[2023-06-13 01:53:52,888] [INFO] DFAST_QC pipeline started.
[2023-06-13 01:53:52,892] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 01:53:52,892] [INFO] DQC Reference Directory: /var/lib/cwl/stgca6f11e8-0a46-4c28-99bb-517bfe5a5eb7/dqc_reference
[2023-06-13 01:53:54,344] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 01:53:54,345] [INFO] Task started: Prodigal
[2023-06-13 01:53:54,346] [INFO] Running command: gunzip -c /var/lib/cwl/stg00b69f2e-16a9-4a49-920a-6df141df001f/GCA_022482305.1_ASM2248230v1_genomic.fna.gz | prodigal -d GCA_022482305.1_ASM2248230v1_genomic.fna/cds.fna -a GCA_022482305.1_ASM2248230v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 01:54:00,562] [INFO] Task succeeded: Prodigal
[2023-06-13 01:54:00,563] [INFO] Task started: HMMsearch
[2023-06-13 01:54:00,563] [INFO] Running command: hmmsearch --tblout GCA_022482305.1_ASM2248230v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca6f11e8-0a46-4c28-99bb-517bfe5a5eb7/dqc_reference/reference_markers.hmm GCA_022482305.1_ASM2248230v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 01:54:00,838] [INFO] Task succeeded: HMMsearch
[2023-06-13 01:54:00,839] [INFO] Found 6/6 markers.
[2023-06-13 01:54:00,873] [INFO] Query marker FASTA was written to GCA_022482305.1_ASM2248230v1_genomic.fna/markers.fasta
[2023-06-13 01:54:00,874] [INFO] Task started: Blastn
[2023-06-13 01:54:00,874] [INFO] Running command: blastn -query GCA_022482305.1_ASM2248230v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca6f11e8-0a46-4c28-99bb-517bfe5a5eb7/dqc_reference/reference_markers.fasta -out GCA_022482305.1_ASM2248230v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:54:01,502] [INFO] Task succeeded: Blastn
[2023-06-13 01:54:01,506] [INFO] Selected 13 target genomes.
[2023-06-13 01:54:01,506] [INFO] Target genome list was writen to GCA_022482305.1_ASM2248230v1_genomic.fna/target_genomes.txt
[2023-06-13 01:54:01,510] [INFO] Task started: fastANI
[2023-06-13 01:54:01,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg00b69f2e-16a9-4a49-920a-6df141df001f/GCA_022482305.1_ASM2248230v1_genomic.fna.gz --refList GCA_022482305.1_ASM2248230v1_genomic.fna/target_genomes.txt --output GCA_022482305.1_ASM2248230v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 01:54:07,545] [INFO] Task succeeded: fastANI
[2023-06-13 01:54:07,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca6f11e8-0a46-4c28-99bb-517bfe5a5eb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 01:54:07,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca6f11e8-0a46-4c28-99bb-517bfe5a5eb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 01:54:07,554] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 01:54:07,555] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 01:54:07,555] [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	81.6818	376	778	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001027985.1	47493	47493	type	True	80.5529	240	778	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001435935.1	47493	47493	type	True	80.3669	238	778	95	below_threshold
Limosilactobacillus antri	strain=DSM 16041	GCA_000160835.1	227943	227943	type	True	79.946	274	778	95	below_threshold
Limosilactobacillus antri	strain=DSM 16041	GCA_001435475.1	227943	227943	type	True	79.9355	256	778	95	below_threshold
Limosilactobacillus oris	strain=DSM 4864	GCA_001434465.1	1632	1632	type	True	79.6475	237	778	95	below_threshold
Limosilactobacillus gorillae	strain=KZ01	GCA_001293735.1	1450649	1450649	type	True	77.6885	86	778	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 01:54:07,561] [INFO] DFAST Taxonomy check result was written to GCA_022482305.1_ASM2248230v1_genomic.fna/tc_result.tsv
[2023-06-13 01:54:07,562] [INFO] ===== Taxonomy check completed =====
[2023-06-13 01:54:07,562] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 01:54:07,562] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca6f11e8-0a46-4c28-99bb-517bfe5a5eb7/dqc_reference/checkm_data
[2023-06-13 01:54:07,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 01:54:07,616] [INFO] Task started: CheckM
[2023-06-13 01:54:07,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022482305.1_ASM2248230v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022482305.1_ASM2248230v1_genomic.fna/checkm_input GCA_022482305.1_ASM2248230v1_genomic.fna/checkm_result
[2023-06-13 01:54:33,531] [INFO] Task succeeded: CheckM
[2023-06-13 01:54:33,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 01:54:33,563] [INFO] ===== Completeness check finished =====
[2023-06-13 01:54:33,564] [INFO] ===== Start GTDB Search =====
[2023-06-13 01:54:33,564] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022482305.1_ASM2248230v1_genomic.fna/markers.fasta)
[2023-06-13 01:54:33,565] [INFO] Task started: Blastn
[2023-06-13 01:54:33,565] [INFO] Running command: blastn -query GCA_022482305.1_ASM2248230v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca6f11e8-0a46-4c28-99bb-517bfe5a5eb7/dqc_reference/reference_markers_gtdb.fasta -out GCA_022482305.1_ASM2248230v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:54:34,354] [INFO] Task succeeded: Blastn
[2023-06-13 01:54:34,359] [INFO] Selected 13 target genomes.
[2023-06-13 01:54:34,359] [INFO] Target genome list was writen to GCA_022482305.1_ASM2248230v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 01:54:34,366] [INFO] Task started: fastANI
[2023-06-13 01:54:34,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg00b69f2e-16a9-4a49-920a-6df141df001f/GCA_022482305.1_ASM2248230v1_genomic.fna.gz --refList GCA_022482305.1_ASM2248230v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022482305.1_ASM2248230v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 01:54:39,125] [INFO] Task succeeded: fastANI
[2023-06-13 01:54:39,137] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 01:54:39,138] [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	82.9585	254	778	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.99	99.99	0.94	0.94	2	-
GCF_001435345.1	s__Limosilactobacillus pontis	81.7045	374	778	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.82	97.66	0.95	0.90	3	-
GCA_019118405.1	s__Limosilactobacillus gallistercoris	81.3966	256	778	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.70	98.67	0.88	0.83	3	-
GCA_002299975.1	s__Limosilactobacillus sp002299975	80.7334	228	778	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	80.5908	308	778	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435935.1	s__Limosilactobacillus panis	80.3669	238	778	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.95	99.95	0.95	0.95	2	-
GCF_000160835.1	s__Limosilactobacillus antri	79.9712	272	778	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.98	99.98	0.99	0.99	3	-
GCA_905214235.1	s__Limosilactobacillus sp905214235	79.7858	255	778	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434465.1	s__Limosilactobacillus oris	79.6582	236	778	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.39	95.80	0.88	0.80	8	-
GCF_900156885.1	s__Limosilactobacillus sp900156885	79.0833	174	778	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001293735.1	s__Limosilactobacillus gorillae	77.6978	85	778	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 01:54:39,141] [INFO] GTDB search result was written to GCA_022482305.1_ASM2248230v1_genomic.fna/result_gtdb.tsv
[2023-06-13 01:54:39,141] [INFO] ===== GTDB Search completed =====
[2023-06-13 01:54:39,146] [INFO] DFAST_QC result json was written to GCA_022482305.1_ASM2248230v1_genomic.fna/dqc_result.json
[2023-06-13 01:54:39,146] [INFO] DFAST_QC completed!
[2023-06-13 01:54:39,146] [INFO] Total running time: 0h0m46s