[2023-06-13 21:20:19,737] [INFO] DFAST_QC pipeline started.
[2023-06-13 21:20:19,739] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 21:20:19,739] [INFO] DQC Reference Directory: /var/lib/cwl/stg2fd86d1f-7b27-41fa-b701-d24873ce6bf2/dqc_reference
[2023-06-13 21:20:21,746] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 21:20:21,747] [INFO] Task started: Prodigal
[2023-06-13 21:20:21,747] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ec24c3c-fd4d-4718-81d8-f960e20c8f0d/GCA_022756445.1_ASM2275644v1_genomic.fna.gz | prodigal -d GCA_022756445.1_ASM2275644v1_genomic.fna/cds.fna -a GCA_022756445.1_ASM2275644v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 21:20:23,232] [INFO] Task succeeded: Prodigal
[2023-06-13 21:20:23,232] [INFO] Task started: HMMsearch
[2023-06-13 21:20:23,233] [INFO] Running command: hmmsearch --tblout GCA_022756445.1_ASM2275644v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2fd86d1f-7b27-41fa-b701-d24873ce6bf2/dqc_reference/reference_markers.hmm GCA_022756445.1_ASM2275644v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 21:20:23,475] [INFO] Task succeeded: HMMsearch
[2023-06-13 21:20:23,476] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2ec24c3c-fd4d-4718-81d8-f960e20c8f0d/GCA_022756445.1_ASM2275644v1_genomic.fna.gz]
[2023-06-13 21:20:23,489] [INFO] Query marker FASTA was written to GCA_022756445.1_ASM2275644v1_genomic.fna/markers.fasta
[2023-06-13 21:20:23,489] [INFO] Task started: Blastn
[2023-06-13 21:20:23,489] [INFO] Running command: blastn -query GCA_022756445.1_ASM2275644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fd86d1f-7b27-41fa-b701-d24873ce6bf2/dqc_reference/reference_markers.fasta -out GCA_022756445.1_ASM2275644v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:20:26,181] [INFO] Task succeeded: Blastn
[2023-06-13 21:20:26,184] [INFO] Selected 15 target genomes.
[2023-06-13 21:20:26,185] [INFO] Target genome list was writen to GCA_022756445.1_ASM2275644v1_genomic.fna/target_genomes.txt
[2023-06-13 21:20:26,185] [INFO] Task started: fastANI
[2023-06-13 21:20:26,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ec24c3c-fd4d-4718-81d8-f960e20c8f0d/GCA_022756445.1_ASM2275644v1_genomic.fna.gz --refList GCA_022756445.1_ASM2275644v1_genomic.fna/target_genomes.txt --output GCA_022756445.1_ASM2275644v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 21:20:29,904] [INFO] Task succeeded: fastANI
[2023-06-13 21:20:29,905] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2fd86d1f-7b27-41fa-b701-d24873ce6bf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 21:20:29,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2fd86d1f-7b27-41fa-b701-d24873ce6bf2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 21:20:29,915] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2023-06-13 21:20:29,915] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-13 21:20:29,915] [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 iners	strain=DSM 13335	GCA_000160875.1	147802	147802	type	True	96.8382	145	266	95	inconclusive
Lactobacillus iners	strain=DSM 13335	GCA_001435015.1	147802	147802	type	True	96.7887	137	266	95	inconclusive
Lactobacillus jensenii	strain=DSM 20557	GCA_001436455.1	109790	109790	type	True	95.9545	123	266	95	inconclusive
Lactobacillus jensenii	strain=ATCC 25258	GCA_018094625.1	109790	109790	type	True	95.7535	125	266	95	inconclusive
Lactobacillus mulieris	strain=c10Ua161M	GCA_007095465.1	2508708	2508708	type	True	85.7244	109	266	95	below_threshold
Lactobacillus psittaci	strain=DSM 15354	GCA_001435695.1	116089	116089	type	True	84.418	75	266	95	below_threshold
Lactobacillus psittaci	strain=DSM 15354	GCA_000425905.1	116089	116089	type	True	83.8632	77	266	95	below_threshold
Lactobacillus gallinarum	strain=DSM 10532	GCA_001434975.1	52242	52242	type	True	78.3842	50	266	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	78.278	53	266	95	below_threshold
