[2024-01-24 11:05:28,066] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:28,068] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:28,076] [INFO] DQC Reference Directory: /var/lib/cwl/stg03d7c1b5-a7c6-4dc6-a517-513a28ed1460/dqc_reference
[2024-01-24 11:05:29,537] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:29,538] [INFO] Task started: Prodigal
[2024-01-24 11:05:29,538] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c7c89e7-59f5-485f-991f-57c8ab9ce3f1/GCF_002837055.1_ASM283705v1_genomic.fna.gz | prodigal -d GCF_002837055.1_ASM283705v1_genomic.fna/cds.fna -a GCF_002837055.1_ASM283705v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:32,689] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:32,690] [INFO] Task started: HMMsearch
[2024-01-24 11:05:32,690] [INFO] Running command: hmmsearch --tblout GCF_002837055.1_ASM283705v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03d7c1b5-a7c6-4dc6-a517-513a28ed1460/dqc_reference/reference_markers.hmm GCF_002837055.1_ASM283705v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:32,915] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:32,916] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6c7c89e7-59f5-485f-991f-57c8ab9ce3f1/GCF_002837055.1_ASM283705v1_genomic.fna.gz]
[2024-01-24 11:05:32,936] [INFO] Query marker FASTA was written to GCF_002837055.1_ASM283705v1_genomic.fna/markers.fasta
[2024-01-24 11:05:32,937] [INFO] Task started: Blastn
[2024-01-24 11:05:32,937] [INFO] Running command: blastn -query GCF_002837055.1_ASM283705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03d7c1b5-a7c6-4dc6-a517-513a28ed1460/dqc_reference/reference_markers.fasta -out GCF_002837055.1_ASM283705v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:33,519] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:33,522] [INFO] Selected 16 target genomes.
[2024-01-24 11:05:33,522] [INFO] Target genome list was writen to GCF_002837055.1_ASM283705v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:33,529] [INFO] Task started: fastANI
[2024-01-24 11:05:33,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c7c89e7-59f5-485f-991f-57c8ab9ce3f1/GCF_002837055.1_ASM283705v1_genomic.fna.gz --refList GCF_002837055.1_ASM283705v1_genomic.fna/target_genomes.txt --output GCF_002837055.1_ASM283705v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:38,890] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:38,890] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03d7c1b5-a7c6-4dc6-a517-513a28ed1460/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:38,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03d7c1b5-a7c6-4dc6-a517-513a28ed1460/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:38,902] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:05:38,902] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:38,902] [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 apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	100.0	493	497	95	conclusive
Lactobacillus apis	strain=CCM 8403	GCA_014635365.1	303541	303541	type	True	99.9897	496	497	95	conclusive
Lactobacillus laiwuensis	strain=F551-2	GCA_019972835.1	2841034	2841034	type	True	79.7146	205	497	95	below_threshold
Lactobacillus huangpiensis	strain=F306-1	GCA_019972815.1	2799571	2799571	type	True	79.4167	195	497	95	below_threshold
Lactobacillus kitasatonis	strain=JCM 1039	GCA_000615285.1	237446	237446	type	True	78.6729	118	497	95	below_threshold
Lactobacillus crispatus	strain=ATCC 33820	GCA_002088015.1	47770	47770	type	True	78.669	111	497	95	below_threshold
Lactobacillus kitasatonis	strain=DSM 16761	GCA_001434435.1	237446	237446	type	True	78.6522	115	497	95	below_threshold
Lactobacillus acetotolerans	strain=JCM 3825	GCA_014648715.1	1600	1600	type	True	78.5903	118	497	95	below_threshold
Lactobacillus crispatus	strain=NCK2488	GCA_008694755.1	47770	47770	type	True	78.5814	109	497	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_000159415.1	227945	227945	type	True	78.5518	103	497	95	below_threshold
Lactobacillus crispatus	strain=DSM 20584	GCA_001434005.1	47770	47770	type	True	78.543	112	497	95	below_threshold
Lactobacillus acetotolerans	strain=DSM 20749	GCA_001436775.1	1600	1600	type	True	78.5288	119	497	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	78.3967	100	497	95	below_threshold
Lactobacillus amylovorus	strain=DSM 20531	GCA_002706375.1	1604	1604	type	True	78.3795	110	497	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:38,904] [INFO] DFAST Taxonomy check result was written to GCF_002837055.1_ASM283705v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:38,905] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:38,905] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:38,906] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03d7c1b5-a7c6-4dc6-a517-513a28ed1460/dqc_reference/checkm_data
[2024-01-24 11:05:38,907] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:38,956] [INFO] Task started: CheckM
[2024-01-24 11:05:38,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002837055.1_ASM283705v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002837055.1_ASM283705v1_genomic.fna/checkm_input GCF_002837055.1_ASM283705v1_genomic.fna/checkm_result
[2024-01-24 11:05:58,127] [INFO] Task succeeded: CheckM
[2024-01-24 11:05:58,128] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:05:58,154] [INFO] ===== Completeness check finished =====
[2024-01-24 11:05:58,155] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:05:58,155] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002837055.1_ASM283705v1_genomic.fna/markers.fasta)
[2024-01-24 11:05:58,159] [INFO] Task started: Blastn
[2024-01-24 11:05:58,160] [INFO] Running command: blastn -query GCF_002837055.1_ASM283705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03d7c1b5-a7c6-4dc6-a517-513a28ed1460/dqc_reference/reference_markers_gtdb.fasta -out GCF_002837055.1_ASM283705v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:59,503] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:59,507] [INFO] Selected 15 target genomes.
[2024-01-24 11:05:59,507] [INFO] Target genome list was writen to GCF_002837055.1_ASM283705v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:05:59,526] [INFO] Task started: fastANI
[2024-01-24 11:05:59,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c7c89e7-59f5-485f-991f-57c8ab9ce3f1/GCF_002837055.1_ASM283705v1_genomic.fna.gz --refList GCF_002837055.1_ASM283705v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002837055.1_ASM283705v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:05,479] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:05,492] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:05,493] [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_002837055.1	s__Lactobacillus apis	100.0	493	497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.63	96.48	0.93	0.86	10	conclusive
GCF_002916935.1	s__Lactobacillus panisapium	80.3465	237	497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000970755.1	s__Lactobacillus kimbladii_A	79.7542	193	497	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	79.7038	199	497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.75	96.46	0.90	0.86	9	-
GCF_014323605.1	s__Lactobacillus kimbladii_B	79.6539	200	497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967195.1	s__Lactobacillus kullabergensis	79.5489	203	497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.65	96.49	0.90	0.88	4	-
GCF_016100975.1	s__Lactobacillus sp016100975	79.4822	209	497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000760615.1	s__Lactobacillus sp000760615	79.4246	213	497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.94	96.94	0.89	0.89	2	-
GCF_000970855.1	s__Lactobacillus helsingborgensis	79.2759	199	497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.65	97.05	0.93	0.90	6	-
GCA_014803915.1	s__Lactobacillus sp014803915	78.8628	91	497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000615285.1	s__Lactobacillus kitasatonis	78.6562	119	497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	-
GCF_001436305.1	s__Lactobacillus ultunensis	78.3967	100	497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
GCF_018987235.1	s__Lactobacillus crispatus	78.2155	122	497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:05,494] [INFO] GTDB search result was written to GCF_002837055.1_ASM283705v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:05,495] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:05,499] [INFO] DFAST_QC result json was written to GCF_002837055.1_ASM283705v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:05,500] [INFO] DFAST_QC completed!
[2024-01-24 11:06:05,500] [INFO] Total running time: 0h0m37s