[2024-01-24 13:18:43,614] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:43,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:43,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f11d3ef-d38f-47ca-bb02-0920403c5160/dqc_reference
[2024-01-24 13:18:44,798] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:44,799] [INFO] Task started: Prodigal
[2024-01-24 13:18:44,800] [INFO] Running command: gunzip -c /var/lib/cwl/stge391c90d-c87c-4ef7-a00d-c389d37e0bdd/GCF_001436455.1_ASM143645v1_genomic.fna.gz | prodigal -d GCF_001436455.1_ASM143645v1_genomic.fna/cds.fna -a GCF_001436455.1_ASM143645v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:47,632] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:47,633] [INFO] Task started: HMMsearch
[2024-01-24 13:18:47,633] [INFO] Running command: hmmsearch --tblout GCF_001436455.1_ASM143645v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f11d3ef-d38f-47ca-bb02-0920403c5160/dqc_reference/reference_markers.hmm GCF_001436455.1_ASM143645v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:47,838] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:47,839] [INFO] Found 6/6 markers.
[2024-01-24 13:18:47,855] [INFO] Query marker FASTA was written to GCF_001436455.1_ASM143645v1_genomic.fna/markers.fasta
[2024-01-24 13:18:47,855] [INFO] Task started: Blastn
[2024-01-24 13:18:47,856] [INFO] Running command: blastn -query GCF_001436455.1_ASM143645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f11d3ef-d38f-47ca-bb02-0920403c5160/dqc_reference/reference_markers.fasta -out GCF_001436455.1_ASM143645v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:48,471] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:48,474] [INFO] Selected 13 target genomes.
[2024-01-24 13:18:48,474] [INFO] Target genome list was writen to GCF_001436455.1_ASM143645v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:48,484] [INFO] Task started: fastANI
[2024-01-24 13:18:48,484] [INFO] Running command: fastANI --query /var/lib/cwl/stge391c90d-c87c-4ef7-a00d-c389d37e0bdd/GCF_001436455.1_ASM143645v1_genomic.fna.gz --refList GCF_001436455.1_ASM143645v1_genomic.fna/target_genomes.txt --output GCF_001436455.1_ASM143645v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:52,481] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:52,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f11d3ef-d38f-47ca-bb02-0920403c5160/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:52,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f11d3ef-d38f-47ca-bb02-0920403c5160/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:52,494] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:52,495] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:52,495] [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 jensenii	strain=DSM 20557	GCA_001436455.1	109790	109790	type	True	100.0	497	499	95	conclusive
Lactobacillus jensenii	strain=ATCC 25258	GCA_018094625.1	109790	109790	type	True	99.9785	495	499	95	conclusive
Lactobacillus mulieris	strain=c10Ua161M	GCA_007095465.1	2508708	2508708	type	True	88.4924	413	499	95	below_threshold
Lactobacillus psittaci	strain=DSM 15354	GCA_001435695.1	116089	116089	type	True	87.243	316	499	95	below_threshold
Lactobacillus psittaci	strain=DSM 15354	GCA_000425905.1	116089	116089	type	True	87.0769	323	499	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_001435665.1	83683	83683	type	True	78.8134	109	499	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	78.7764	129	499	95	below_threshold
Lactobacillus acidophilus	strain=DSM 20079	GCA_001433895.1	1579	1579	type	True	78.5223	145	499	95	below_threshold
Lactobacillus acidophilus	strain=ATCC 4356	GCA_000786395.1	1579	1579	type	True	78.2907	150	499	95	below_threshold
Lactobacillus laiwuensis	strain=F551-2	GCA_019972835.1	2841034	2841034	type	True	77.1377	74	499	95	below_threshold
Lactobacillus huangpiensis	strain=F306-1	GCA_019972815.1	2799571	2799571	type	True	76.7759	69	499	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:52,497] [INFO] DFAST Taxonomy check result was written to GCF_001436455.1_ASM143645v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:52,497] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:52,497] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:52,498] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f11d3ef-d38f-47ca-bb02-0920403c5160/dqc_reference/checkm_data
[2024-01-24 13:18:52,499] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:52,517] [INFO] Task started: CheckM
[2024-01-24 13:18:52,517] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001436455.1_ASM143645v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001436455.1_ASM143645v1_genomic.fna/checkm_input GCF_001436455.1_ASM143645v1_genomic.fna/checkm_result
[2024-01-24 13:19:08,504] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:08,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:08,528] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:08,528] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:08,528] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001436455.1_ASM143645v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:08,529] [INFO] Task started: Blastn
[2024-01-24 13:19:08,529] [INFO] Running command: blastn -query GCF_001436455.1_ASM143645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f11d3ef-d38f-47ca-bb02-0920403c5160/dqc_reference/reference_markers_gtdb.fasta -out GCF_001436455.1_ASM143645v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:09,327] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:09,344] [INFO] Selected 16 target genomes.
[2024-01-24 13:19:09,344] [INFO] Target genome list was writen to GCF_001436455.1_ASM143645v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:09,363] [INFO] Task started: fastANI
[2024-01-24 13:19:09,363] [INFO] Running command: fastANI --query /var/lib/cwl/stge391c90d-c87c-4ef7-a00d-c389d37e0bdd/GCF_001436455.1_ASM143645v1_genomic.fna.gz --refList GCF_001436455.1_ASM143645v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001436455.1_ASM143645v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:14,987] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:15,000] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:15,000] [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_001436455.1	s__Lactobacillus jensenii	100.0	497	499	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.86	99.75	0.93	0.88	31	conclusive
GCF_007095465.1	s__Lactobacillus mulieris	88.4924	413	499	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.54	96.91	0.92	0.85	18	-
GCF_000425905.1	s__Lactobacillus psittaci	87.0769	323	499	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.95	99.95	0.99	0.99	2	-
GCF_000615285.1	s__Lactobacillus kitasatonis	78.9026	117	499	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	-
GCF_000160855.1	s__Lactobacillus helveticus	78.8002	127	499	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_000178475.1	s__Lactobacillus amylolyticus	78.7588	107	499	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.45	98.00	0.96	0.87	8	-
GCF_001435325.1	s__Lactobacillus intestinalis	78.7219	125	499	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.33	96.07	0.89	0.82	9	-
GCF_004009905.1	s__Lactobacillus xujianguonis	78.7068	120	499	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	78.698	129	499	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_001434335.1	s__Lactobacillus kalixensis	78.5908	128	499	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883635.1	s__Lactobacillus pullistercoris	78.5245	115	499	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	78.4998	114	499	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.80	98.01	0.90	0.86	31	-
GCF_001591845.1	s__Lactobacillus acidophilus	78.4893	143	499	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCA_014803895.1	s__Lactobacillus sp014803895	77.8969	113	499	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001436775.1	s__Lactobacillus acetotolerans	77.8318	86	499	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.88	98.02	0.91	0.85	26	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:15,139] [INFO] GTDB search result was written to GCF_001436455.1_ASM143645v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:15,140] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:15,145] [INFO] DFAST_QC result json was written to GCF_001436455.1_ASM143645v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:15,145] [INFO] DFAST_QC completed!
[2024-01-24 13:19:15,145] [INFO] Total running time: 0h0m32s