[2024-01-24 11:27:04,762] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:04,765] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:04,765] [INFO] DQC Reference Directory: /var/lib/cwl/stg01c1d41a-ae5f-4189-9d42-e2f7f716f8e4/dqc_reference
[2024-01-24 11:27:05,963] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:05,964] [INFO] Task started: Prodigal
[2024-01-24 11:27:05,965] [INFO] Running command: gunzip -c /var/lib/cwl/stg974fe1db-0fa2-4b1c-bb70-13da21ecc57a/GCF_014648715.1_ASM1464871v1_genomic.fna.gz | prodigal -d GCF_014648715.1_ASM1464871v1_genomic.fna/cds.fna -a GCF_014648715.1_ASM1464871v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:08,778] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:08,778] [INFO] Task started: HMMsearch
[2024-01-24 11:27:08,779] [INFO] Running command: hmmsearch --tblout GCF_014648715.1_ASM1464871v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01c1d41a-ae5f-4189-9d42-e2f7f716f8e4/dqc_reference/reference_markers.hmm GCF_014648715.1_ASM1464871v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:08,975] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:08,977] [INFO] Found 6/6 markers.
[2024-01-24 11:27:08,998] [INFO] Query marker FASTA was written to GCF_014648715.1_ASM1464871v1_genomic.fna/markers.fasta
[2024-01-24 11:27:08,999] [INFO] Task started: Blastn
[2024-01-24 11:27:08,999] [INFO] Running command: blastn -query GCF_014648715.1_ASM1464871v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01c1d41a-ae5f-4189-9d42-e2f7f716f8e4/dqc_reference/reference_markers.fasta -out GCF_014648715.1_ASM1464871v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:09,580] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:09,583] [INFO] Selected 25 target genomes.
[2024-01-24 11:27:09,583] [INFO] Target genome list was writen to GCF_014648715.1_ASM1464871v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:09,673] [INFO] Task started: fastANI
[2024-01-24 11:27:09,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg974fe1db-0fa2-4b1c-bb70-13da21ecc57a/GCF_014648715.1_ASM1464871v1_genomic.fna.gz --refList GCF_014648715.1_ASM1464871v1_genomic.fna/target_genomes.txt --output GCF_014648715.1_ASM1464871v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:17,518] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:17,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01c1d41a-ae5f-4189-9d42-e2f7f716f8e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:17,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01c1d41a-ae5f-4189-9d42-e2f7f716f8e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:17,538] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:27:17,538] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:17,538] [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 acetotolerans	strain=JCM 3825	GCA_014648715.1	1600	1600	type	True	100.0	478	483	95	conclusive
Lactobacillus acetotolerans	strain=DSM 20749	GCA_001436775.1	1600	1600	type	True	99.9669	449	483	95	conclusive
Lactobacillus xujianguonis	strain=HT111-2	GCA_004009905.1	2495899	2495899	type	True	79.2657	145	483	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_004354545.1	83683	83683	type	True	79.0	147	483	95	below_threshold
Lactobacillus kefiranofaciens subsp. kefirgranum	strain=DSM 10550	GCA_001434195.1	190906	267818	type	True	78.9843	161	483	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_001435665.1	83683	83683	type	True	78.9558	145	483	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_000178475.1	83683	83683	type	True	78.9195	147	483	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_000159415.1	227945	227945	type	True	78.8645	178	483	95	below_threshold
Lactobacillus helveticus	strain=DSM 20075	GCA_000160855.1	1587	1587	type	True	78.8563	154	483	95	below_threshold
Lactobacillus kefiranofaciens	strain=ATCC 43761	GCA_900103655.1	267818	267818	type	True	78.8429	177	483	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	78.8099	175	483	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	78.7691	173	483	95	below_threshold
Lactobacillus helveticus	strain=CGMCC 1.1877	GCA_001434945.1	1587	1587	type	True	78.7167	150	483	95	below_threshold
Lactobacillus helveticus	strain=JCM 1120	GCA_015698225.1	1587	1587	type	True	78.6756	162	483	95	below_threshold
Lactobacillus kitasatonis	strain=JCM 1039	GCA_000615285.1	237446	237446	type	True	78.6719	161	483	95	below_threshold
Lactobacillus kitasatonis	strain=DSM 16761	GCA_001434435.1	237446	237446	type	True	78.6354	166	483	95	below_threshold
Lactobacillus hamsteri	strain=DSM 5661	GCA_001434515.1	96565	96565	type	True	78.6162	179	483	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	78.5418	112	483	95	below_threshold
