[2023-06-05 00:53:08,191] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:53:08,194] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:53:08,194] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dd24661-bd29-4cff-af0d-ef7cf6803797/dqc_reference
[2023-06-05 00:53:09,411] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:53:09,413] [INFO] Task started: Prodigal
[2023-06-05 00:53:09,413] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d7a7969-4d23-429d-bd7f-f7afa486fd19/GCA_004552585.1_ASM455258v1_genomic.fna.gz | prodigal -d GCA_004552585.1_ASM455258v1_genomic.fna/cds.fna -a GCA_004552585.1_ASM455258v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:53:12,973] [INFO] Task succeeded: Prodigal
[2023-06-05 00:53:12,973] [INFO] Task started: HMMsearch
[2023-06-05 00:53:12,974] [INFO] Running command: hmmsearch --tblout GCA_004552585.1_ASM455258v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dd24661-bd29-4cff-af0d-ef7cf6803797/dqc_reference/reference_markers.hmm GCA_004552585.1_ASM455258v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:53:13,245] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:53:13,246] [INFO] Found 6/6 markers.
[2023-06-05 00:53:13,293] [INFO] Query marker FASTA was written to GCA_004552585.1_ASM455258v1_genomic.fna/markers.fasta
[2023-06-05 00:53:13,293] [INFO] Task started: Blastn
[2023-06-05 00:53:13,294] [INFO] Running command: blastn -query GCA_004552585.1_ASM455258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dd24661-bd29-4cff-af0d-ef7cf6803797/dqc_reference/reference_markers.fasta -out GCA_004552585.1_ASM455258v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:53:14,026] [INFO] Task succeeded: Blastn
[2023-06-05 00:53:14,038] [INFO] Selected 11 target genomes.
[2023-06-05 00:53:14,039] [INFO] Target genome list was writen to GCA_004552585.1_ASM455258v1_genomic.fna/target_genomes.txt
[2023-06-05 00:53:14,061] [INFO] Task started: fastANI
[2023-06-05 00:53:14,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d7a7969-4d23-429d-bd7f-f7afa486fd19/GCA_004552585.1_ASM455258v1_genomic.fna.gz --refList GCA_004552585.1_ASM455258v1_genomic.fna/target_genomes.txt --output GCA_004552585.1_ASM455258v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:53:18,516] [INFO] Task succeeded: fastANI
[2023-06-05 00:53:18,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dd24661-bd29-4cff-af0d-ef7cf6803797/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:53:18,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dd24661-bd29-4cff-af0d-ef7cf6803797/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:53:18,526] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2023-06-05 00:53:18,526] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 00:53:18,526] [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 amylovorus	strain=DSM 20531	GCA_001433985.1	1604	1604	type	True	97.4189	432	532	95	conclusive
Lactobacillus amylovorus	strain=DSM 20531	GCA_002706375.1	1604	1604	type	True	97.3478	451	532	95	conclusive
Lactobacillus kitasatonis	strain=DSM 16761	GCA_001434435.1	237446	237446	type	True	92.4512	416	532	95	below_threshold
Lactobacillus kitasatonis	strain=JCM 1039	GCA_000615285.1	237446	237446	type	True	92.3067	419	532	95	below_threshold
Lactobacillus gallinarum	strain=DSM 10532	GCA_001434975.1	52242	52242	type	True	85.7524	348	532	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	84.2244	341	532	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	80.3673	218	532	95	below_threshold
Lactobacillus laiwuensis	strain=F551-2	GCA_019972835.1	2841034	2841034	type	True	77.6259	93	532	95	below_threshold
Lactobacillus huangpiensis	strain=F306-1	GCA_019972815.1	2799571	2799571	type	True	77.5998	83	532	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 00:53:18,532] [INFO] DFAST Taxonomy check result was written to GCA_004552585.1_ASM455258v1_genomic.fna/tc_result.tsv
[2023-06-05 00:53:18,533] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:53:18,533] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:53:18,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dd24661-bd29-4cff-af0d-ef7cf6803797/dqc_reference/checkm_data
[2023-06-05 00:53:18,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:53:18,558] [INFO] Task started: CheckM
[2023-06-05 00:53:18,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004552585.1_ASM455258v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004552585.1_ASM455258v1_genomic.fna/checkm_input GCA_004552585.1_ASM455258v1_genomic.fna/checkm_result
[2023-06-05 00:53:37,781] [INFO] Task succeeded: CheckM
[2023-06-05 00:53:37,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.25%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:53:37,806] [INFO] ===== Completeness check finished =====
[2023-06-05 00:53:37,806] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:53:37,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004552585.1_ASM455258v1_genomic.fna/markers.fasta)
[2023-06-05 00:53:37,807] [INFO] Task started: Blastn
[2023-06-05 00:53:37,808] [INFO] Running command: blastn -query GCA_004552585.1_ASM455258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dd24661-bd29-4cff-af0d-ef7cf6803797/dqc_reference/reference_markers_gtdb.fasta -out GCA_004552585.1_ASM455258v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:53:38,719] [INFO] Task succeeded: Blastn
[2023-06-05 00:53:38,723] [INFO] Selected 11 target genomes.
[2023-06-05 00:53:38,724] [INFO] Target genome list was writen to GCA_004552585.1_ASM455258v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:53:38,799] [INFO] Task started: fastANI
[2023-06-05 00:53:38,799] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d7a7969-4d23-429d-bd7f-f7afa486fd19/GCA_004552585.1_ASM455258v1_genomic.fna.gz --refList GCA_004552585.1_ASM455258v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004552585.1_ASM455258v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:53:43,371] [INFO] Task succeeded: fastANI
[2023-06-05 00:53:43,382] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:53:43,382] [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_002706375.1	s__Lactobacillus amylovorus	97.3478	451	532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.43	96.81	0.87	0.78	24	conclusive
GCF_000615285.1	s__Lactobacillus kitasatonis	92.2648	420	532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	-
GCF_001434975.1	s__Lactobacillus gallinarum	85.7094	350	532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_001436305.1	s__Lactobacillus ultunensis	84.209	342	532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
GCF_000160855.1	s__Lactobacillus helveticus	83.6202	334	532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_001591845.1	s__Lactobacillus acidophilus	83.0913	358	532	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	82.7755	325	532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	-
GCF_000178475.1	s__Lactobacillus amylolyticus	81.2615	202	532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.45	98.00	0.96	0.87	8	-
GCF_000615445.1	s__Lactobacillus hamsteri	80.9484	226	532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_004009905.1	s__Lactobacillus xujianguonis	80.8953	220	532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.83	99.82	0.94	0.92	3	-
GCF_001434335.1	s__Lactobacillus kalixensis	80.6457	227	532	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 00:53:43,384] [INFO] GTDB search result was written to GCA_004552585.1_ASM455258v1_genomic.fna/result_gtdb.tsv
[2023-06-05 00:53:43,385] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:53:43,407] [INFO] DFAST_QC result json was written to GCA_004552585.1_ASM455258v1_genomic.fna/dqc_result.json
[2023-06-05 00:53:43,408] [INFO] DFAST_QC completed!
[2023-06-05 00:53:43,408] [INFO] Total running time: 0h0m35s