[2024-01-25 18:50:50,544] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:50,611] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:50,611] [INFO] DQC Reference Directory: /var/lib/cwl/stg9008b646-9d0a-47b8-bdea-8c1bd32ae45e/dqc_reference
[2024-01-25 18:50:51,832] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:51,833] [INFO] Task started: Prodigal
[2024-01-25 18:50:51,833] [INFO] Running command: gunzip -c /var/lib/cwl/stg59299057-69b7-43dd-8265-83d0ebce5941/GCF_002902235.1_ASM290223v1_genomic.fna.gz | prodigal -d GCF_002902235.1_ASM290223v1_genomic.fna/cds.fna -a GCF_002902235.1_ASM290223v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:55,725] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:55,725] [INFO] Task started: HMMsearch
[2024-01-25 18:50:55,725] [INFO] Running command: hmmsearch --tblout GCF_002902235.1_ASM290223v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9008b646-9d0a-47b8-bdea-8c1bd32ae45e/dqc_reference/reference_markers.hmm GCF_002902235.1_ASM290223v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:55,951] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:55,952] [INFO] Found 6/6 markers.
[2024-01-25 18:50:55,981] [INFO] Query marker FASTA was written to GCF_002902235.1_ASM290223v1_genomic.fna/markers.fasta
[2024-01-25 18:50:55,981] [INFO] Task started: Blastn
[2024-01-25 18:50:55,981] [INFO] Running command: blastn -query GCF_002902235.1_ASM290223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9008b646-9d0a-47b8-bdea-8c1bd32ae45e/dqc_reference/reference_markers.fasta -out GCF_002902235.1_ASM290223v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:56,569] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:56,572] [INFO] Selected 16 target genomes.
[2024-01-25 18:50:56,572] [INFO] Target genome list was writen to GCF_002902235.1_ASM290223v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:56,593] [INFO] Task started: fastANI
[2024-01-25 18:50:56,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg59299057-69b7-43dd-8265-83d0ebce5941/GCF_002902235.1_ASM290223v1_genomic.fna.gz --refList GCF_002902235.1_ASM290223v1_genomic.fna/target_genomes.txt --output GCF_002902235.1_ASM290223v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:51:05,819] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:05,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9008b646-9d0a-47b8-bdea-8c1bd32ae45e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:51:05,820] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9008b646-9d0a-47b8-bdea-8c1bd32ae45e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:51:05,826] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:51:05,826] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:51:05,826] [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 ureilyticus	strain=DSM 6718	GCA_002902235.1	94138	94138	type	True	100.0	808	812	95	conclusive
Staphylococcus cohnii subsp. cohnii	strain=NCTC 11041	GCA_002902365.1	74704	29382	suspected-type	True	92.2152	714	812	95	below_threshold
Staphylococcus cohnii	strain=NCTC11041	GCA_900458255.1	29382	29382	type	True	92.1529	733	812	95	below_threshold
Staphylococcus cohnii subsp. barensis	strain=SC5	GCA_014180735.1	2834574	29382	type	True	91.8612	739	812	95	below_threshold
Staphylococcus nepalensis	strain=NCTC13834	GCA_900458695.1	214473	214473	type	True	83.2393	665	812	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	80.4818	480	812	95	below_threshold
Staphylococcus succinus subsp. succinus	strain=DSM 14617	GCA_001006765.1	224030	61015	type	True	80.1119	456	812	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:51:05,830] [INFO] DFAST Taxonomy check result was written to GCF_002902235.1_ASM290223v1_genomic.fna/tc_result.tsv
[2024-01-25 18:51:05,831] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:51:05,831] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:51:05,831] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9008b646-9d0a-47b8-bdea-8c1bd32ae45e/dqc_reference/checkm_data
[2024-01-25 18:51:05,832] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:51:05,865] [INFO] Task started: CheckM
[2024-01-25 18:51:05,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002902235.1_ASM290223v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002902235.1_ASM290223v1_genomic.fna/checkm_input GCF_002902235.1_ASM290223v1_genomic.fna/checkm_result
[2024-01-25 18:51:23,948] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:23,949] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:23,967] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:23,967] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:23,968] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002902235.1_ASM290223v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:23,968] [INFO] Task started: Blastn
[2024-01-25 18:51:23,968] [INFO] Running command: blastn -query GCF_002902235.1_ASM290223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9008b646-9d0a-47b8-bdea-8c1bd32ae45e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002902235.1_ASM290223v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:24,695] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:24,699] [INFO] Selected 18 target genomes.
[2024-01-25 18:51:24,699] [INFO] Target genome list was writen to GCF_002902235.1_ASM290223v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:24,731] [INFO] Task started: fastANI
[2024-01-25 18:51:24,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg59299057-69b7-43dd-8265-83d0ebce5941/GCF_002902235.1_ASM290223v1_genomic.fna.gz --refList GCF_002902235.1_ASM290223v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002902235.1_ASM290223v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:35,217] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:35,230] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:35,230] [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_002902235.1	s__Staphylococcus ureilyticus	100.0	808	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.76	98.26	0.93	0.88	107	conclusive
GCF_002902365.1	s__Staphylococcus cohnii	92.24	713	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.14	95.73	0.92	0.88	59	-
GCF_014635045.1	s__Staphylococcus nepalensis	83.3342	651	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.49	99.27	0.96	0.93	23	-
GCF_900458565.1	s__Staphylococcus equorum	80.5856	483	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.19	97.35	0.94	0.89	49	-
GCF_000010125.1	s__Staphylococcus saprophyticus	80.5145	467	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.41	98.75	0.94	0.91	167	-
GCF_002732165.1	s__Staphylococcus xylosus	80.4752	460	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.41	97.01	0.95	0.90	48	-
GCF_016774515.1	s__Staphylococcus xylosus_A	80.4536	497	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	99.08	0.95	0.91	11	-
GCF_001431205.1	s__Staphylococcus sp001431205	80.4127	457	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391405.1	s__Staphylococcus sp013391405	80.3832	459	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747895.1	s__Staphylococcus equorum_A	80.3577	488	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	98.64	0.94	0.92	4	-
GCF_003697915.1	s__Staphylococcus pseudoxylosus	80.3153	469	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.50	97.12	0.92	0.87	9	-
GCF_000338275.1	s__Staphylococcus xylosus_B	80.2492	474	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.09	97.23	0.94	0.90	8	-
GCF_001006765.1	s__Staphylococcus succinus	80.1164	457	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.99	95.53	0.94	0.89	24	-
GCF_003491325.1	s__Staphylococcus warneri_A	78.6306	258	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.32	98.95	0.94	0.90	22	-
GCF_002902685.1	s__Staphylococcus pettenkoferi	77.9621	169	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.48	96.01	0.95	0.89	21	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:35,234] [INFO] GTDB search result was written to GCF_002902235.1_ASM290223v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:35,234] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:35,237] [INFO] DFAST_QC result json was written to GCF_002902235.1_ASM290223v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:35,237] [INFO] DFAST_QC completed!
[2024-01-25 18:51:35,237] [INFO] Total running time: 0h0m45s