[2023-06-13 20:23:36,215] [INFO] DFAST_QC pipeline started.
[2023-06-13 20:23:36,217] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 20:23:36,217] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cd4cc81-8150-4caf-9be6-98d8d13ac99b/dqc_reference
[2023-06-13 20:23:37,396] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 20:23:37,397] [INFO] Task started: Prodigal
[2023-06-13 20:23:37,397] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f30895d-057d-4c0a-8b9d-bd8ec1c8827c/GCA_022755265.1_ASM2275526v1_genomic.fna.gz | prodigal -d GCA_022755265.1_ASM2275526v1_genomic.fna/cds.fna -a GCA_022755265.1_ASM2275526v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 20:23:39,518] [INFO] Task succeeded: Prodigal
[2023-06-13 20:23:39,518] [INFO] Task started: HMMsearch
[2023-06-13 20:23:39,519] [INFO] Running command: hmmsearch --tblout GCA_022755265.1_ASM2275526v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cd4cc81-8150-4caf-9be6-98d8d13ac99b/dqc_reference/reference_markers.hmm GCA_022755265.1_ASM2275526v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 20:23:39,710] [INFO] Task succeeded: HMMsearch
[2023-06-13 20:23:39,712] [INFO] Found 6/6 markers.
[2023-06-13 20:23:39,734] [INFO] Query marker FASTA was written to GCA_022755265.1_ASM2275526v1_genomic.fna/markers.fasta
[2023-06-13 20:23:39,734] [INFO] Task started: Blastn
[2023-06-13 20:23:39,735] [INFO] Running command: blastn -query GCA_022755265.1_ASM2275526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cd4cc81-8150-4caf-9be6-98d8d13ac99b/dqc_reference/reference_markers.fasta -out GCA_022755265.1_ASM2275526v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:23:40,329] [INFO] Task succeeded: Blastn
[2023-06-13 20:23:40,333] [INFO] Selected 20 target genomes.
[2023-06-13 20:23:40,333] [INFO] Target genome list was writen to GCA_022755265.1_ASM2275526v1_genomic.fna/target_genomes.txt
[2023-06-13 20:23:40,334] [INFO] Task started: fastANI
[2023-06-13 20:23:40,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f30895d-057d-4c0a-8b9d-bd8ec1c8827c/GCA_022755265.1_ASM2275526v1_genomic.fna.gz --refList GCA_022755265.1_ASM2275526v1_genomic.fna/target_genomes.txt --output GCA_022755265.1_ASM2275526v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 20:23:45,626] [INFO] Task succeeded: fastANI
[2023-06-13 20:23:45,627] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cd4cc81-8150-4caf-9be6-98d8d13ac99b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 20:23:45,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cd4cc81-8150-4caf-9be6-98d8d13ac99b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 20:23:45,639] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2023-06-13 20:23:45,639] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 20:23:45,639] [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	98.8334	327	361	95	conclusive
Lactobacillus iners	strain=DSM 13335	GCA_001435015.1	147802	147802	type	True	98.7676	319	361	95	conclusive
Lactobacillus gasseri	strain=ATCC 33323	GCA_000014425.1	1596	1596	type	True	78.2476	80	361	95	below_threshold
Lactobacillus paragasseri	strain=JCM 5343	GCA_003584685.1	2107999	2107999	type	True	78.0472	87	361	95	below_threshold
Lactobacillus hominis	strain=DSM 23910	GCA_001436125.1	1203033	1203033	type	True	78.0026	83	361	95	below_threshold
Lactobacillus paragasseri	strain=JCM 5343	GCA_003307275.1	2107999	2107999	type	True	77.9836	91	361	95	below_threshold
Lactobacillus hominis	strain=type strain:CRBIP 24.179	GCA_000296835.1	1203033	1203033	type	True	77.9272	87	361	95	below_threshold
Lactobacillus gallinarum	strain=DSM 10532	GCA_001434975.1	52242	52242	type	True	77.3671	68	361	95	below_threshold
Lactobacillus crispatus	strain=NCK2488	GCA_008694755.1	47770	47770	type	True	77.1606	56	361	95	below_threshold
Lactobacillus crispatus	strain=DSM 20584	GCA_001434005.1	47770	47770	type	True	77.1124	57	361	95	below_threshold
Lactobacillus jensenii	strain=ATCC 25258	GCA_018094625.1	109790	109790	type	True	76.8406	76	361	95	below_threshold
Lactobacillus mulieris	strain=c10Ua161M	GCA_007095465.1	2508708	2508708	type	True	76.7294	69	361	95	below_threshold
Lactobacillus jensenii	strain=DSM 20557	GCA_001436455.1	109790	109790	type	True	76.6966	72	361	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 20:23:45,641] [INFO] DFAST Taxonomy check result was written to GCA_022755265.1_ASM2275526v1_genomic.fna/tc_result.tsv
