[2024-01-24 11:12:58,080] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:58,083] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:58,084] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d30982d-c951-4386-83fa-7f31f25f088e/dqc_reference
[2024-01-24 11:12:59,519] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,520] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,521] [INFO] Running command: gunzip -c /var/lib/cwl/stgf28590a2-1632-4223-b2dd-39704b127d77/GCF_017874575.1_ASM1787457v1_genomic.fna.gz | prodigal -d GCF_017874575.1_ASM1787457v1_genomic.fna/cds.fna -a GCF_017874575.1_ASM1787457v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:03,503] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:03,504] [INFO] Task started: HMMsearch
[2024-01-24 11:13:03,504] [INFO] Running command: hmmsearch --tblout GCF_017874575.1_ASM1787457v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d30982d-c951-4386-83fa-7f31f25f088e/dqc_reference/reference_markers.hmm GCF_017874575.1_ASM1787457v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:03,793] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:03,794] [INFO] Found 6/6 markers.
[2024-01-24 11:13:03,828] [INFO] Query marker FASTA was written to GCF_017874575.1_ASM1787457v1_genomic.fna/markers.fasta
[2024-01-24 11:13:03,829] [INFO] Task started: Blastn
[2024-01-24 11:13:03,829] [INFO] Running command: blastn -query GCF_017874575.1_ASM1787457v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d30982d-c951-4386-83fa-7f31f25f088e/dqc_reference/reference_markers.fasta -out GCF_017874575.1_ASM1787457v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:04,434] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:04,441] [INFO] Selected 23 target genomes.
[2024-01-24 11:13:04,441] [INFO] Target genome list was writen to GCF_017874575.1_ASM1787457v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:04,494] [INFO] Task started: fastANI
[2024-01-24 11:13:04,494] [INFO] Running command: fastANI --query /var/lib/cwl/stgf28590a2-1632-4223-b2dd-39704b127d77/GCF_017874575.1_ASM1787457v1_genomic.fna.gz --refList GCF_017874575.1_ASM1787457v1_genomic.fna/target_genomes.txt --output GCF_017874575.1_ASM1787457v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:12,142] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:12,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d30982d-c951-4386-83fa-7f31f25f088e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:12,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d30982d-c951-4386-83fa-7f31f25f088e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:12,159] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:12,159] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:12,159] [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 colini	strain=DSM 101872	GCA_017874575.1	1819254	1819254	type	True	100.0	722	724	95	conclusive
Lactobacillus johnsonii	strain=ATCC 33200	GCA_000159355.1	33959	33959	type	True	79.6727	181	724	95	below_threshold
Lactobacillus hominis	strain=type strain:CRBIP 24.179	GCA_000296835.1	1203033	1203033	type	True	79.6086	180	724	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	79.5829	153	724	95	below_threshold
Lactobacillus hominis	strain=DSM 23910	GCA_001436125.1	1203033	1203033	type	True	79.5704	171	724	95	below_threshold
Lactobacillus johnsonii	strain=ATCC 33200	GCA_001433975.1	33959	33959	type	True	79.5314	177	724	95	below_threshold
Lactobacillus paragasseri	strain=JCM 5343	GCA_003584685.1	2107999	2107999	type	True	79.5102	186	724	95	below_threshold
Lactobacillus paragasseri	strain=JCM 5343	GCA_003307275.1	2107999	2107999	type	True	79.4997	189	724	95	below_threshold
Lactobacillus taiwanensis	strain=DSM 21401	GCA_001436695.1	508451	508451	type	True	79.41	179	724	95	below_threshold
Lactobacillus helveticus	strain=JCM 1120	GCA_015698225.1	1587	1587	type	True	78.8442	129	724	95	below_threshold
Lactobacillus helveticus	strain=DSM 20075	GCA_000160855.1	1587	1587	type	True	78.8249	138	724	95	below_threshold
Lactobacillus helveticus	strain=CGMCC 1.1877	GCA_001434945.1	1587	1587	type	True	78.7808	127	724	95	below_threshold
Lactobacillus hamsteri	strain=DSM 5661	GCA_001434515.1	96565	96565	type	True	78.6904	138	724	95	below_threshold
Lactobacillus hamsteri	strain=JCM 6256	GCA_000615445.1	96565	96565	type	True	78.6854	139	724	95	below_threshold
Lactobacillus amylovorus	strain=DSM 20531	GCA_001433985.1	1604	1604	type	True	78.5334	128	724	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	78.3764	150	724	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_000159415.1	227945	227945	type	True	78.3404	156	724	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	78.3338	150	724	95	below_threshold
