[2023-06-13 02:47:54,501] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:47:54,510] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:47:54,510] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9e5128c-df1d-4c1e-b7a8-952e112d5274/dqc_reference
[2023-06-13 02:47:55,913] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:47:55,914] [INFO] Task started: Prodigal
[2023-06-13 02:47:55,914] [INFO] Running command: gunzip -c /var/lib/cwl/stga9a41a9c-e197-46e5-ac02-e587268a78fa/GCA_022754875.1_ASM2275487v1_genomic.fna.gz | prodigal -d GCA_022754875.1_ASM2275487v1_genomic.fna/cds.fna -a GCA_022754875.1_ASM2275487v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:47:57,822] [INFO] Task succeeded: Prodigal
[2023-06-13 02:47:57,822] [INFO] Task started: HMMsearch
[2023-06-13 02:47:57,822] [INFO] Running command: hmmsearch --tblout GCA_022754875.1_ASM2275487v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9e5128c-df1d-4c1e-b7a8-952e112d5274/dqc_reference/reference_markers.hmm GCA_022754875.1_ASM2275487v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:47:58,120] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:47:58,127] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga9a41a9c-e197-46e5-ac02-e587268a78fa/GCA_022754875.1_ASM2275487v1_genomic.fna.gz]
[2023-06-13 02:47:58,153] [INFO] Query marker FASTA was written to GCA_022754875.1_ASM2275487v1_genomic.fna/markers.fasta
[2023-06-13 02:47:58,153] [INFO] Task started: Blastn
[2023-06-13 02:47:58,153] [INFO] Running command: blastn -query GCA_022754875.1_ASM2275487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9e5128c-df1d-4c1e-b7a8-952e112d5274/dqc_reference/reference_markers.fasta -out GCA_022754875.1_ASM2275487v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:47:58,966] [INFO] Task succeeded: Blastn
[2023-06-13 02:47:58,970] [INFO] Selected 19 target genomes.
[2023-06-13 02:47:58,970] [INFO] Target genome list was writen to GCA_022754875.1_ASM2275487v1_genomic.fna/target_genomes.txt
[2023-06-13 02:47:58,971] [INFO] Task started: fastANI
[2023-06-13 02:47:58,971] [INFO] Running command: fastANI --query /var/lib/cwl/stga9a41a9c-e197-46e5-ac02-e587268a78fa/GCA_022754875.1_ASM2275487v1_genomic.fna.gz --refList GCA_022754875.1_ASM2275487v1_genomic.fna/target_genomes.txt --output GCA_022754875.1_ASM2275487v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:48:04,795] [INFO] Task succeeded: fastANI
[2023-06-13 02:48:04,795] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9e5128c-df1d-4c1e-b7a8-952e112d5274/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:48:04,795] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9e5128c-df1d-4c1e-b7a8-952e112d5274/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:48:04,806] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2023-06-13 02:48:04,807] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 02:48:04,807] [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_001435015.1	147802	147802	type	True	98.816	306	336	95	conclusive
Lactobacillus iners	strain=DSM 13335	GCA_000160875.1	147802	147802	type	True	98.7387	311	336	95	conclusive
Lactobacillus paragasseri	strain=JCM 5343	GCA_003584685.1	2107999	2107999	type	True	78.2766	82	336	95	below_threshold
Lactobacillus paragasseri	strain=JCM 5343	GCA_003307275.1	2107999	2107999	type	True	78.1351	82	336	95	below_threshold
Lactobacillus hominis	strain=type strain:CRBIP 24.179	GCA_000296835.1	1203033	1203033	type	True	78.05	71	336	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	78.0427	75	336	95	below_threshold
Lactobacillus hominis	strain=DSM 23910	GCA_001436125.1	1203033	1203033	type	True	78.0071	73	336	95	below_threshold
Lactobacillus gasseri	strain=ATCC 33323	GCA_000014425.1	1596	1596	type	True	77.8904	78	336	95	below_threshold
Lactobacillus crispatus	strain=DSM 20584	GCA_001434005.1	47770	47770	type	True	77.1743	52	336	95	below_threshold
Lactobacillus crispatus	strain=NCK2488	GCA_008694755.1	47770	47770	type	True	77.1575	51	336	95	below_threshold
