[2024-01-24 13:28:01,287] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:01,293] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:01,293] [INFO] DQC Reference Directory: /var/lib/cwl/stged6ee4e4-1507-45b4-88c5-9fa455d88761/dqc_reference
[2024-01-24 13:28:02,665] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:02,666] [INFO] Task started: Prodigal
[2024-01-24 13:28:02,667] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0cf4c7b-f8e5-4156-9070-321a75c9eec8/GCF_013394085.1_ASM1339408v1_genomic.fna.gz | prodigal -d GCF_013394085.1_ASM1339408v1_genomic.fna/cds.fna -a GCF_013394085.1_ASM1339408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:07,518] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:07,518] [INFO] Task started: HMMsearch
[2024-01-24 13:28:07,518] [INFO] Running command: hmmsearch --tblout GCF_013394085.1_ASM1339408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged6ee4e4-1507-45b4-88c5-9fa455d88761/dqc_reference/reference_markers.hmm GCF_013394085.1_ASM1339408v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:07,736] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:07,737] [INFO] Found 6/6 markers.
[2024-01-24 13:28:07,756] [INFO] Query marker FASTA was written to GCF_013394085.1_ASM1339408v1_genomic.fna/markers.fasta
[2024-01-24 13:28:07,756] [INFO] Task started: Blastn
[2024-01-24 13:28:07,756] [INFO] Running command: blastn -query GCF_013394085.1_ASM1339408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged6ee4e4-1507-45b4-88c5-9fa455d88761/dqc_reference/reference_markers.fasta -out GCF_013394085.1_ASM1339408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:08,323] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:08,326] [INFO] Selected 16 target genomes.
[2024-01-24 13:28:08,327] [INFO] Target genome list was writen to GCF_013394085.1_ASM1339408v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:08,371] [INFO] Task started: fastANI
[2024-01-24 13:28:08,372] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0cf4c7b-f8e5-4156-9070-321a75c9eec8/GCF_013394085.1_ASM1339408v1_genomic.fna.gz --refList GCF_013394085.1_ASM1339408v1_genomic.fna/target_genomes.txt --output GCF_013394085.1_ASM1339408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:16,434] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:16,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged6ee4e4-1507-45b4-88c5-9fa455d88761/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:16,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged6ee4e4-1507-45b4-88c5-9fa455d88761/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:16,444] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:28:16,445] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:16,445] [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 fermentum	strain=DSM 20052	GCA_013394085.1	1613	1613	type	True	100.0	629	629	95	conclusive
Limosilactobacillus fermentum	strain=B1 28	GCA_005341425.1	1613	1613	type	True	99.9362	622	629	95	conclusive
Limosilactobacillus fermentum	strain=ATCC 14931	GCA_000159215.1	1613	1613	type	True	99.8241	591	629	95	conclusive
Limosilactobacillus gorillae	strain=KZ01	GCA_001293735.1	1450649	1450649	type	True	81.3106	327	629	95	below_threshold
Limosilactobacillus avistercoris	strain=Sa3CUN2	GCA_014836425.1	2762243	2762243	type	True	78.8443	54	629	95	below_threshold
Limosilactobacillus antri	strain=DSM 16041	GCA_000160835.1	227943	227943	type	True	78.8141	102	629	95	below_threshold
Limosilactobacillus antri	strain=DSM 16041	GCA_001435475.1	227943	227943	type	True	78.593	94	629	95	below_threshold
Limosilactobacillus ingluviei	strain=DSM 15946	GCA_001435775.1	148604	148604	type	True	78.053	143	629	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001027985.1	47493	47493	type	True	77.857	98	629	95	below_threshold
Limosilactobacillus oris	strain=DSM 4864	GCA_001434465.1	1632	1632	type	True	77.7816	99	629	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:16,447] [INFO] DFAST Taxonomy check result was written to GCF_013394085.1_ASM1339408v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:16,447] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:16,447] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:16,448] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged6ee4e4-1507-45b4-88c5-9fa455d88761/dqc_reference/checkm_data
[2024-01-24 13:28:16,449] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:16,470] [INFO] Task started: CheckM
[2024-01-24 13:28:16,470] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013394085.1_ASM1339408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013394085.1_ASM1339408v1_genomic.fna/checkm_input GCF_013394085.1_ASM1339408v1_genomic.fna/checkm_result
[2024-01-24 13:28:36,642] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:36,643] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:36,669] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:36,669] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:36,670] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013394085.1_ASM1339408v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:36,670] [INFO] Task started: Blastn
[2024-01-24 13:28:36,670] [INFO] Running command: blastn -query GCF_013394085.1_ASM1339408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged6ee4e4-1507-45b4-88c5-9fa455d88761/dqc_reference/reference_markers_gtdb.fasta -out GCF_013394085.1_ASM1339408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:37,486] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:37,489] [INFO] Selected 18 target genomes.
[2024-01-24 13:28:37,489] [INFO] Target genome list was writen to GCF_013394085.1_ASM1339408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:37,519] [INFO] Task started: fastANI
[2024-01-24 13:28:37,519] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0cf4c7b-f8e5-4156-9070-321a75c9eec8/GCF_013394085.1_ASM1339408v1_genomic.fna.gz --refList GCF_013394085.1_ASM1339408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013394085.1_ASM1339408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:43,524] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:43,535] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:43,536] [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_013394085.1	s__Limosilactobacillus fermentum	100.0	628	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.65	97.32	0.90	0.60	102	conclusive
GCF_001293735.1	s__Limosilactobacillus gorillae	81.302	327	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000160835.1	s__Limosilactobacillus antri	78.8141	102	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.98	99.98	0.99	0.99	3	-
GCF_001436025.1	s__Limosilactobacillus mucosae	78.341	84	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.05	95.70	0.88	0.73	22	-
GCF_002940945.1	s__Limosilactobacillus pontis_A	78.1715	80	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435775.1	s__Limosilactobacillus ingluviei	78.0579	143	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.51	97.11	0.84	0.81	5	-
GCF_001434465.1	s__Limosilactobacillus oris	77.7816	99	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.39	95.80	0.88	0.80	8	-
GCA_019117285.1	s__Limosilactobacillus intestinigallinarum	77.6278	91	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.99	99.99	0.94	0.94	2	-
GCA_905214235.1	s__Limosilactobacillus sp905214235	77.6196	100	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012843675.1	s__Limosilactobacillus sp012843675	77.5848	94	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.07	98.07	0.86	0.86	2	-
GCF_001435935.1	s__Limosilactobacillus panis	77.49	97	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.95	99.95	0.95	0.95	2	-
GCA_019117185.1	s__Limosilactobacillus intestinipullorum	76.8789	88	629	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.21	99.14	0.84	0.80	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:43,537] [INFO] GTDB search result was written to GCF_013394085.1_ASM1339408v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:43,538] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:43,542] [INFO] DFAST_QC result json was written to GCF_013394085.1_ASM1339408v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:43,543] [INFO] DFAST_QC completed!
[2024-01-24 13:28:43,543] [INFO] Total running time: 0h0m42s