Lactobacillus hamsteri	strain=DSM 5661	GCA_001434515.1	96565	96565	type	True	77.7979	57	266	95	below_threshold
Lactobacillus hamsteri	strain=JCM 6256	GCA_000615445.1	96565	96565	type	True	77.6984	58	266	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 21:20:29,917] [INFO] DFAST Taxonomy check result was written to GCA_022756445.1_ASM2275644v1_genomic.fna/tc_result.tsv
[2023-06-13 21:20:29,918] [INFO] ===== Taxonomy check completed =====
[2023-06-13 21:20:29,918] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 21:20:29,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2fd86d1f-7b27-41fa-b701-d24873ce6bf2/dqc_reference/checkm_data
[2023-06-13 21:20:29,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 21:20:29,931] [INFO] Task started: CheckM
[2023-06-13 21:20:29,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022756445.1_ASM2275644v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022756445.1_ASM2275644v1_genomic.fna/checkm_input GCA_022756445.1_ASM2275644v1_genomic.fna/checkm_result
[2023-06-13 21:20:42,863] [INFO] Task succeeded: CheckM
[2023-06-13 21:20:42,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 21:20:42,884] [INFO] ===== Completeness check finished =====
[2023-06-13 21:20:42,885] [INFO] ===== Start GTDB Search =====
[2023-06-13 21:20:42,885] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022756445.1_ASM2275644v1_genomic.fna/markers.fasta)
[2023-06-13 21:20:42,885] [INFO] Task started: Blastn
[2023-06-13 21:20:42,885] [INFO] Running command: blastn -query GCA_022756445.1_ASM2275644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fd86d1f-7b27-41fa-b701-d24873ce6bf2/dqc_reference/reference_markers_gtdb.fasta -out GCA_022756445.1_ASM2275644v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:20:43,333] [INFO] Task succeeded: Blastn
[2023-06-13 21:20:43,338] [INFO] Selected 12 target genomes.
[2023-06-13 21:20:43,338] [INFO] Target genome list was writen to GCA_022756445.1_ASM2275644v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 21:20:43,340] [INFO] Task started: fastANI
[2023-06-13 21:20:43,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ec24c3c-fd4d-4718-81d8-f960e20c8f0d/GCA_022756445.1_ASM2275644v1_genomic.fna.gz --refList GCA_022756445.1_ASM2275644v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022756445.1_ASM2275644v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 21:20:46,742] [INFO] Task succeeded: fastANI
[2023-06-13 21:20:46,750] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-13 21:20:46,750] [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_000160875.1	s__Lactobacillus iners	96.8382	145	266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.75	98.36	0.94	0.90	32	inconclusive
GCF_001436455.1	s__Lactobacillus jensenii	95.9545	123	266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.86	99.75	0.93	0.88	31	inconclusive
GCF_007095465.1	s__Lactobacillus mulieris	85.7739	108	266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.54	96.91	0.92	0.85	18	-
GCF_000425905.1	s__Lactobacillus psittaci	83.8632	77	266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.95	99.95	0.99	0.99	2	-
GCF_001434975.1	s__Lactobacillus gallinarum	78.3842	50	266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_000615445.1	s__Lactobacillus hamsteri	77.6984	58	266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_007570935.1	s__Lactobacillus sp007570935	77.608	55	266	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 21:20:46,752] [INFO] GTDB search result was written to GCA_022756445.1_ASM2275644v1_genomic.fna/result_gtdb.tsv
[2023-06-13 21:20:46,753] [INFO] ===== GTDB Search completed =====
[2023-06-13 21:20:46,756] [INFO] DFAST_QC result json was written to GCA_022756445.1_ASM2275644v1_genomic.fna/dqc_result.json
[2023-06-13 21:20:46,756] [INFO] DFAST_QC completed!
[2023-06-13 21:20:46,756] [INFO] Total running time: 0h0m27s