Lactobacillus gallinarum	strain=DSM 10532	GCA_001434975.1	52242	52242	type	True	77.1432	64	336	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 02:48:04,809] [INFO] DFAST Taxonomy check result was written to GCA_022754875.1_ASM2275487v1_genomic.fna/tc_result.tsv
[2023-06-13 02:48:04,809] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:48:04,810] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:48:04,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9e5128c-df1d-4c1e-b7a8-952e112d5274/dqc_reference/checkm_data
[2023-06-13 02:48:04,811] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:48:04,844] [INFO] Task started: CheckM
[2023-06-13 02:48:04,844] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022754875.1_ASM2275487v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022754875.1_ASM2275487v1_genomic.fna/checkm_input GCA_022754875.1_ASM2275487v1_genomic.fna/checkm_result
[2023-06-13 02:48:19,423] [INFO] Task succeeded: CheckM
[2023-06-13 02:48:19,427] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 02:48:19,464] [INFO] ===== Completeness check finished =====
[2023-06-13 02:48:19,465] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:48:19,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022754875.1_ASM2275487v1_genomic.fna/markers.fasta)
[2023-06-13 02:48:19,465] [INFO] Task started: Blastn
[2023-06-13 02:48:19,466] [INFO] Running command: blastn -query GCA_022754875.1_ASM2275487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9e5128c-df1d-4c1e-b7a8-952e112d5274/dqc_reference/reference_markers_gtdb.fasta -out GCA_022754875.1_ASM2275487v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:48:20,186] [INFO] Task succeeded: Blastn
[2023-06-13 02:48:20,192] [INFO] Selected 19 target genomes.
[2023-06-13 02:48:20,192] [INFO] Target genome list was writen to GCA_022754875.1_ASM2275487v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:48:20,193] [INFO] Task started: fastANI
[2023-06-13 02:48:20,194] [INFO] Running command: fastANI --query /var/lib/cwl/stga9a41a9c-e197-46e5-ac02-e587268a78fa/GCA_022754875.1_ASM2275487v1_genomic.fna.gz --refList GCA_022754875.1_ASM2275487v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022754875.1_ASM2275487v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:48:26,537] [INFO] Task succeeded: fastANI
[2023-06-13 02:48:26,549] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 02:48:26,549] [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	98.7387	311	336	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_003584685.1	s__Lactobacillus paragasseri	78.2766	82	336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.70	97.96	0.91	0.84	40	-
GCF_000296835.1	s__Lactobacillus hominis	78.05	71	336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.73	99.20	0.96	0.89	4	-
GCF_003423665.1	s__Lactobacillus rodentium	78.0161	76	336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014425.1	s__Lactobacillus gasseri	77.8904	78	336	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	77.5927	79	336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018987235.1	s__Lactobacillus crispatus	77.1587	51	336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	-
GCF_001434975.1	s__Lactobacillus gallinarum	77.1432	64	336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCA_018883635.1	s__Lactobacillus pullistercoris	76.8673	52	336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591845.1	s__Lactobacillus acidophilus	76.8642	69	336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
--------------------------------------------------------------------------------
[2023-06-13 02:48:26,552] [INFO] GTDB search result was written to GCA_022754875.1_ASM2275487v1_genomic.fna/result_gtdb.tsv
[2023-06-13 02:48:26,552] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:48:26,556] [INFO] DFAST_QC result json was written to GCA_022754875.1_ASM2275487v1_genomic.fna/dqc_result.json
[2023-06-13 02:48:26,556] [INFO] DFAST_QC completed!
[2023-06-13 02:48:26,556] [INFO] Total running time: 0h0m32s