Lactobacillus amylovorus	strain=DSM 20531	GCA_002706375.1	1604	1604	type	True	78.3143	137	724	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	77.7646	75	724	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:12,160] [INFO] DFAST Taxonomy check result was written to GCF_017874575.1_ASM1787457v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:12,161] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:12,161] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:12,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d30982d-c951-4386-83fa-7f31f25f088e/dqc_reference/checkm_data
[2024-01-24 11:13:12,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:12,186] [INFO] Task started: CheckM
[2024-01-24 11:13:12,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874575.1_ASM1787457v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874575.1_ASM1787457v1_genomic.fna/checkm_input GCF_017874575.1_ASM1787457v1_genomic.fna/checkm_result
[2024-01-24 11:13:32,412] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:32,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:32,439] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:32,440] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:32,440] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874575.1_ASM1787457v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:32,440] [INFO] Task started: Blastn
[2024-01-24 11:13:32,441] [INFO] Running command: blastn -query GCF_017874575.1_ASM1787457v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d30982d-c951-4386-83fa-7f31f25f088e/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874575.1_ASM1787457v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:33,253] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:33,256] [INFO] Selected 14 target genomes.
[2024-01-24 11:13:33,256] [INFO] Target genome list was writen to GCF_017874575.1_ASM1787457v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:33,278] [INFO] Task started: fastANI
[2024-01-24 11:13:33,278] [INFO] Running command: fastANI --query /var/lib/cwl/stgf28590a2-1632-4223-b2dd-39704b127d77/GCF_017874575.1_ASM1787457v1_genomic.fna.gz --refList GCF_017874575.1_ASM1787457v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874575.1_ASM1787457v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:38,553] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:38,567] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:38,568] [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_017874575.1	s__Lactobacillus colini	100.0	722	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014803895.1	s__Lactobacillus sp014803895	81.7987	330	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589175.1	s__Lactobacillus sp910589175	79.7505	171	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000159355.1	s__Lactobacillus johnsonii	79.6787	180	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.89	95.28	0.86	0.57	61	-
GCF_000296835.1	s__Lactobacillus hominis	79.6086	180	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.73	99.20	0.96	0.89	4	-
GCF_003584685.1	s__Lactobacillus paragasseri	79.5441	185	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.70	97.96	0.91	0.84	40	-
GCF_001436695.1	s__Lactobacillus taiwanensis	79.4146	178	724	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	79.2868	183	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.12	96.79	0.93	0.86	41	-
GCF_000160855.1	s__Lactobacillus helveticus	78.8249	138	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_007570935.1	s__Lactobacillus sp007570935	78.5699	157	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014803915.1	s__Lactobacillus sp014803915	78.4411	102	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007095465.1	s__Lactobacillus mulieris	78.4323	109	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.54	96.91	0.92	0.85	18	-
GCF_001436305.1	s__Lactobacillus ultunensis	78.3764	150	724	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	78.3692	135	724	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.43	96.81	0.87	0.78	24	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:38,569] [INFO] GTDB search result was written to GCF_017874575.1_ASM1787457v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:38,570] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:38,574] [INFO] DFAST_QC result json was written to GCF_017874575.1_ASM1787457v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:38,574] [INFO] DFAST_QC completed!
[2024-01-24 11:13:38,574] [INFO] Total running time: 0h0m40s