[2024-01-24 12:40:06,253] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:06,255] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:06,255] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ec89c69-9180-4465-b83a-9b536aa99a87/dqc_reference
[2024-01-24 12:40:07,547] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:07,548] [INFO] Task started: Prodigal
[2024-01-24 12:40:07,549] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0564d36-7a31-46b6-8872-7c2c127ee2f9/GCF_000469705.1_LaCIP7613V1_genomic.fna.gz | prodigal -d GCF_000469705.1_LaCIP7613V1_genomic.fna/cds.fna -a GCF_000469705.1_LaCIP7613V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:11,293] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:11,294] [INFO] Task started: HMMsearch
[2024-01-24 12:40:11,294] [INFO] Running command: hmmsearch --tblout GCF_000469705.1_LaCIP7613V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ec89c69-9180-4465-b83a-9b536aa99a87/dqc_reference/reference_markers.hmm GCF_000469705.1_LaCIP7613V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:11,501] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:11,503] [INFO] Found 6/6 markers.
[2024-01-24 12:40:11,522] [INFO] Query marker FASTA was written to GCF_000469705.1_LaCIP7613V1_genomic.fna/markers.fasta
[2024-01-24 12:40:11,523] [INFO] Task started: Blastn
[2024-01-24 12:40:11,523] [INFO] Running command: blastn -query GCF_000469705.1_LaCIP7613V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ec89c69-9180-4465-b83a-9b536aa99a87/dqc_reference/reference_markers.fasta -out GCF_000469705.1_LaCIP7613V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:12,123] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:12,127] [INFO] Selected 10 target genomes.
[2024-01-24 12:40:12,127] [INFO] Target genome list was writen to GCF_000469705.1_LaCIP7613V1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:12,132] [INFO] Task started: fastANI
[2024-01-24 12:40:12,132] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0564d36-7a31-46b6-8872-7c2c127ee2f9/GCF_000469705.1_LaCIP7613V1_genomic.fna.gz --refList GCF_000469705.1_LaCIP7613V1_genomic.fna/target_genomes.txt --output GCF_000469705.1_LaCIP7613V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:16,216] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:16,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ec89c69-9180-4465-b83a-9b536aa99a87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:16,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ec89c69-9180-4465-b83a-9b536aa99a87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:16,225] [INFO] Found 7 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:40:16,226] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:16,226] [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 acidophilus	strain=CIP 76.13	GCA_000469705.1	1579	1579	type	True	100.0	633	634	95	conclusive
Lactobacillus acidophilus	strain=NBRC 13951	GCA_001591845.1	1579	1579	type	True	99.9894	623	634	95	conclusive
Lactobacillus acidophilus	strain=DSM 20079	GCA_003047065.1	1579	1579	type	True	99.9879	634	634	95	conclusive
Lactobacillus acidophilus	strain=ATCC 4356	GCA_000786395.1	1579	1579	type	True	99.9861	632	634	95	conclusive
Lactobacillus acidophilus	strain=DSM 20079	GCA_001433895.1	1579	1579	type	True	99.9849	629	634	95	conclusive
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	80.3254	275	634	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	78.1152	122	634	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:16,228] [INFO] DFAST Taxonomy check result was written to GCF_000469705.1_LaCIP7613V1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:16,229] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:16,229] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:16,229] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ec89c69-9180-4465-b83a-9b536aa99a87/dqc_reference/checkm_data
[2024-01-24 12:40:16,230] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:16,253] [INFO] Task started: CheckM
[2024-01-24 12:40:16,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000469705.1_LaCIP7613V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000469705.1_LaCIP7613V1_genomic.fna/checkm_input GCF_000469705.1_LaCIP7613V1_genomic.fna/checkm_result
[2024-01-24 12:40:34,173] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:34,174] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:34,191] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:34,192] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:34,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000469705.1_LaCIP7613V1_genomic.fna/markers.fasta)
[2024-01-24 12:40:34,193] [INFO] Task started: Blastn
[2024-01-24 12:40:34,193] [INFO] Running command: blastn -query GCF_000469705.1_LaCIP7613V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ec89c69-9180-4465-b83a-9b536aa99a87/dqc_reference/reference_markers_gtdb.fasta -out GCF_000469705.1_LaCIP7613V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:34,943] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:34,947] [INFO] Selected 10 target genomes.
[2024-01-24 12:40:34,947] [INFO] Target genome list was writen to GCF_000469705.1_LaCIP7613V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:34,953] [INFO] Task started: fastANI
[2024-01-24 12:40:34,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0564d36-7a31-46b6-8872-7c2c127ee2f9/GCF_000469705.1_LaCIP7613V1_genomic.fna.gz --refList GCF_000469705.1_LaCIP7613V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000469705.1_LaCIP7613V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:38,800] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:38,809] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:38,810] [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_001591845.1	s__Lactobacillus acidophilus	99.9894	623	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	conclusive
GCF_002706375.1	s__Lactobacillus amylovorus	83.3616	416	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.43	96.81	0.87	0.78	24	-
GCF_000615285.1	s__Lactobacillus kitasatonis	83.3332	400	634	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	82.6349	371	634	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	82.2219	377	634	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	82.0265	365	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_900103655.1	s__Lactobacillus kefiranofaciens	81.2345	348	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.62	99.18	0.95	0.85	9	-
GCF_000615445.1	s__Lactobacillus hamsteri	80.5486	270	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_003423665.1	s__Lactobacillus rodentium	78.2402	148	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:38,812] [INFO] GTDB search result was written to GCF_000469705.1_LaCIP7613V1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:38,812] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:38,816] [INFO] DFAST_QC result json was written to GCF_000469705.1_LaCIP7613V1_genomic.fna/dqc_result.json
[2024-01-24 12:40:38,816] [INFO] DFAST_QC completed!
[2024-01-24 12:40:38,816] [INFO] Total running time: 0h0m33s