[2024-01-24 11:59:22,962] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:22,964] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:22,964] [INFO] DQC Reference Directory: /var/lib/cwl/stgf17a3d72-b611-4453-978c-759790311e40/dqc_reference
[2024-01-24 11:59:25,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:25,642] [INFO] Task started: Prodigal
[2024-01-24 11:59:25,642] [INFO] Running command: gunzip -c /var/lib/cwl/stgb06c48f8-6a75-405e-b950-aa360e0a683b/GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna.gz | prodigal -d GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/cds.fna -a GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:29,929] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:29,929] [INFO] Task started: HMMsearch
[2024-01-24 11:59:29,929] [INFO] Running command: hmmsearch --tblout GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf17a3d72-b611-4453-978c-759790311e40/dqc_reference/reference_markers.hmm GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:30,319] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:30,320] [INFO] Found 6/6 markers.
[2024-01-24 11:59:30,340] [INFO] Query marker FASTA was written to GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/markers.fasta
[2024-01-24 11:59:30,341] [INFO] Task started: Blastn
[2024-01-24 11:59:30,341] [INFO] Running command: blastn -query GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/markers.fasta -db /var/lib/cwl/stgf17a3d72-b611-4453-978c-759790311e40/dqc_reference/reference_markers.fasta -out GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:32,383] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:32,386] [INFO] Selected 25 target genomes.
[2024-01-24 11:59:32,387] [INFO] Target genome list was writen to GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/target_genomes.txt
[2024-01-24 11:59:32,481] [INFO] Task started: fastANI
[2024-01-24 11:59:32,481] [INFO] Running command: fastANI --query /var/lib/cwl/stgb06c48f8-6a75-405e-b950-aa360e0a683b/GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna.gz --refList GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/target_genomes.txt --output GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:39,548] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:39,549] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf17a3d72-b611-4453-978c-759790311e40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:39,549] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf17a3d72-b611-4453-978c-759790311e40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:39,564] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:59:39,564] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:59:39,564] [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
Limosilactobacillus pontis	strain=DSM 8475	GCA_001435345.1	35787	35787	type	True	79.1486	61	559	95	below_threshold
Limosilactobacillus secaliphilus	strain=DSM 17896	GCA_001437055.1	396268	396268	type	True	78.864	107	559	95	below_threshold
Limosilactobacillus rudii	strain=STM3_1	GCA_014145455.1	2759755	2759755	type	True	78.8225	73	559	95	below_threshold
Limosilactobacillus vaginalis	strain=ATCC 49540	GCA_000159435.1	1633	1633	type	True	78.6691	81	559	95	below_threshold
Limosilactobacillus vaginalis	strain=DSM 5837	GCA_001435915.1	1633	1633	type	True	78.6578	79	559	95	below_threshold
Limosilactobacillus reuteri subsp. suis	strain=ATCC 53608	GCA_000236455.2	927703	1598	type	True	78.6571	78	559	95	below_threshold
Limosilactobacillus albertensis	strain=Lr3000	GCA_014145555.1	2759752	2759752	type	True	78.5501	78	559	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=JCM 1112	GCA_000010005.1	557436	1598	type	True	78.4908	82	559	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001435935.1	47493	47493	type	True	78.4374	88	559	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001027985.1	47493	47493	type	True	78.4215	86	559	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=DSM 20016	GCA_001434615.1	557436	1598	type	True	78.2513	82	559	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=DSM 20016	GCA_000016825.1	557436	1598	type	True	78.1754	83	559	95	below_threshold
Limosilactobacillus gorillae	strain=KZ01	GCA_001293735.1	1450649	1450649	type	True	78.1205	68	559	95	below_threshold
Limosilactobacillus ingluviei	strain=DSM 15946	GCA_001435775.1	148604	148604	type	True	78.0326	75	559	95	below_threshold
Limosilactobacillus mucosae	strain=DSM 13345	GCA_001436025.1	97478	97478	type	True	77.8694	75	559	95	below_threshold
[Lactobacillus] timonensis	strain=Marseille-P3825	GCA_900240275.1	1970790	1970790	type	True	77.593	57	559	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:39,566] [INFO] DFAST Taxonomy check result was written to GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/tc_result.tsv
[2024-01-24 11:59:39,566] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:39,566] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:39,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf17a3d72-b611-4453-978c-759790311e40/dqc_reference/checkm_data
[2024-01-24 11:59:39,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:39,586] [INFO] Task started: CheckM
[2024-01-24 11:59:39,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/checkm_input GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/checkm_result
[2024-01-24 12:00:00,002] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:00,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:00,022] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:00,023] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:00,023] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/markers.fasta)
[2024-01-24 12:00:00,023] [INFO] Task started: Blastn
[2024-01-24 12:00:00,024] [INFO] Running command: blastn -query GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/markers.fasta -db /var/lib/cwl/stgf17a3d72-b611-4453-978c-759790311e40/dqc_reference/reference_markers_gtdb.fasta -out GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:00,763] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:00,767] [INFO] Selected 22 target genomes.
