[2024-01-25 19:50:35,892] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:35,893] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:35,893] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9108f07-8a61-4745-b542-11d9087d13c1/dqc_reference
[2024-01-25 19:50:37,044] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:37,044] [INFO] Task started: Prodigal
[2024-01-25 19:50:37,045] [INFO] Running command: gunzip -c /var/lib/cwl/stg76440b01-673c-4bdd-a492-b424e3252ad3/GCF_026413145.1_ASM2641314v1_genomic.fna.gz | prodigal -d GCF_026413145.1_ASM2641314v1_genomic.fna/cds.fna -a GCF_026413145.1_ASM2641314v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:50:41,527] [INFO] Task succeeded: Prodigal
[2024-01-25 19:50:41,528] [INFO] Task started: HMMsearch
[2024-01-25 19:50:41,528] [INFO] Running command: hmmsearch --tblout GCF_026413145.1_ASM2641314v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9108f07-8a61-4745-b542-11d9087d13c1/dqc_reference/reference_markers.hmm GCF_026413145.1_ASM2641314v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:50:41,743] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:50:41,744] [INFO] Found 6/6 markers.
[2024-01-25 19:50:41,766] [INFO] Query marker FASTA was written to GCF_026413145.1_ASM2641314v1_genomic.fna/markers.fasta
[2024-01-25 19:50:41,767] [INFO] Task started: Blastn
[2024-01-25 19:50:41,767] [INFO] Running command: blastn -query GCF_026413145.1_ASM2641314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9108f07-8a61-4745-b542-11d9087d13c1/dqc_reference/reference_markers.fasta -out GCF_026413145.1_ASM2641314v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:42,334] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:42,337] [INFO] Selected 12 target genomes.
[2024-01-25 19:50:42,338] [INFO] Target genome list was writen to GCF_026413145.1_ASM2641314v1_genomic.fna/target_genomes.txt
[2024-01-25 19:50:42,361] [INFO] Task started: fastANI
[2024-01-25 19:50:42,361] [INFO] Running command: fastANI --query /var/lib/cwl/stg76440b01-673c-4bdd-a492-b424e3252ad3/GCF_026413145.1_ASM2641314v1_genomic.fna.gz --refList GCF_026413145.1_ASM2641314v1_genomic.fna/target_genomes.txt --output GCF_026413145.1_ASM2641314v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:50:47,304] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:47,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9108f07-8a61-4745-b542-11d9087d13c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:50:47,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9108f07-8a61-4745-b542-11d9087d13c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:50:47,312] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:50:47,312] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:50:47,312] [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	81.33	322	648	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001027985.1	47493	47493	type	True	79.9048	211	648	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001435935.1	47493	47493	type	True	79.8675	209	648	95	below_threshold
Limosilactobacillus antri	strain=DSM 16041	GCA_000160835.1	227943	227943	type	True	79.6947	230	648	95	below_threshold
Limosilactobacillus oris	strain=DSM 4864	GCA_001434465.1	1632	1632	type	True	79.6882	210	648	95	below_threshold
Limosilactobacillus antri	strain=DSM 16041	GCA_001435475.1	227943	227943	type	True	79.6386	217	648	95	below_threshold
Limosilactobacillus fermentum	strain=DSM 20052	GCA_013394085.1	1613	1613	type	True	77.8762	124	648	95	below_threshold
Limosilactobacillus fermentum	strain=B1 28	GCA_005341425.1	1613	1613	type	True	77.8723	123	648	95	below_threshold
Limosilactobacillus fermentum	strain=ATCC 14931	GCA_000159215.1	1613	1613	type	True	77.7961	117	648	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:50:47,314] [INFO] DFAST Taxonomy check result was written to GCF_026413145.1_ASM2641314v1_genomic.fna/tc_result.tsv
[2024-01-25 19:50:47,320] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:50:47,320] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:50:47,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9108f07-8a61-4745-b542-11d9087d13c1/dqc_reference/checkm_data
[2024-01-25 19:50:47,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:50:47,347] [INFO] Task started: CheckM
[2024-01-25 19:50:47,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026413145.1_ASM2641314v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026413145.1_ASM2641314v1_genomic.fna/checkm_input GCF_026413145.1_ASM2641314v1_genomic.fna/checkm_result
[2024-01-25 19:51:07,157] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:07,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:07,180] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:07,180] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:07,180] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026413145.1_ASM2641314v1_genomic.fna/markers.fasta)
[2024-01-25 19:51:07,181] [INFO] Task started: Blastn
[2024-01-25 19:51:07,181] [INFO] Running command: blastn -query GCF_026413145.1_ASM2641314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9108f07-8a61-4745-b542-11d9087d13c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_026413145.1_ASM2641314v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:07,950] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:07,953] [INFO] Selected 10 target genomes.
[2024-01-25 19:51:07,953] [INFO] Target genome list was writen to GCF_026413145.1_ASM2641314v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:07,963] [INFO] Task started: fastANI
[2024-01-25 19:51:07,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg76440b01-673c-4bdd-a492-b424e3252ad3/GCF_026413145.1_ASM2641314v1_genomic.fna.gz --refList GCF_026413145.1_ASM2641314v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026413145.1_ASM2641314v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:11,438] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:11,445] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:51:11,445] [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
GCA_019117285.1	s__Limosilactobacillus intestinigallinarum	82.1694	235	648	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.99	99.99	0.94	0.94	2	-
GCA_019118405.1	s__Limosilactobacillus gallistercoris	81.4	236	648	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.70	98.67	0.88	0.83	3	-
GCF_001435345.1	s__Limosilactobacillus pontis	81.3298	322	648	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.82	97.66	0.95	0.90	3	-
GCA_002299975.1	s__Limosilactobacillus sp002299975	80.9425	218	648	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.38	99.38	0.84	0.84	2	-
GCF_002940945.1	s__Limosilactobacillus pontis_A	80.7073	274	648	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214235.1	s__Limosilactobacillus sp905214235	80.0935	221	648	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016825.1	s__Limosilactobacillus reuteri	79.7295	103	648	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	96.73	95.25	0.84	0.75	135	-
GCF_001434465.1	s__Limosilactobacillus oris	79.6882	210	648	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.39	95.80	0.88	0.80	8	-
GCF_001436025.1	s__Limosilactobacillus mucosae	78.4023	90	648	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.05	95.70	0.88	0.73	22	-
GCA_019113965.1	s__Limosilactobacillus merdipullorum	77.6543	81	648	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:51:11,446] [INFO] GTDB search result was written to GCF_026413145.1_ASM2641314v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:11,447] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:11,449] [INFO] DFAST_QC result json was written to GCF_026413145.1_ASM2641314v1_genomic.fna/dqc_result.json
[2024-01-25 19:51:11,450] [INFO] DFAST_QC completed!
[2024-01-25 19:51:11,450] [INFO] Total running time: 0h0m36s