1	33959	33959	type	True	96.2304	432	522	95	conclusive
Lactobacillus taiwanensis	strain=DSM 21401	GCA_001436695.1	508451	508451	type	True	87.7932	421	522	95	below_threshold
Lactobacillus gasseri	strain=ATCC 33323	GCA_008868295.1	1596	1596	type	True	85.6933	380	522	95	below_threshold
Lactobacillus paragasseri	strain=JCM 5343	GCA_003584685.1	2107999	2107999	type	True	85.6899	395	522	95	below_threshold
Lactobacillus paragasseri	strain=JCM 5343	GCA_003307275.1	2107999	2107999	type	True	85.6478	396	522	95	below_threshold
Lactobacillus gasseri	strain=ATCC 33323	GCA_000014425.1	1596	1596	type	True	85.6475	387	522	95	below_threshold
Lactobacillus gasseri	strain=NCTC13722	GCA_900452355.1	1596	1596	type	True	85.6392	388	522	95	below_threshold
Lactobacillus colini	strain=DSM 101872	GCA_017874575.1	1819254	1819254	type	True	79.3846	173	522	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	79.3123	139	522	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 04:00:05,296] [INFO] DFAST Taxonomy check result was written to GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 04:00:05,296] [INFO] ===== Taxonomy check completed =====
[2023-06-08 04:00:05,296] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 04:00:05,296] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged6c9aef-3099-4942-b2aa-6f2595a5e9cd/dqc_reference/checkm_data
[2023-06-08 04:00:05,297] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 04:00:05,322] [INFO] Task started: CheckM
[2023-06-08 04:00:05,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 04:00:22,640] [INFO] Task succeeded: CheckM
[2023-06-08 04:00:22,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 04:00:22,657] [INFO] ===== Completeness check finished =====
[2023-06-08 04:00:22,658] [INFO] ===== Start GTDB Search =====
[2023-06-08 04:00:22,658] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 04:00:22,659] [INFO] Task started: Blastn
[2023-06-08 04:00:22,659] [INFO] Running command: blastn -query GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stged6c9aef-3099-4942-b2aa-6f2595a5e9cd/dqc_reference/reference_markers_gtdb.fasta -out GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:00:23,433] [INFO] Task succeeded: Blastn
[2023-06-08 04:00:23,437] [INFO] Selected 8 target genomes.
[2023-06-08 04:00:23,437] [INFO] Target genome list was writen to GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 04:00:23,438] [INFO] Task started: fastANI
[2023-06-08 04:00:23,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e339358-e947-4550-bc79-3f9c7a9d2a7d/GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 04:00:26,876] [INFO] Task succeeded: fastANI
[2023-06-08 04:00:26,885] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-08 04:00:26,886] [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_000159355.1	s__Lactobacillus johnsonii	96.2304	432	522	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.89	95.28	0.86	0.57	61	inconclusive
GCA_910589175.1	s__Lactobacillus sp910589175	95.536	447	522	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_910589675.1	s__Lactobacillus sp910589675	94.7836	312	522	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.13	0.73	0.71	7	-
GCF_001436695.1	s__Lactobacillus taiwanensis	87.7932	421	522	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.80	98.01	0.90	0.86	31	-
GCF_003584685.1	s__Lactobacillus paragasseri	85.6899	395	522	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.70	97.96	0.91	0.84	40	-
GCF_000014425.1	s__Lactobacillus gasseri	85.6475	387	522	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.12	96.79	0.93	0.86	41	-
GCF_017874575.1	s__Lactobacillus colini	79.3846	173	522	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001436305.1	s__Lactobacillus ultunensis	79.2788	140	522	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
--------------------------------------------------------------------------------
[2023-06-08 04:00:26,888] [INFO] GTDB search result was written to GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 04:00:26,889] [INFO] ===== GTDB Search completed =====
[2023-06-08 04:00:26,904] [INFO] DFAST_QC result json was written to GCA_945910455.1_SRR11489783_bin.71_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 04:00:26,904] [INFO] DFAST_QC completed!
[2023-06-08 04:00:26,904] [INFO] Total running time: 0h0m32s