[2024-01-24 12:37:25,068] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:25,069] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:25,070] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1f79e1e-fff2-4501-875b-a316efd1d7e7/dqc_reference
[2024-01-24 12:37:26,376] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:26,376] [INFO] Task started: Prodigal
[2024-01-24 12:37:26,377] [INFO] Running command: gunzip -c /var/lib/cwl/stg13f746b4-32ba-407c-b589-c50a57ef4b83/GCF_024397795.1_ASM2439779v1_genomic.fna.gz | prodigal -d GCF_024397795.1_ASM2439779v1_genomic.fna/cds.fna -a GCF_024397795.1_ASM2439779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:30,386] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:30,387] [INFO] Task started: HMMsearch
[2024-01-24 12:37:30,387] [INFO] Running command: hmmsearch --tblout GCF_024397795.1_ASM2439779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1f79e1e-fff2-4501-875b-a316efd1d7e7/dqc_reference/reference_markers.hmm GCF_024397795.1_ASM2439779v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:30,652] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:30,653] [INFO] Found 6/6 markers.
[2024-01-24 12:37:30,675] [INFO] Query marker FASTA was written to GCF_024397795.1_ASM2439779v1_genomic.fna/markers.fasta
[2024-01-24 12:37:30,676] [INFO] Task started: Blastn
[2024-01-24 12:37:30,676] [INFO] Running command: blastn -query GCF_024397795.1_ASM2439779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1f79e1e-fff2-4501-875b-a316efd1d7e7/dqc_reference/reference_markers.fasta -out GCF_024397795.1_ASM2439779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:31,292] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:31,302] [INFO] Selected 19 target genomes.
[2024-01-24 12:37:31,302] [INFO] Target genome list was writen to GCF_024397795.1_ASM2439779v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:31,387] [INFO] Task started: fastANI
[2024-01-24 12:37:31,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg13f746b4-32ba-407c-b589-c50a57ef4b83/GCF_024397795.1_ASM2439779v1_genomic.fna.gz --refList GCF_024397795.1_ASM2439779v1_genomic.fna/target_genomes.txt --output GCF_024397795.1_ASM2439779v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:37,592] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:37,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1f79e1e-fff2-4501-875b-a316efd1d7e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:37,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1f79e1e-fff2-4501-875b-a316efd1d7e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:37,612] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:37:37,613] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:37,613] [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 intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	100.0	676	678	95	conclusive
Lactobacillus intestinalis	strain=DSM 6629	GCA_001435325.1	151781	151781	type	True	99.9388	648	678	95	conclusive
Lactobacillus amylolyticus	strain=DSM 11664	GCA_004354545.1	83683	83683	type	True	80.6951	210	678	95	below_threshold
Lactobacillus hamsteri	strain=JCM 6256	GCA_000615445.1	96565	96565	type	True	80.5494	261	678	95	below_threshold
Lactobacillus hamsteri	strain=DSM 5661	GCA_001434515.1	96565	96565	type	True	80.524	261	678	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_000178475.1	83683	83683	type	True	80.4064	195	678	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_001435665.1	83683	83683	type	True	80.3867	200	678	95	below_threshold
Lactobacillus helveticus	strain=JCM 1120	GCA_015698225.1	1587	1587	type	True	80.3475	218	678	95	below_threshold
Lactobacillus gallinarum	strain=DSM 10532	GCA_001434975.1	52242	52242	type	True	80.3465	240	678	95	below_threshold
Lactobacillus helveticus	strain=CGMCC 1.1877	GCA_001434945.1	1587	1587	type	True	80.3187	210	678	95	below_threshold
Lactobacillus xujianguonis	strain=HT111-2	GCA_004009905.1	2495899	2495899	type	True	80.3164	241	678	95	below_threshold
Lactobacillus crispatus	strain=NCK2488	GCA_008694755.1	47770	47770	type	True	79.9987	229	678	95	below_threshold
Lactobacillus kalixensis	strain=DSM 16043	GCA_001434335.1	227944	227944	type	True	79.966	251	678	95	below_threshold
Lactobacillus gasseri	strain=ATCC 33323	GCA_000014425.1	1596	1596	type	True	79.6899	179	678	95	below_threshold
Lactobacillus gasseri	strain=ATCC 33323	GCA_008868295.1	1596	1596	type	True	78.9257	169	678	95	below_threshold
Lactobacillus laiwuensis	strain=F551-2	GCA_019972835.1	2841034	2841034	type	True	78.4206	101	678	95	below_threshold
