[2023-06-08 01:27:38,108] [INFO] DFAST_QC pipeline started.
[2023-06-08 01:27:38,111] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 01:27:38,111] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e974bb0-dca3-4214-9d3b-18640b52b99f/dqc_reference
[2023-06-08 01:27:39,324] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 01:27:39,325] [INFO] Task started: Prodigal
[2023-06-08 01:27:39,325] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1f5c8ae-3141-4414-85b6-93de294d2164/GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 01:27:43,178] [INFO] Task succeeded: Prodigal
[2023-06-08 01:27:43,178] [INFO] Task started: HMMsearch
[2023-06-08 01:27:43,178] [INFO] Running command: hmmsearch --tblout GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e974bb0-dca3-4214-9d3b-18640b52b99f/dqc_reference/reference_markers.hmm GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 01:27:43,398] [INFO] Task succeeded: HMMsearch
[2023-06-08 01:27:43,400] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb1f5c8ae-3141-4414-85b6-93de294d2164/GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 01:27:43,428] [INFO] Query marker FASTA was written to GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 01:27:43,428] [INFO] Task started: Blastn
[2023-06-08 01:27:43,429] [INFO] Running command: blastn -query GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e974bb0-dca3-4214-9d3b-18640b52b99f/dqc_reference/reference_markers.fasta -out GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:27:44,067] [INFO] Task succeeded: Blastn
[2023-06-08 01:27:44,071] [INFO] Selected 22 target genomes.
[2023-06-08 01:27:44,071] [INFO] Target genome list was writen to GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 01:27:44,079] [INFO] Task started: fastANI
[2023-06-08 01:27:44,080] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1f5c8ae-3141-4414-85b6-93de294d2164/GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 01:27:52,882] [INFO] Task succeeded: fastANI
[2023-06-08 01:27:52,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e974bb0-dca3-4214-9d3b-18640b52b99f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 01:27:52,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e974bb0-dca3-4214-9d3b-18640b52b99f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 01:27:52,890] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 01:27:52,891] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 01:27:52,891] [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 mucosae	strain=DSM 13345	GCA_001436025.1	97478	97478	type	True	98.0633	427	472	95	conclusive
Limosilactobacillus secaliphilus	strain=DSM 17896	GCA_001437055.1	396268	396268	type	True	78.4449	72	472	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001435935.1	47493	47493	type	True	78.1558	63	472	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001027985.1	47493	47493	type	True	78.0434	64	472	95	below_threshold
Limosilactobacillus gorillae	strain=KZ01	GCA_001293735.1	1450649	1450649	type	True	78.0238	55	472	95	below_threshold
Limosilactobacillus oris	strain=DSM 4864	GCA_001434465.1	1632	1632	type	True	78.0049	75	472	95	below_threshold
Limosilactobacillus portuensis	strain=c11Ua_112_M	GCA_014838735.1	2742601	2742601	type	True	77.9772	56	472	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 01:27:52,893] [INFO] DFAST Taxonomy check result was written to GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 01:27:52,893] [INFO] ===== Taxonomy check completed =====
[2023-06-08 01:27:52,893] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 01:27:52,894] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e974bb0-dca3-4214-9d3b-18640b52b99f/dqc_reference/checkm_data
[2023-06-08 01:27:52,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 01:27:52,916] [INFO] Task started: CheckM
[2023-06-08 01:27:52,916] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 01:28:12,789] [INFO] Task succeeded: CheckM
[2023-06-08 01:28:12,790] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 01:28:12,809] [INFO] ===== Completeness check finished =====
[2023-06-08 01:28:12,809] [INFO] ===== Start GTDB Search =====
[2023-06-08 01:28:12,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 01:28:12,810] [INFO] Task started: Blastn
[2023-06-08 01:28:12,810] [INFO] Running command: blastn -query GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e974bb0-dca3-4214-9d3b-18640b52b99f/dqc_reference/reference_markers_gtdb.fasta -out GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:28:13,673] [INFO] Task succeeded: Blastn
[2023-06-08 01:28:13,677] [INFO] Selected 18 target genomes.
[2023-06-08 01:28:13,677] [INFO] Target genome list was writen to GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 01:28:13,687] [INFO] Task started: fastANI
[2023-06-08 01:28:13,687] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1f5c8ae-3141-4414-85b6-93de294d2164/GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 01:28:20,498] [INFO] Task succeeded: fastANI
[2023-06-08 01:28:20,510] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 01:28:20,510] [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_001436025.1	s__Limosilactobacillus mucosae	98.0633	427	472	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.05	95.70	0.88	0.73	22	conclusive
GCF_012843675.1	s__Limosilactobacillus sp012843675	87.7451	376	472	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.07	98.07	0.86	0.86	2	-
GCF_001435345.1	s__Limosilactobacillus pontis	78.6521	61	472	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.82	97.66	0.95	0.90	3	-
GCA_019114515.1	s__Limosilactobacillus merdigallinarum	78.5203	55	472	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019117285.1	s__Limosilactobacillus intestinigallinarum	78.5194	52	472	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.99	99.99	0.94	0.94	2	-
GCF_001437055.1	s__Limosilactobacillus secaliphilus	78.4622	71	472	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	78.3359	65	472	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014838745.1	s__Limosilactobacillus urinaemulieris	78.2792	52	472	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.61	97.61	0.86	0.86	2	-
GCF_000160835.1	s__Limosilactobacillus antri	78.2775	74	472	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	78.1558	63	472	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	78.1061	69	472	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	78.0238	55	472	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	78.0049	75	472	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.39	95.80	0.88	0.80	8	-
GCA_019118405.1	s__Limosilactobacillus gallistercoris	77.2301	51	472	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.70	98.67	0.88	0.83	3	-
--------------------------------------------------------------------------------
[2023-06-08 01:28:20,516] [INFO] GTDB search result was written to GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 01:28:20,517] [INFO] ===== GTDB Search completed =====
[2023-06-08 01:28:20,521] [INFO] DFAST_QC result json was written to GCA_945830835.1_SRR5240742_bin.12_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 01:28:20,521] [INFO] DFAST_QC completed!
[2023-06-08 01:28:20,521] [INFO] Total running time: 0h0m42s