[2024-01-24 13:31:44,310] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,311] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,312] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd28f0e9-832d-4c9b-93dd-278988c811e5/dqc_reference
[2024-01-24 13:31:45,669] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,670] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,670] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b690347-3c80-4601-9bbf-633b98cdcb7b/GCF_003968865.1_ASM396886v1_genomic.fna.gz | prodigal -d GCF_003968865.1_ASM396886v1_genomic.fna/cds.fna -a GCF_003968865.1_ASM396886v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:50,343] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:50,343] [INFO] Task started: HMMsearch
[2024-01-24 13:31:50,343] [INFO] Running command: hmmsearch --tblout GCF_003968865.1_ASM396886v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd28f0e9-832d-4c9b-93dd-278988c811e5/dqc_reference/reference_markers.hmm GCF_003968865.1_ASM396886v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:50,631] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:50,632] [INFO] Found 6/6 markers.
[2024-01-24 13:31:50,669] [INFO] Query marker FASTA was written to GCF_003968865.1_ASM396886v1_genomic.fna/markers.fasta
[2024-01-24 13:31:50,671] [INFO] Task started: Blastn
[2024-01-24 13:31:50,671] [INFO] Running command: blastn -query GCF_003968865.1_ASM396886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd28f0e9-832d-4c9b-93dd-278988c811e5/dqc_reference/reference_markers.fasta -out GCF_003968865.1_ASM396886v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:51,295] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:51,299] [INFO] Selected 12 target genomes.
[2024-01-24 13:31:51,299] [INFO] Target genome list was writen to GCF_003968865.1_ASM396886v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:51,309] [INFO] Task started: fastANI
[2024-01-24 13:31:51,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b690347-3c80-4601-9bbf-633b98cdcb7b/GCF_003968865.1_ASM396886v1_genomic.fna.gz --refList GCF_003968865.1_ASM396886v1_genomic.fna/target_genomes.txt --output GCF_003968865.1_ASM396886v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:31:57,444] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:57,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd28f0e9-832d-4c9b-93dd-278988c811e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:31:57,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd28f0e9-832d-4c9b-93dd-278988c811e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:31:57,458] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:31:57,459] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:31:57,459] [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 schleiferi subsp. schleiferi	strain=NCTC 12218	GCA_003968865.1	74707	1295	type	True	100.0	761	765	95	inconclusive
Staphylococcus schleiferi	strain=NCTC12218	GCA_900458895.2	1295	1295	type	True	99.99	763	765	95	inconclusive
Staphylococcus schleiferi	strain=ATCC 43808	GCA_011137195.1	1295	1295	type	True	99.8974	739	765	95	inconclusive
Staphylococcus coagulans	strain=DSM 6628	GCA_002901995.1	74706	74706	type	True	95.1425	686	765	95	inconclusive
Staphylococcus pseudintermedius	strain=LMG 22219	GCA_001792775.2	283734	283734	type	True	80.3573	383	765	95	below_threshold
Staphylococcus delphini	strain=NCTC 12225	GCA_002902785.1	53344	53344	type	True	80.1527	378	765	95	below_threshold
Staphylococcus intermedius	strain=NCTC 11048	GCA_000308095.1	1285	1285	type	True	80.1434	362	765	95	below_threshold
Staphylococcus lutrae	strain=DSM 10244	GCA_002902165.1	155085	155085	type	True	79.5823	323	765	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:31:57,461] [INFO] DFAST Taxonomy check result was written to GCF_003968865.1_ASM396886v1_genomic.fna/tc_result.tsv
[2024-01-24 13:31:57,461] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:31:57,462] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:31:57,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd28f0e9-832d-4c9b-93dd-278988c811e5/dqc_reference/checkm_data
[2024-01-24 13:31:57,463] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:31:57,499] [INFO] Task started: CheckM
[2024-01-24 13:31:57,500] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003968865.1_ASM396886v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003968865.1_ASM396886v1_genomic.fna/checkm_input GCF_003968865.1_ASM396886v1_genomic.fna/checkm_result
[2024-01-24 13:32:19,727] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:19,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:19,746] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:19,747] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:19,747] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003968865.1_ASM396886v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:19,748] [INFO] Task started: Blastn
[2024-01-24 13:32:19,748] [INFO] Running command: blastn -query GCF_003968865.1_ASM396886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd28f0e9-832d-4c9b-93dd-278988c811e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003968865.1_ASM396886v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:20,635] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:20,640] [INFO] Selected 11 target genomes.
[2024-01-24 13:32:20,640] [INFO] Target genome list was writen to GCF_003968865.1_ASM396886v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:20,654] [INFO] Task started: fastANI
[2024-01-24 13:32:20,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b690347-3c80-4601-9bbf-633b98cdcb7b/GCF_003968865.1_ASM396886v1_genomic.fna.gz --refList GCF_003968865.1_ASM396886v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003968865.1_ASM396886v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:26,608] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:26,623] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:32:26,623] [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_900458895.2	s__Staphylococcus schleiferi	99.99	763	765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	99.86	99.80	0.99	0.98	25	inconclusive
GCF_002901995.1	s__Staphylococcus coagulans	95.1425	686	765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0878	98.48	97.57	0.97	0.93	43	inconclusive
GCF_010365305.1	s__Staphylococcus sp010365305	81.1364	412	765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001792775.2	s__Staphylococcus pseudintermedius	80.3761	381	765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.31	98.36	0.94	0.88	431	-
GCF_900183575.1	s__Staphylococcus cornubiensis	80.2044	404	765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900636325.1	s__Staphylococcus delphini	80.1285	394	765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.77	95.78	0.92	0.86	24	-
GCF_002902385.1	s__Staphylococcus intermedius	80.0898	379	765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.80	99.54	0.96	0.94	8	-
GCF_002101335.1	s__Staphylococcus lutrae	79.6083	336	765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000934465.1	s__Staphylococcus microti	78.9798	244	765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.97	0.98	0.96	3	-
GCF_002902145.1	s__Staphylococcus rostri	78.9598	221	765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000816085.1	s__Staphylococcus hyicus	78.7223	247	765	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.46	99.24	0.96	0.94	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:26,625] [INFO] GTDB search result was written to GCF_003968865.1_ASM396886v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:26,626] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:26,629] [INFO] DFAST_QC result json was written to GCF_003968865.1_ASM396886v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:26,629] [INFO] DFAST_QC completed!
[2024-01-24 13:32:26,629] [INFO] Total running time: 0h0m42s