[2023-06-08 03:42:22,675] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:42:22,677] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:42:22,677] [INFO] DQC Reference Directory: /var/lib/cwl/stg14bc1891-e1bc-41cb-bca5-730ddbf0ab15/dqc_reference
[2023-06-08 03:42:24,034] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:42:24,035] [INFO] Task started: Prodigal
[2023-06-08 03:42:24,035] [INFO] Running command: gunzip -c /var/lib/cwl/stg684d18ac-3196-458e-ac37-d39dad720e79/GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:42:27,681] [INFO] Task succeeded: Prodigal
[2023-06-08 03:42:27,681] [INFO] Task started: HMMsearch
[2023-06-08 03:42:27,681] [INFO] Running command: hmmsearch --tblout GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14bc1891-e1bc-41cb-bca5-730ddbf0ab15/dqc_reference/reference_markers.hmm GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:42:27,903] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:42:27,905] [INFO] Found 6/6 markers.
[2023-06-08 03:42:27,927] [INFO] Query marker FASTA was written to GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 03:42:27,928] [INFO] Task started: Blastn
[2023-06-08 03:42:27,928] [INFO] Running command: blastn -query GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg14bc1891-e1bc-41cb-bca5-730ddbf0ab15/dqc_reference/reference_markers.fasta -out GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:42:28,560] [INFO] Task succeeded: Blastn
[2023-06-08 03:42:28,564] [INFO] Selected 12 target genomes.
[2023-06-08 03:42:28,564] [INFO] Target genome list was writen to GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 03:42:28,566] [INFO] Task started: fastANI
[2023-06-08 03:42:28,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg684d18ac-3196-458e-ac37-d39dad720e79/GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:42:32,909] [INFO] Task succeeded: fastANI
[2023-06-08 03:42:32,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14bc1891-e1bc-41cb-bca5-730ddbf0ab15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:42:32,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14bc1891-e1bc-41cb-bca5-730ddbf0ab15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:42:32,926] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:42:32,926] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 03:42:32,927] [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	82.6767	339	477	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001027985.1	47493	47493	type	True	79.68	177	477	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001435935.1	47493	47493	type	True	79.4884	186	477	95	below_threshold
Limosilactobacillus oris	strain=DSM 4864	GCA_001434465.1	1632	1632	type	True	79.4167	164	477	95	below_threshold
Limosilactobacillus antri	strain=DSM 16041	GCA_000160835.1	227943	227943	type	True	79.2122	164	477	95	below_threshold
Limosilactobacillus antri	strain=DSM 16041	GCA_001435475.1	227943	227943	type	True	79.0868	163	477	95	below_threshold
Limosilactobacillus avistercoris	strain=Sa3CUN2	GCA_014836425.1	2762243	2762243	type	True	78.8682	97	477	95	below_threshold
Limosilactobacillus fastidiosus	strain=WF-MO7-1	GCA_014145505.1	2759855	2759855	type	True	78.7342	77	477	95	below_threshold
Limosilactobacillus urinaemulieris	strain=c9Ua_26_M	GCA_014838745.1	2742600	2742600	type	True	78.4774	96	477	95	below_threshold
Limosilactobacillus fermentum	strain=DSM 20052	GCA_013394085.1	1613	1613	type	True	77.6427	71	477	95	below_threshold
Limosilactobacillus fermentum	strain=B1 28	GCA_005341425.1	1613	1613	type	True	77.5852	73	477	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 03:42:32,929] [INFO] DFAST Taxonomy check result was written to GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 03:42:32,929] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:42:32,929] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:42:32,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14bc1891-e1bc-41cb-bca5-730ddbf0ab15/dqc_reference/checkm_data
[2023-06-08 03:42:32,931] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:42:32,952] [INFO] Task started: CheckM
[2023-06-08 03:42:32,952] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 03:42:51,838] [INFO] Task succeeded: CheckM
[2023-06-08 03:42:51,839] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.51%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 03:42:51,855] [INFO] ===== Completeness check finished =====
[2023-06-08 03:42:51,855] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:42:51,856] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 03:42:51,856] [INFO] Task started: Blastn
[2023-06-08 03:42:51,856] [INFO] Running command: blastn -query GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg14bc1891-e1bc-41cb-bca5-730ddbf0ab15/dqc_reference/reference_markers_gtdb.fasta -out GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:42:52,890] [INFO] Task succeeded: Blastn
[2023-06-08 03:42:52,894] [INFO] Selected 10 target genomes.
[2023-06-08 03:42:52,895] [INFO] Target genome list was writen to GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:42:52,897] [INFO] Task started: fastANI
[2023-06-08 03:42:52,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg684d18ac-3196-458e-ac37-d39dad720e79/GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:42:55,944] [INFO] Task succeeded: fastANI
[2023-06-08 03:42:55,953] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 03:42:55,954] [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_002299975.1	s__Limosilactobacillus sp002299975	89.7733	271	477	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.38	99.38	0.84	0.84	2	-
GCA_019118405.1	s__Limosilactobacillus gallistercoris	87.3956	277	477	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.70	98.67	0.88	0.83	3	-
GCA_019117285.1	s__Limosilactobacillus intestinigallinarum	83.7407	226	477	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	82.7009	338	477	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.82	97.66	0.95	0.90	3	-
GCF_002940945.1	s__Limosilactobacillus pontis_A	82.0619	329	477	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902834055.1	s__Limosilactobacillus sp902834055	79.7614	87	477	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	79.5429	184	477	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.95	99.95	0.95	0.95	2	-
GCF_900156885.1	s__Limosilactobacillus sp900156885	78.7585	167	477	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145505.1	s__Limosilactobacillus fastidiosus	78.7342	77	477	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.58	99.58	0.93	0.93	2	-
GCF_014838745.1	s__Limosilactobacillus urinaemulieris	78.4349	97	477	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.61	97.61	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-08 03:42:55,956] [INFO] GTDB search result was written to GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 03:42:55,956] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:42:55,959] [INFO] DFAST_QC result json was written to GCA_945873395.1_SRR15732360_bin.36_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 03:42:55,960] [INFO] DFAST_QC completed!
[2023-06-08 03:42:55,960] [INFO] Total running time: 0h0m33s