[2024-01-24 13:33:10,171] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:10,173] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:10,173] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e2ce0d1-eb71-46b3-b4c5-1ab18ed5805e/dqc_reference
[2024-01-24 13:33:11,346] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:11,347] [INFO] Task started: Prodigal
[2024-01-24 13:33:11,347] [INFO] Running command: gunzip -c /var/lib/cwl/stg163b52f3-d2aa-4cff-af79-e138ea6b0ec1/GCF_001436215.1_ASM143621v1_genomic.fna.gz | prodigal -d GCF_001436215.1_ASM143621v1_genomic.fna/cds.fna -a GCF_001436215.1_ASM143621v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:15,181] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:15,182] [INFO] Task started: HMMsearch
[2024-01-24 13:33:15,182] [INFO] Running command: hmmsearch --tblout GCF_001436215.1_ASM143621v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e2ce0d1-eb71-46b3-b4c5-1ab18ed5805e/dqc_reference/reference_markers.hmm GCF_001436215.1_ASM143621v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:15,404] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:15,405] [INFO] Found 6/6 markers.
[2024-01-24 13:33:15,427] [INFO] Query marker FASTA was written to GCF_001436215.1_ASM143621v1_genomic.fna/markers.fasta
[2024-01-24 13:33:15,427] [INFO] Task started: Blastn
[2024-01-24 13:33:15,427] [INFO] Running command: blastn -query GCF_001436215.1_ASM143621v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e2ce0d1-eb71-46b3-b4c5-1ab18ed5805e/dqc_reference/reference_markers.fasta -out GCF_001436215.1_ASM143621v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:16,002] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:16,006] [INFO] Selected 25 target genomes.
[2024-01-24 13:33:16,007] [INFO] Target genome list was writen to GCF_001436215.1_ASM143621v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:16,074] [INFO] Task started: fastANI
[2024-01-24 13:33:16,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg163b52f3-d2aa-4cff-af79-e138ea6b0ec1/GCF_001436215.1_ASM143621v1_genomic.fna.gz --refList GCF_001436215.1_ASM143621v1_genomic.fna/target_genomes.txt --output GCF_001436215.1_ASM143621v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:25,470] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:25,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e2ce0d1-eb71-46b3-b4c5-1ab18ed5805e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:25,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e2ce0d1-eb71-46b3-b4c5-1ab18ed5805e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:25,485] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:25,485] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:25,485] [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
Ligilactobacillus agilis	strain=DSM 20509	GCA_001436215.1	1601	1601	type	True	100.0	660	661	95	conclusive
Ligilactobacillus equi	strain=JCM 10991	GCA_000615765.1	137357	137357	type	True	79.0545	104	661	95	below_threshold
Ligilactobacillus hayakitensis	strain=JCM 14209	GCA_000615845.1	396716	396716	type	True	78.9456	81	661	95	below_threshold
Ligilactobacillus aviarius	strain=DSM 20655	GCA_001436315.1	1606	1606	type	True	78.8829	60	661	95	below_threshold
Ligilactobacillus equi	strain=DSM 15833	GCA_001435735.1	137357	137357	type	True	78.8818	105	661	95	below_threshold
Ligilactobacillus aviarius	strain=NBRC 102162	GCA_007989665.1	1606	1606	type	True	78.7515	56	661	95	below_threshold
Ligilactobacillus salivarius	strain=DSM 20554	GCA_002079585.1	1624	1624	type	True	78.6398	83	661	95	below_threshold
Ligilactobacillus salivarius	strain=DSM 20555	GCA_001435955.1	1624	1624	type	True	78.6236	74	661	95	below_threshold
Ligilactobacillus araffinosus	strain=DSM 20653	GCA_001435375.1	147809	147809	type	True	78.5395	57	661	95	below_threshold
Ligilactobacillus hayakitensis	strain=DSM 18933	GCA_001434455.1	396716	396716	type	True	78.4817	75	661	95	below_threshold
Ligilactobacillus apodemi	strain=DSM 16634	GCA_001434405.1	307126	307126	type	True	78.3205	87	661	95	below_threshold
Ligilactobacillus apodemi	strain=JCM 16172	GCA_000615885.1	307126	307126	type	True	78.3144	88	661	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:25,487] [INFO] DFAST Taxonomy check result was written to GCF_001436215.1_ASM143621v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:25,488] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:25,488] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:25,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e2ce0d1-eb71-46b3-b4c5-1ab18ed5805e/dqc_reference/checkm_data
[2024-01-24 13:33:25,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:25,512] [INFO] Task started: CheckM
[2024-01-24 13:33:25,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001436215.1_ASM143621v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001436215.1_ASM143621v1_genomic.fna/checkm_input GCF_001436215.1_ASM143621v1_genomic.fna/checkm_result
[2024-01-24 13:33:44,009] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:44,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:44,030] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:44,031] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:44,031] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001436215.1_ASM143621v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:44,032] [INFO] Task started: Blastn
[2024-01-24 13:33:44,032] [INFO] Running command: blastn -query GCF_001436215.1_ASM143621v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e2ce0d1-eb71-46b3-b4c5-1ab18ed5805e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001436215.1_ASM143621v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:44,769] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:44,774] [INFO] Selected 25 target genomes.
[2024-01-24 13:33:44,774] [INFO] Target genome list was writen to GCF_001436215.1_ASM143621v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:44,814] [INFO] Task started: fastANI
[2024-01-24 13:33:44,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg163b52f3-d2aa-4cff-af79-e138ea6b0ec1/GCF_001436215.1_ASM143621v1_genomic.fna.gz --refList GCF_001436215.1_ASM143621v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001436215.1_ASM143621v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:54,001] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:54,014] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:54,014] [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_001436215.1	s__Ligilactobacillus agilis	100.0	660	661	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.37	95.88	0.84	0.79	29	conclusive
GCF_900113455.1	s__Ligilactobacillus ruminis	79.3083	52	661	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.28	96.58	0.88	0.79	57	-
GCF_001654615.1	s__Ligilactobacillus aviarius_B	79.262	53	661	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.09	96.72	0.90	0.88	16	-
GCF_000615765.1	s__Ligilactobacillus equi	79.0545	104	661	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.27	98.57	0.92	0.85	3	-
GCF_000615845.1	s__Ligilactobacillus hayakitensis	79.0082	80	661	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.97	99.97	0.98	0.98	2	-
GCF_001436315.1	s__Ligilactobacillus aviarius	78.8829	60	661	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.10	96.00	0.94	0.89	5	-
GCF_001435955.1	s__Ligilactobacillus salivarius	78.6236	74	661	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.81	97.07	0.87	0.79	193	-
GCA_905204935.1	s__Ligilactobacillus sp900765635	78.5725	74	661	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.97	99.97	0.92	0.92	2	-
GCF_001435375.1	s__Ligilactobacillus araffinosus	78.5395	57	661	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434405.1	s__Ligilactobacillus apodemi	78.3032	88	661	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.97	99.97	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:54,016] [INFO] GTDB search result was written to GCF_001436215.1_ASM143621v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:54,016] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:54,020] [INFO] DFAST_QC result json was written to GCF_001436215.1_ASM143621v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:54,020] [INFO] DFAST_QC completed!
[2024-01-24 13:33:54,020] [INFO] Total running time: 0h0m44s