[2023-06-13 11:03:43,990] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:03:43,994] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:03:43,995] [INFO] DQC Reference Directory: /var/lib/cwl/stg83b46a3a-7d78-4c24-ac89-4f500c93dad4/dqc_reference
[2023-06-13 11:03:45,238] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:03:45,239] [INFO] Task started: Prodigal
[2023-06-13 11:03:45,240] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a384380-0bbf-4129-811f-baf31d6de422/GCA_022756065.1_ASM2275606v1_genomic.fna.gz | prodigal -d GCA_022756065.1_ASM2275606v1_genomic.fna/cds.fna -a GCA_022756065.1_ASM2275606v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:03:49,387] [INFO] Task succeeded: Prodigal
[2023-06-13 11:03:49,387] [INFO] Task started: HMMsearch
[2023-06-13 11:03:49,387] [INFO] Running command: hmmsearch --tblout GCA_022756065.1_ASM2275606v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83b46a3a-7d78-4c24-ac89-4f500c93dad4/dqc_reference/reference_markers.hmm GCA_022756065.1_ASM2275606v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:03:49,675] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:03:49,676] [INFO] Found 6/6 markers.
[2023-06-13 11:03:49,707] [INFO] Query marker FASTA was written to GCA_022756065.1_ASM2275606v1_genomic.fna/markers.fasta
[2023-06-13 11:03:49,707] [INFO] Task started: Blastn
[2023-06-13 11:03:49,707] [INFO] Running command: blastn -query GCA_022756065.1_ASM2275606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83b46a3a-7d78-4c24-ac89-4f500c93dad4/dqc_reference/reference_markers.fasta -out GCA_022756065.1_ASM2275606v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:03:50,330] [INFO] Task succeeded: Blastn
[2023-06-13 11:03:50,334] [INFO] Selected 13 target genomes.
[2023-06-13 11:03:50,334] [INFO] Target genome list was writen to GCA_022756065.1_ASM2275606v1_genomic.fna/target_genomes.txt
[2023-06-13 11:03:50,335] [INFO] Task started: fastANI
[2023-06-13 11:03:50,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a384380-0bbf-4129-811f-baf31d6de422/GCA_022756065.1_ASM2275606v1_genomic.fna.gz --refList GCA_022756065.1_ASM2275606v1_genomic.fna/target_genomes.txt --output GCA_022756065.1_ASM2275606v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:03:55,328] [INFO] Task succeeded: fastANI
[2023-06-13 11:03:55,329] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83b46a3a-7d78-4c24-ac89-4f500c93dad4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:03:55,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83b46a3a-7d78-4c24-ac89-4f500c93dad4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:03:55,343] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2023-06-13 11:03:55,344] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 11:03:55,344] [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 crispatus	strain=DSM 20584	GCA_001434005.1	47770	47770	type	True	97.7146	496	669	95	conclusive
Lactobacillus crispatus	strain=ATCC 33820	GCA_002088015.1	47770	47770	type	True	97.7138	495	669	95	conclusive
Lactobacillus crispatus	strain=NCK2488	GCA_008694755.1	47770	47770	type	True	97.6397	490	669	95	conclusive
Lactobacillus crispatus	strain=ATCC 33820	GCA_018987235.1	47770	47770	suspected-type	True	97.4989	524	669	95	conclusive
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	81.8828	336	669	95	below_threshold
Lactobacillus acidophilus	strain=ATCC 4356	GCA_000786395.1	1579	1579	type	True	81.8249	330	669	95	below_threshold
Lactobacillus kefiranofaciens	strain=ATCC 43761	GCA_900103655.1	267818	267818	type	True	81.4962	343	669	95	below_threshold
Lactobacillus kefiranofaciens subsp. kefirgranum	strain=DSM 10550	GCA_001434195.1	190906	267818	type	True	81.4292	338	669	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	79.9025	231	669	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	78.4458	99	669	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	78.1491	105	669	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 11:03:55,347] [INFO] DFAST Taxonomy check result was written to GCA_022756065.1_ASM2275606v1_genomic.fna/tc_result.tsv
[2023-06-13 11:03:55,348] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:03:55,348] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:03:55,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83b46a3a-7d78-4c24-ac89-4f500c93dad4/dqc_reference/checkm_data
[2023-06-13 11:03:55,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:03:55,379] [INFO] Task started: CheckM
[2023-06-13 11:03:55,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022756065.1_ASM2275606v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022756065.1_ASM2275606v1_genomic.fna/checkm_input GCA_022756065.1_ASM2275606v1_genomic.fna/checkm_result
[2023-06-13 11:04:15,575] [INFO] Task succeeded: CheckM
[2023-06-13 11:04:15,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 11:04:15,600] [INFO] ===== Completeness check finished =====
[2023-06-13 11:04:15,600] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:04:15,601] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022756065.1_ASM2275606v1_genomic.fna/markers.fasta)
[2023-06-13 11:04:15,601] [INFO] Task started: Blastn
[2023-06-13 11:04:15,601] [INFO] Running command: blastn -query GCA_022756065.1_ASM2275606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83b46a3a-7d78-4c24-ac89-4f500c93dad4/dqc_reference/reference_markers_gtdb.fasta -out GCA_022756065.1_ASM2275606v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:04:16,356] [INFO] Task succeeded: Blastn
[2023-06-13 11:04:16,361] [INFO] Selected 10 target genomes.
[2023-06-13 11:04:16,362] [INFO] Target genome list was writen to GCA_022756065.1_ASM2275606v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:04:16,362] [INFO] Task started: fastANI
[2023-06-13 11:04:16,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a384380-0bbf-4129-811f-baf31d6de422/GCA_022756065.1_ASM2275606v1_genomic.fna.gz --refList GCA_022756065.1_ASM2275606v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022756065.1_ASM2275606v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:04:20,509] [INFO] Task succeeded: fastANI
[2023-06-13 11:04:20,519] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 11:04:20,520] [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_018987235.1	s__Lactobacillus crispatus	97.5108	523	669	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	conclusive
GCF_000615285.1	s__Lactobacillus kitasatonis	82.9325	340	669	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	82.7528	343	669	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_002706375.1	s__Lactobacillus amylovorus	82.626	359	669	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.43	96.81	0.87	0.78	24	-
GCF_000160855.1	s__Lactobacillus helveticus	82.1685	333	669	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_001436305.1	s__Lactobacillus ultunensis	81.861	337	669	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
GCF_001591845.1	s__Lactobacillus acidophilus	81.8174	330	669	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_900103655.1	s__Lactobacillus kefiranofaciens	81.5038	343	669	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.62	99.18	0.95	0.85	9	-
GCF_001436455.1	s__Lactobacillus jensenii	78.0527	124	669	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.86	99.75	0.93	0.88	31	-
GCF_013346935.1	s__Lactobacillus melliventris	77.6899	93	669	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.75	96.46	0.90	0.86	9	-
--------------------------------------------------------------------------------
[2023-06-13 11:04:20,522] [INFO] GTDB search result was written to GCA_022756065.1_ASM2275606v1_genomic.fna/result_gtdb.tsv
[2023-06-13 11:04:20,522] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:04:20,526] [INFO] DFAST_QC result json was written to GCA_022756065.1_ASM2275606v1_genomic.fna/dqc_result.json
[2023-06-13 11:04:20,526] [INFO] DFAST_QC completed!
[2023-06-13 11:04:20,526] [INFO] Total running time: 0h0m37s