[2024-01-24 12:00:00,767] [INFO] Target genome list was writen to GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:00,794] [INFO] Task started: fastANI
[2024-01-24 12:00:00,795] [INFO] Running command: fastANI --query /var/lib/cwl/stgb06c48f8-6a75-405e-b950-aa360e0a683b/GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna.gz --refList GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/target_genomes_gtdb.txt --output GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:07,002] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:07,018] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:00:07,018] [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_000161935.1	s__Limosilactobacillus coleohominis_A	79.9838	233	559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901675.1	s__Limosilactobacillus coleohominis	79.9261	176	559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.52	96.59	0.81	0.71	8	-
GCA_019117445.1	s__Limosilactobacillus excrementigallinarum	79.7265	192	559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	96.52	96.52	0.81	0.81	2	-
GCF_001435345.1	s__Limosilactobacillus pontis	79.1486	61	559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.82	97.66	0.95	0.90	3	-
GCF_014145455.1	s__Limosilactobacillus rudii	78.8841	72	559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001437055.1	s__Limosilactobacillus secaliphilus	78.864	107	559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014838735.1	s__Limosilactobacillus portuensis	78.6702	83	559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.50	97.46	0.87	0.84	6	-
GCF_000159435.1	s__Limosilactobacillus vaginalis	78.6691	81	559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.80	96.39	0.94	0.86	8	-
GCA_019114515.1	s__Limosilactobacillus merdigallinarum	78.6376	99	559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013694365.1	s__Limosilactobacillus reuteri_E	78.2105	73	559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.28	96.40	0.80	0.72	58	-
GCF_000016825.1	s__Limosilactobacillus reuteri	78.176	83	559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	96.73	95.25	0.84	0.75	135	-
GCF_016900115.1	s__Limosilactobacillus alvi	78.1622	83	559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.65	97.65	0.93	0.93	2	-
GCF_001436025.1	s__Limosilactobacillus mucosae	77.8694	75	559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.05	95.70	0.88	0.73	22	-
GCA_018883805.1	s__Limosilactobacillus merdavium	77.8491	57	559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	96.07	96.07	0.81	0.81	2	-
GCF_012843675.1	s__Limosilactobacillus sp012843675	77.5841	70	559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.07	98.07	0.86	0.86	2	-
GCA_019118465.1	s__Limosilactobacillus faecipullorum	77.2852	84	559	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:07,020] [INFO] GTDB search result was written to GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:07,020] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:07,024] [INFO] DFAST_QC result json was written to GCF_943192935.1_Limosilactobacillus_sp_nov1_DSM110982_genomic.fna/dqc_result.json
[2024-01-24 12:00:07,024] [INFO] DFAST_QC completed!
[2024-01-24 12:00:07,024] [INFO] Total running time: 0h0m44s