Lactobacillus huangpiensis	strain=F306-1	GCA_019972815.1	2799571	2799571	type	True	78.3852	101	678	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:37,614] [INFO] DFAST Taxonomy check result was written to GCF_024397795.1_ASM2439779v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:37,615] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:37,615] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:37,615] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1f79e1e-fff2-4501-875b-a316efd1d7e7/dqc_reference/checkm_data
[2024-01-24 12:37:37,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:37,638] [INFO] Task started: CheckM
[2024-01-24 12:37:37,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024397795.1_ASM2439779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024397795.1_ASM2439779v1_genomic.fna/checkm_input GCF_024397795.1_ASM2439779v1_genomic.fna/checkm_result
[2024-01-24 12:37:57,039] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:57,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:57,056] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:57,056] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:57,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024397795.1_ASM2439779v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:57,057] [INFO] Task started: Blastn
[2024-01-24 12:37:57,058] [INFO] Running command: blastn -query GCF_024397795.1_ASM2439779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1f79e1e-fff2-4501-875b-a316efd1d7e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_024397795.1_ASM2439779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:57,824] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:57,829] [INFO] Selected 16 target genomes.
[2024-01-24 12:37:57,829] [INFO] Target genome list was writen to GCF_024397795.1_ASM2439779v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:57,847] [INFO] Task started: fastANI
[2024-01-24 12:37:57,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg13f746b4-32ba-407c-b589-c50a57ef4b83/GCF_024397795.1_ASM2439779v1_genomic.fna.gz --refList GCF_024397795.1_ASM2439779v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024397795.1_ASM2439779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:03,754] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:03,767] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:03,767] [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_001435325.1	s__Lactobacillus intestinalis	99.9388	648	678	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.33	96.07	0.89	0.82	9	conclusive
GCA_910589675.1	s__Lactobacillus sp910589675	89.7624	285	678	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.13	0.73	0.71	7	-
GCF_007570935.1	s__Lactobacillus sp007570935	80.7475	312	678	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000615445.1	s__Lactobacillus hamsteri	80.5956	259	678	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCA_018883635.1	s__Lactobacillus pullistercoris	80.5935	229	678	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	80.5468	269	678	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_000178475.1	s__Lactobacillus amylolyticus	80.4357	194	678	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.45	98.00	0.96	0.87	8	-
GCF_000160855.1	s__Lactobacillus helveticus	80.383	244	678	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_001434975.1	s__Lactobacillus gallinarum	80.3465	240	678	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_004009905.1	s__Lactobacillus xujianguonis	80.2924	242	678	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.83	99.82	0.94	0.92	3	-
GCF_018987235.1	s__Lactobacillus crispatus	80.1601	248	678	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	-
GCF_900103655.1	s__Lactobacillus kefiranofaciens	80.0821	211	678	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.62	99.18	0.95	0.85	9	-
GCF_001434335.1	s__Lactobacillus kalixensis	79.9565	251	678	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001436695.1	s__Lactobacillus taiwanensis	79.6928	186	678	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.80	98.01	0.90	0.86	31	-
GCF_000014425.1	s__Lactobacillus gasseri	79.6627	181	678	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.12	96.79	0.93	0.86	41	-
GCA_014803895.1	s__Lactobacillus sp014803895	78.6325	153	678	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 12:38:03,769] [INFO] GTDB search result was written to GCF_024397795.1_ASM2439779v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:03,769] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:03,773] [INFO] DFAST_QC result json was written to GCF_024397795.1_ASM2439779v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:03,773] [INFO] DFAST_QC completed!
[2024-01-24 12:38:03,773] [INFO] Total running time: 0h0m39s