[2024-01-24 15:19:04,371] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:04,373] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:04,373] [INFO] DQC Reference Directory: /var/lib/cwl/stg31488828-3bad-415b-94f8-d6b0ceee7c61/dqc_reference
[2024-01-24 15:19:05,603] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:05,604] [INFO] Task started: Prodigal
[2024-01-24 15:19:05,604] [INFO] Running command: gunzip -c /var/lib/cwl/stg514ffe60-42c5-4481-ab16-fbc754355f9a/GCF_001435345.1_ASM143534v1_genomic.fna.gz | prodigal -d GCF_001435345.1_ASM143534v1_genomic.fna/cds.fna -a GCF_001435345.1_ASM143534v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:09,796] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:09,797] [INFO] Task started: HMMsearch
[2024-01-24 15:19:09,797] [INFO] Running command: hmmsearch --tblout GCF_001435345.1_ASM143534v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31488828-3bad-415b-94f8-d6b0ceee7c61/dqc_reference/reference_markers.hmm GCF_001435345.1_ASM143534v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:10,045] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:10,046] [INFO] Found 6/6 markers.
[2024-01-24 15:19:10,086] [INFO] Query marker FASTA was written to GCF_001435345.1_ASM143534v1_genomic.fna/markers.fasta
[2024-01-24 15:19:10,087] [INFO] Task started: Blastn
[2024-01-24 15:19:10,087] [INFO] Running command: blastn -query GCF_001435345.1_ASM143534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31488828-3bad-415b-94f8-d6b0ceee7c61/dqc_reference/reference_markers.fasta -out GCF_001435345.1_ASM143534v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:10,718] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:10,721] [INFO] Selected 20 target genomes.
[2024-01-24 15:19:10,721] [INFO] Target genome list was writen to GCF_001435345.1_ASM143534v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:10,771] [INFO] Task started: fastANI
[2024-01-24 15:19:10,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg514ffe60-42c5-4481-ab16-fbc754355f9a/GCF_001435345.1_ASM143534v1_genomic.fna.gz --refList GCF_001435345.1_ASM143534v1_genomic.fna/target_genomes.txt --output GCF_001435345.1_ASM143534v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:20,330] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:20,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31488828-3bad-415b-94f8-d6b0ceee7c61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:20,331] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31488828-3bad-415b-94f8-d6b0ceee7c61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:20,351] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:20,351] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:20,352] [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
Limosilactobacillus pontis	strain=DSM 8475	GCA_001435345.1	35787	35787	type	True	100.0	530	531	95	conclusive
Limosilactobacillus rudii	strain=STM3_1	GCA_014145455.1	2759755	2759755	type	True	79.7393	84	531	95	below_threshold
Limosilactobacillus portuensis	strain=c11Ua_112_M	GCA_014838735.1	2742601	2742601	type	True	79.7362	95	531	95	below_threshold
Limosilactobacillus vaginalis	strain=ATCC 49540	GCA_000159435.1	1633	1633	type	True	79.7321	104	531	95	below_threshold
Limosilactobacillus antri	strain=DSM 16041	GCA_000160835.1	227943	227943	type	True	79.6649	206	531	95	below_threshold
Limosilactobacillus oris	strain=DSM 4864	GCA_001434465.1	1632	1632	type	True	79.5691	192	531	95	below_threshold
Limosilactobacillus vaginalis	strain=DSM 5837	GCA_001435915.1	1633	1633	type	True	79.5449	96	531	95	below_threshold
Limosilactobacillus antri	strain=DSM 16041	GCA_001435475.1	227943	227943	type	True	79.5327	200	531	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001027985.1	47493	47493	type	True	79.4899	204	531	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001435935.1	47493	47493	type	True	79.3714	207	531	95	below_threshold
Limosilactobacillus gorillae	strain=KZ01	GCA_001293735.1	1450649	1450649	type	True	77.9154	78	531	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:20,844] [INFO] DFAST Taxonomy check result was written to GCF_001435345.1_ASM143534v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:20,845] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:20,845] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:20,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31488828-3bad-415b-94f8-d6b0ceee7c61/dqc_reference/checkm_data
[2024-01-24 15:19:20,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:20,873] [INFO] Task started: CheckM
[2024-01-24 15:19:20,873] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001435345.1_ASM143534v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001435345.1_ASM143534v1_genomic.fna/checkm_input GCF_001435345.1_ASM143534v1_genomic.fna/checkm_result
[2024-01-24 15:19:40,130] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:40,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:40,148] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:40,148] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:40,149] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001435345.1_ASM143534v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:40,149] [INFO] Task started: Blastn
[2024-01-24 15:19:40,149] [INFO] Running command: blastn -query GCF_001435345.1_ASM143534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31488828-3bad-415b-94f8-d6b0ceee7c61/dqc_reference/reference_markers_gtdb.fasta -out GCF_001435345.1_ASM143534v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:40,924] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:40,928] [INFO] Selected 10 target genomes.
[2024-01-24 15:19:40,928] [INFO] Target genome list was writen to GCF_001435345.1_ASM143534v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:40,939] [INFO] Task started: fastANI
[2024-01-24 15:19:40,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg514ffe60-42c5-4481-ab16-fbc754355f9a/GCF_001435345.1_ASM143534v1_genomic.fna.gz --refList GCF_001435345.1_ASM143534v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001435345.1_ASM143534v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:45,409] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:45,427] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:45,427] [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_001435345.1	s__Limosilactobacillus pontis	100.0	530	531	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.82	97.66	0.95	0.90	3	conclusive
GCA_019117285.1	s__Limosilactobacillus intestinigallinarum	87.8437	289	531	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.99	99.99	0.94	0.94	2	-
GCF_002940945.1	s__Limosilactobacillus pontis_A	84.1387	444	531	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118405.1	s__Limosilactobacillus gallistercoris	83.4377	290	531	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.70	98.67	0.88	0.83	3	-
GCA_002299975.1	s__Limosilactobacillus sp002299975	82.8178	271	531	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.38	99.38	0.84	0.84	2	-
GCA_905214235.1	s__Limosilactobacillus sp905214235	79.9747	213	531	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000159435.1	s__Limosilactobacillus vaginalis	79.7321	104	531	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.80	96.39	0.94	0.86	8	-
GCA_902834055.1	s__Limosilactobacillus sp902834055	79.3607	88	531	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435935.1	s__Limosilactobacillus panis	79.3486	208	531	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.95	99.95	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:45,429] [INFO] GTDB search result was written to GCF_001435345.1_ASM143534v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:45,430] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:45,434] [INFO] DFAST_QC result json was written to GCF_001435345.1_ASM143534v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:45,435] [INFO] DFAST_QC completed!
[2024-01-24 15:19:45,435] [INFO] Total running time: 0h0m41s