[2024-01-24 11:44:23,003] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,005] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,006] [INFO] DQC Reference Directory: /var/lib/cwl/stgeab9b4b3-05c7-41c4-a1ea-87969fccc1a1/dqc_reference
[2024-01-24 11:44:26,344] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,345] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,346] [INFO] Running command: gunzip -c /var/lib/cwl/stg2810aa4c-dc22-4a52-b9ac-d1e6c945e3e4/GCF_018327645.1_ASM1832764v1_genomic.fna.gz | prodigal -d GCF_018327645.1_ASM1832764v1_genomic.fna/cds.fna -a GCF_018327645.1_ASM1832764v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:30,535] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:30,535] [INFO] Task started: HMMsearch
[2024-01-24 11:44:30,535] [INFO] Running command: hmmsearch --tblout GCF_018327645.1_ASM1832764v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeab9b4b3-05c7-41c4-a1ea-87969fccc1a1/dqc_reference/reference_markers.hmm GCF_018327645.1_ASM1832764v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:30,790] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:30,791] [INFO] Found 6/6 markers.
[2024-01-24 11:44:30,810] [INFO] Query marker FASTA was written to GCF_018327645.1_ASM1832764v1_genomic.fna/markers.fasta
[2024-01-24 11:44:30,810] [INFO] Task started: Blastn
[2024-01-24 11:44:30,810] [INFO] Running command: blastn -query GCF_018327645.1_ASM1832764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeab9b4b3-05c7-41c4-a1ea-87969fccc1a1/dqc_reference/reference_markers.fasta -out GCF_018327645.1_ASM1832764v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:31,438] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:31,442] [INFO] Selected 22 target genomes.
[2024-01-24 11:44:31,443] [INFO] Target genome list was writen to GCF_018327645.1_ASM1832764v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:31,543] [INFO] Task started: fastANI
[2024-01-24 11:44:31,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg2810aa4c-dc22-4a52-b9ac-d1e6c945e3e4/GCF_018327645.1_ASM1832764v1_genomic.fna.gz --refList GCF_018327645.1_ASM1832764v1_genomic.fna/target_genomes.txt --output GCF_018327645.1_ASM1832764v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:37,513] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:37,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeab9b4b3-05c7-41c4-a1ea-87969fccc1a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:37,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeab9b4b3-05c7-41c4-a1ea-87969fccc1a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:37,529] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:37,530] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:37,530] [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 corticis	strain=B40	GCA_018327645.1	2201249	2201249	type	True	100.0	580	581	95	conclusive
Lactobacillus acidophilus	strain=ATCC 4356	GCA_000786395.1	1579	1579	type	True	79.0959	110	581	95	below_threshold
Lactobacillus kitasatonis	strain=JCM 1039	GCA_000615285.1	237446	237446	type	True	79.0918	133	581	95	below_threshold
Lactobacillus kitasatonis	strain=DSM 16761	GCA_001434435.1	237446	237446	type	True	79.0519	133	581	95	below_threshold
Lactobacillus acidophilus	strain=CIP 76.13	GCA_000469705.1	1579	1579	type	True	79.0052	112	581	95	below_threshold
Lactobacillus acidophilus	strain=DSM 20079	GCA_003047065.1	1579	1579	type	True	79.0005	116	581	95	below_threshold
Lactobacillus amylovorus	strain=DSM 20531	GCA_002706375.1	1604	1604	type	True	78.997	130	581	95	below_threshold
Lactobacillus amylovorus	strain=DSM 20531	GCA_001433985.1	1604	1604	type	True	78.9558	129	581	95	below_threshold
Lactobacillus acidophilus	strain=DSM 20079	GCA_001433895.1	1579	1579	type	True	78.8517	109	581	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_004354545.1	83683	83683	type	True	78.8113	117	581	95	below_threshold
Lactobacillus equicursoris	strain=JCM 14600	GCA_001311765.1	420645	420645	type	True	78.7667	79	581	95	below_threshold
Lactobacillus xujianguonis	strain=HT111-2	GCA_004009905.1	2495899	2495899	type	True	78.7602	129	581	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_000178475.1	83683	83683	type	True	78.6604	114	581	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_001435665.1	83683	83683	type	True	78.6398	114	581	95	below_threshold
Lactobacillus mulieris	strain=c10Ua161M	GCA_007095465.1	2508708	2508708	type	True	78.4373	91	581	95	below_threshold
Lactobacillus equicursoris	strain=type strain:CIP 110162	GCA_000312645.1	420645	420645	type	True	78.3803	81	581	95	below_threshold
Lactobacillus equicursoris	strain=DSM 19284	GCA_001434815.1	420645	420645	type	True	78.3208	80	581	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	78.165	66	581	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	78.0111	68	581	95	below_threshold
