[2023-06-08 06:51:56,574] [INFO] DFAST_QC pipeline started.
[2023-06-08 06:51:56,579] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 06:51:56,579] [INFO] DQC Reference Directory: /var/lib/cwl/stgf199e486-f920-487a-9792-5e430234e472/dqc_reference
[2023-06-08 06:51:58,195] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 06:51:58,195] [INFO] Task started: Prodigal
[2023-06-08 06:51:58,196] [INFO] Running command: gunzip -c /var/lib/cwl/stg522bbc17-a36b-4154-9ab1-987583f729de/GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 06:52:03,049] [INFO] Task succeeded: Prodigal
[2023-06-08 06:52:03,049] [INFO] Task started: HMMsearch
[2023-06-08 06:52:03,050] [INFO] Running command: hmmsearch --tblout GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf199e486-f920-487a-9792-5e430234e472/dqc_reference/reference_markers.hmm GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 06:52:03,342] [INFO] Task succeeded: HMMsearch
[2023-06-08 06:52:03,344] [INFO] Found 6/6 markers.
[2023-06-08 06:52:03,374] [INFO] Query marker FASTA was written to GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 06:52:03,375] [INFO] Task started: Blastn
[2023-06-08 06:52:03,375] [INFO] Running command: blastn -query GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf199e486-f920-487a-9792-5e430234e472/dqc_reference/reference_markers.fasta -out GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 06:52:04,051] [INFO] Task succeeded: Blastn
[2023-06-08 06:52:04,055] [INFO] Selected 12 target genomes.
[2023-06-08 06:52:04,055] [INFO] Target genome list was writen to GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 06:52:04,056] [INFO] Task started: fastANI
[2023-06-08 06:52:04,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg522bbc17-a36b-4154-9ab1-987583f729de/GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 06:52:10,139] [INFO] Task succeeded: fastANI
[2023-06-08 06:52:10,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf199e486-f920-487a-9792-5e430234e472/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 06:52:10,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf199e486-f920-487a-9792-5e430234e472/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 06:52:10,151] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2023-06-08 06:52:10,151] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 06:52:10,151] [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
Staphylococcus nepalensis	strain=NCTC13834	GCA_900458695.1	214473	214473	type	True	99.5819	858	879	95	conclusive
Staphylococcus nepalensis	strain=CCM 7045	GCA_014635045.1	214473	214473	type	True	99.5765	857	879	95	conclusive
Staphylococcus nepalensis	strain=DSM 15150	GCA_002902745.1	214473	214473	type	True	99.2364	713	879	95	conclusive
Staphylococcus cohnii subsp. barensis	strain=SC5	GCA_014180735.1	2834574	29382	type	True	83.461	672	879	95	below_threshold
Staphylococcus cohnii subsp. cohnii	strain=NCTC 11041	GCA_002902365.1	74704	29382	suspected-type	True	83.3498	651	879	95	below_threshold
Staphylococcus cohnii	strain=NCTC11041	GCA_900458255.1	29382	29382	type	True	83.309	661	879	95	below_threshold
Staphylococcus ureilyticus	strain=DSM 6718	GCA_002902235.1	94138	94138	type	True	83.2406	633	879	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	80.629	533	879	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 06:52:10,153] [INFO] DFAST Taxonomy check result was written to GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 06:52:10,154] [INFO] ===== Taxonomy check completed =====
[2023-06-08 06:52:10,155] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 06:52:10,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf199e486-f920-487a-9792-5e430234e472/dqc_reference/checkm_data
[2023-06-08 06:52:10,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 06:52:10,201] [INFO] Task started: CheckM
[2023-06-08 06:52:10,202] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 06:52:32,358] [INFO] Task succeeded: CheckM
[2023-06-08 06:52:32,359] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 06:52:32,397] [INFO] ===== Completeness check finished =====
[2023-06-08 06:52:32,397] [INFO] ===== Start GTDB Search =====
[2023-06-08 06:52:32,398] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 06:52:32,398] [INFO] Task started: Blastn
[2023-06-08 06:52:32,398] [INFO] Running command: blastn -query GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf199e486-f920-487a-9792-5e430234e472/dqc_reference/reference_markers_gtdb.fasta -out GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 06:52:33,153] [INFO] Task succeeded: Blastn
[2023-06-08 06:52:33,158] [INFO] Selected 14 target genomes.
[2023-06-08 06:52:33,158] [INFO] Target genome list was writen to GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 06:52:33,170] [INFO] Task started: fastANI
[2023-06-08 06:52:33,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg522bbc17-a36b-4154-9ab1-987583f729de/GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 06:52:41,400] [INFO] Task succeeded: fastANI
[2023-06-08 06:52:41,425] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 06:52:41,425] [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_014635045.1	s__Staphylococcus nepalensis	99.5765	857	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.49	99.27	0.96	0.93	23	conclusive
GCF_002902365.1	s__Staphylococcus cohnii	83.3498	651	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.14	95.73	0.92	0.88	59	-
GCF_002902235.1	s__Staphylococcus ureilyticus	83.239	633	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.76	98.26	0.93	0.88	107	-
GCF_016774515.1	s__Staphylococcus xylosus_A	80.5804	529	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	99.08	0.95	0.91	11	-
GCF_001747895.1	s__Staphylococcus equorum_A	80.3257	515	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	98.64	0.94	0.92	4	-
GCF_900458565.1	s__Staphylococcus equorum	80.2616	521	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.19	97.35	0.94	0.89	49	-
GCF_003697915.1	s__Staphylococcus pseudoxylosus	80.1666	516	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.50	97.12	0.92	0.87	9	-
GCF_002732165.1	s__Staphylococcus xylosus	80.098	501	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.41	97.01	0.95	0.90	48	-
GCF_000010125.1	s__Staphylococcus saprophyticus	80.0908	486	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.41	98.75	0.94	0.91	167	-
GCF_013391405.1	s__Staphylococcus sp013391405	80.0612	493	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001006765.1	s__Staphylococcus succinus	80.0087	480	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.99	95.53	0.94	0.89	24	-
GCF_001431205.1	s__Staphylococcus sp001431205	79.9697	522	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000338275.1	s__Staphylococcus xylosus_B	79.8597	535	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.09	97.23	0.94	0.90	8	-
GCF_004785665.1	s__Staphylococcus pragensis	78.3816	239	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.69	99.09	0.98	0.94	4	-
--------------------------------------------------------------------------------
[2023-06-08 06:52:41,427] [INFO] GTDB search result was written to GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 06:52:41,427] [INFO] ===== GTDB Search completed =====
[2023-06-08 06:52:41,431] [INFO] DFAST_QC result json was written to GCA_947643975.1_SRR17794290_bin.17_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 06:52:41,431] [INFO] DFAST_QC completed!
[2023-06-08 06:52:41,431] [INFO] Total running time: 0h0m45s