Lactobacillus kalixensis	strain=DSM 16043	GCA_001434335.1	227944	227944	type	True	78.4062	147	483	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:17,540] [INFO] DFAST Taxonomy check result was written to GCF_014648715.1_ASM1464871v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:17,540] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:17,540] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:17,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01c1d41a-ae5f-4189-9d42-e2f7f716f8e4/dqc_reference/checkm_data
[2024-01-24 11:27:17,542] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:17,565] [INFO] Task started: CheckM
[2024-01-24 11:27:17,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648715.1_ASM1464871v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648715.1_ASM1464871v1_genomic.fna/checkm_input GCF_014648715.1_ASM1464871v1_genomic.fna/checkm_result
[2024-01-24 11:27:33,751] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:33,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:33,769] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:33,770] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:33,771] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648715.1_ASM1464871v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:33,771] [INFO] Task started: Blastn
[2024-01-24 11:27:33,771] [INFO] Running command: blastn -query GCF_014648715.1_ASM1464871v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01c1d41a-ae5f-4189-9d42-e2f7f716f8e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648715.1_ASM1464871v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:34,531] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:34,536] [INFO] Selected 18 target genomes.
[2024-01-24 11:27:34,536] [INFO] Target genome list was writen to GCF_014648715.1_ASM1464871v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:34,553] [INFO] Task started: fastANI
[2024-01-24 11:27:34,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg974fe1db-0fa2-4b1c-bb70-13da21ecc57a/GCF_014648715.1_ASM1464871v1_genomic.fna.gz --refList GCF_014648715.1_ASM1464871v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648715.1_ASM1464871v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:40,629] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:40,647] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:40,647] [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_001436775.1	s__Lactobacillus acetotolerans	99.9669	449	483	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.88	98.02	0.91	0.85	26	conclusive
GCF_004009905.1	s__Lactobacillus xujianguonis	79.2178	146	483	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.83	99.82	0.94	0.92	3	-
GCF_001434975.1	s__Lactobacillus gallinarum	78.8758	161	483	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_000178475.1	s__Lactobacillus amylolyticus	78.8724	149	483	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.45	98.00	0.96	0.87	8	-
GCF_900103655.1	s__Lactobacillus kefiranofaciens	78.8192	175	483	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.62	99.18	0.95	0.85	9	-
GCF_000160855.1	s__Lactobacillus helveticus	78.8024	156	483	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	78.7972	176	483	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
GCF_002706375.1	s__Lactobacillus amylovorus	78.7903	162	483	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	78.658	162	483	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	-
GCF_000615445.1	s__Lactobacillus hamsteri	78.5867	179	483	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_018987235.1	s__Lactobacillus crispatus	78.5823	168	483	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	-
GCF_001434335.1	s__Lactobacillus kalixensis	78.4062	147	483	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000970855.1	s__Lactobacillus helsingborgensis	78.3851	118	483	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.65	97.05	0.93	0.90	6	-
GCA_018883635.1	s__Lactobacillus pullistercoris	78.2303	157	483	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013346935.1	s__Lactobacillus melliventris	78.12	123	483	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.75	96.46	0.90	0.86	9	-
GCA_910589675.1	s__Lactobacillus sp910589675	77.8804	100	483	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.13	0.73	0.71	7	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:40,649] [INFO] GTDB search result was written to GCF_014648715.1_ASM1464871v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:40,649] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:40,653] [INFO] DFAST_QC result json was written to GCF_014648715.1_ASM1464871v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:40,653] [INFO] DFAST_QC completed!
[2024-01-24 11:27:40,653] [INFO] Total running time: 0h0m36s