Lactobacillus apis	strain=CCM 8403	GCA_014635365.1	303541	303541	type	True	77.9675	72	581	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:37,531] [INFO] DFAST Taxonomy check result was written to GCF_018327645.1_ASM1832764v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:37,532] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:37,532] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:37,532] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeab9b4b3-05c7-41c4-a1ea-87969fccc1a1/dqc_reference/checkm_data
[2024-01-24 11:44:37,533] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:37,552] [INFO] Task started: CheckM
[2024-01-24 11:44:37,553] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018327645.1_ASM1832764v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018327645.1_ASM1832764v1_genomic.fna/checkm_input GCF_018327645.1_ASM1832764v1_genomic.fna/checkm_result
[2024-01-24 11:44:57,296] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:57,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:57,318] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:57,318] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:57,319] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018327645.1_ASM1832764v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:57,319] [INFO] Task started: Blastn
[2024-01-24 11:44:57,319] [INFO] Running command: blastn -query GCF_018327645.1_ASM1832764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeab9b4b3-05c7-41c4-a1ea-87969fccc1a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_018327645.1_ASM1832764v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:58,113] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:58,123] [INFO] Selected 23 target genomes.
[2024-01-24 11:44:58,123] [INFO] Target genome list was writen to GCF_018327645.1_ASM1832764v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:58,141] [INFO] Task started: fastANI
[2024-01-24 11:44:58,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg2810aa4c-dc22-4a52-b9ac-d1e6c945e3e4/GCF_018327645.1_ASM1832764v1_genomic.fna.gz --refList GCF_018327645.1_ASM1832764v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018327645.1_ASM1832764v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:05,365] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:05,385] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:05,386] [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_018327645.1	s__Lactobacillus corticis	100.0	580	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001591845.1	s__Lactobacillus acidophilus	79.1223	109	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_000615285.1	s__Lactobacillus kitasatonis	79.0781	135	581	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	79.0771	106	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_001434975.1	s__Lactobacillus gallinarum	79.0662	120	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_002706375.1	s__Lactobacillus amylovorus	78.9898	130	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.43	96.81	0.87	0.78	24	-
GCF_004009905.1	s__Lactobacillus xujianguonis	78.7602	129	581	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	78.7104	132	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	-
GCF_000178475.1	s__Lactobacillus amylolyticus	78.648	115	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.45	98.00	0.96	0.87	8	-
GCF_007095465.1	s__Lactobacillus mulieris	78.4373	91	581	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	78.4314	122	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
GCF_007570935.1	s__Lactobacillus sp007570935	78.3254	106	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434815.1	s__Lactobacillus equicursoris	78.2849	80	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.84	97.67	0.88	0.82	5	-
GCF_009695985.1	s__Lactobacillus porci	78.1942	69	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.20	0.91	0.90	4	-
GCA_002418055.1	s__Lactobacillus sp002418055	78.0472	77	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.84	99.82	0.90	0.90	3	-
GCF_001436775.1	s__Lactobacillus acetotolerans	78.0195	83	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.88	98.02	0.91	0.85	26	-
GCF_002837055.1	s__Lactobacillus apis	78.0155	68	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.63	96.48	0.93	0.86	10	-
GCF_003423665.1	s__Lactobacillus rodentium	77.9876	67	581	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 11:45:05,387] [INFO] GTDB search result was written to GCF_018327645.1_ASM1832764v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:05,388] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:05,396] [INFO] DFAST_QC result json was written to GCF_018327645.1_ASM1832764v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:05,396] [INFO] DFAST_QC completed!
[2024-01-24 11:45:05,397] [INFO] Total running time: 0h0m42s