[2023-06-13 20:23:45,642] [INFO] ===== Taxonomy check completed =====
[2023-06-13 20:23:45,642] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 20:23:45,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cd4cc81-8150-4caf-9be6-98d8d13ac99b/dqc_reference/checkm_data
[2023-06-13 20:23:45,643] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 20:23:45,658] [INFO] Task started: CheckM
[2023-06-13 20:23:45,658] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022755265.1_ASM2275526v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022755265.1_ASM2275526v1_genomic.fna/checkm_input GCA_022755265.1_ASM2275526v1_genomic.fna/checkm_result
[2023-06-13 20:23:59,640] [INFO] Task succeeded: CheckM
[2023-06-13 20:23:59,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 20:23:59,661] [INFO] ===== Completeness check finished =====
[2023-06-13 20:23:59,661] [INFO] ===== Start GTDB Search =====
[2023-06-13 20:23:59,662] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022755265.1_ASM2275526v1_genomic.fna/markers.fasta)
[2023-06-13 20:23:59,662] [INFO] Task started: Blastn
[2023-06-13 20:23:59,662] [INFO] Running command: blastn -query GCA_022755265.1_ASM2275526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cd4cc81-8150-4caf-9be6-98d8d13ac99b/dqc_reference/reference_markers_gtdb.fasta -out GCA_022755265.1_ASM2275526v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:24:00,453] [INFO] Task succeeded: Blastn
[2023-06-13 20:24:00,458] [INFO] Selected 24 target genomes.
[2023-06-13 20:24:00,458] [INFO] Target genome list was writen to GCA_022755265.1_ASM2275526v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 20:24:00,460] [INFO] Task started: fastANI
[2023-06-13 20:24:00,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f30895d-057d-4c0a-8b9d-bd8ec1c8827c/GCA_022755265.1_ASM2275526v1_genomic.fna.gz --refList GCA_022755265.1_ASM2275526v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022755265.1_ASM2275526v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 20:24:07,573] [INFO] Task succeeded: fastANI
[2023-06-13 20:24:07,585] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 20:24:07,585] [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	98.8334	327	361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.75	98.36	0.94	0.90	32	conclusive
GCF_000014425.1	s__Lactobacillus gasseri	78.2476	80	361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.12	96.79	0.93	0.86	41	-
GCF_003584685.1	s__Lactobacillus paragasseri	78.0472	87	361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.70	97.96	0.91	0.84	40	-
GCF_017874575.1	s__Lactobacillus colini	78.0444	66	361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296835.1	s__Lactobacillus hominis	77.966	86	361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.73	99.20	0.96	0.89	4	-
GCA_910589675.1	s__Lactobacillus sp910589675	77.541	85	361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.13	0.73	0.71	7	-
GCF_001434975.1	s__Lactobacillus gallinarum	77.3671	68	361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_004009905.1	s__Lactobacillus xujianguonis	77.2542	52	361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.83	99.82	0.94	0.92	3	-
GCF_001591845.1	s__Lactobacillus acidophilus	77.1684	68	361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_018987235.1	s__Lactobacillus crispatus	77.0681	58	361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	-
GCA_018883635.1	s__Lactobacillus pullistercoris	77.0129	53	361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007095465.1	s__Lactobacillus mulieris	76.7294	69	361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.54	96.91	0.92	0.85	18	-
GCF_001436455.1	s__Lactobacillus jensenii	76.6966	72	361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.86	99.75	0.93	0.88	31	-
--------------------------------------------------------------------------------
[2023-06-13 20:24:07,587] [INFO] GTDB search result was written to GCA_022755265.1_ASM2275526v1_genomic.fna/result_gtdb.tsv
[2023-06-13 20:24:07,588] [INFO] ===== GTDB Search completed =====
[2023-06-13 20:24:07,592] [INFO] DFAST_QC result json was written to GCA_022755265.1_ASM2275526v1_genomic.fna/dqc_result.json
[2023-06-13 20:24:07,592] [INFO] DFAST_QC completed!
[2023-06-13 20:24:07,592] [INFO] Total running time: 0h0m31s