[2023-06-13 07:32:12,815] [INFO] DFAST_QC pipeline started.
[2023-06-13 07:32:12,817] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 07:32:12,817] [INFO] DQC Reference Directory: /var/lib/cwl/stg1eaed6eb-181b-4a73-b257-68b3f52d0445/dqc_reference
[2023-06-13 07:32:14,108] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 07:32:14,109] [INFO] Task started: Prodigal
[2023-06-13 07:32:14,109] [INFO] Running command: gunzip -c /var/lib/cwl/stg03988aee-3d01-4bc5-8f31-ff3e120be70e/GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 07:32:17,072] [INFO] Task succeeded: Prodigal
[2023-06-13 07:32:17,072] [INFO] Task started: HMMsearch
[2023-06-13 07:32:17,072] [INFO] Running command: hmmsearch --tblout GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1eaed6eb-181b-4a73-b257-68b3f52d0445/dqc_reference/reference_markers.hmm GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 07:32:17,291] [INFO] Task succeeded: HMMsearch
[2023-06-13 07:32:17,292] [INFO] Found 6/6 markers.
[2023-06-13 07:32:17,310] [INFO] Query marker FASTA was written to GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 07:32:17,310] [INFO] Task started: Blastn
[2023-06-13 07:32:17,310] [INFO] Running command: blastn -query GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1eaed6eb-181b-4a73-b257-68b3f52d0445/dqc_reference/reference_markers.fasta -out GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 07:32:17,941] [INFO] Task succeeded: Blastn
[2023-06-13 07:32:17,945] [INFO] Selected 13 target genomes.
[2023-06-13 07:32:17,946] [INFO] Target genome list was writen to GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 07:32:17,950] [INFO] Task started: fastANI
[2023-06-13 07:32:17,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg03988aee-3d01-4bc5-8f31-ff3e120be70e/GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 07:32:21,505] [INFO] Task succeeded: fastANI
[2023-06-13 07:32:21,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1eaed6eb-181b-4a73-b257-68b3f52d0445/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 07:32:21,507] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1eaed6eb-181b-4a73-b257-68b3f52d0445/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 07:32:21,519] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 07:32:21,519] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 07:32:21,520] [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 oris	strain=DSM 4864	GCA_001434465.1	1632	1632	type	True	79.0047	97	213	95	below_threshold
Limosilactobacillus antri	strain=DSM 16041	GCA_000160835.1	227943	227943	type	True	78.753	103	213	95	below_threshold
Limosilactobacillus antri	strain=DSM 16041	GCA_001435475.1	227943	227943	type	True	78.7188	101	213	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001435935.1	47493	47493	type	True	78.3078	102	213	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001027985.1	47493	47493	type	True	78.2059	102	213	95	below_threshold
Limosilactobacillus pontis	strain=DSM 8475	GCA_001435345.1	35787	35787	type	True	77.0811	61	213	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 07:32:21,522] [INFO] DFAST Taxonomy check result was written to GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 07:32:21,523] [INFO] ===== Taxonomy check completed =====
[2023-06-13 07:32:21,523] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 07:32:21,523] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1eaed6eb-181b-4a73-b257-68b3f52d0445/dqc_reference/checkm_data
[2023-06-13 07:32:21,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 07:32:21,548] [INFO] Task started: CheckM
[2023-06-13 07:32:21,549] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 07:32:38,007] [INFO] Task succeeded: CheckM
[2023-06-13 07:32:38,009] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 07:32:38,031] [INFO] ===== Completeness check finished =====
[2023-06-13 07:32:38,032] [INFO] ===== Start GTDB Search =====
[2023-06-13 07:32:38,032] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 07:32:38,033] [INFO] Task started: Blastn
[2023-06-13 07:32:38,033] [INFO] Running command: blastn -query GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg1eaed6eb-181b-4a73-b257-68b3f52d0445/dqc_reference/reference_markers_gtdb.fasta -out GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 07:32:38,995] [INFO] Task succeeded: Blastn
[2023-06-13 07:32:39,000] [INFO] Selected 14 target genomes.
[2023-06-13 07:32:39,000] [INFO] Target genome list was writen to GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 07:32:39,006] [INFO] Task started: fastANI
[2023-06-13 07:32:39,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg03988aee-3d01-4bc5-8f31-ff3e120be70e/GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 07:32:42,940] [INFO] Task succeeded: fastANI
[2023-06-13 07:32:42,952] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 07:32:42,952] [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_019117185.1	s__Limosilactobacillus intestinipullorum	98.9581	195	213	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.21	99.14	0.84	0.80	3	conclusive
GCA_902834055.1	s__Limosilactobacillus sp902834055	92.8587	74	213	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	79.0047	97	213	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.39	95.80	0.88	0.80	8	-
GCA_905214235.1	s__Limosilactobacillus sp905214235	78.9542	102	213	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	78.8358	101	213	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.98	99.98	0.99	0.99	3	-
GCF_001435935.1	s__Limosilactobacillus panis	78.3852	100	213	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.95	99.95	0.95	0.95	2	-
GCF_002940945.1	s__Limosilactobacillus pontis_A	77.2696	54	213	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 07:32:42,954] [INFO] GTDB search result was written to GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 07:32:42,955] [INFO] ===== GTDB Search completed =====
[2023-06-13 07:32:42,958] [INFO] DFAST_QC result json was written to GCA_938041665.1_ERR1430499_bin.12_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 07:32:42,958] [INFO] DFAST_QC completed!
[2023-06-13 07:32:42,958] [INFO] Total running time: 0h0m30s