[2024-01-24 13:27:31,895] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:31,897] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:31,897] [INFO] DQC Reference Directory: /var/lib/cwl/stg6dcf16bb-efb8-4726-9534-3e3c1a165f4d/dqc_reference
[2024-01-24 13:27:33,270] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:33,271] [INFO] Task started: Prodigal
[2024-01-24 13:27:33,272] [INFO] Running command: gunzip -c /var/lib/cwl/stg85311e1d-00e1-4a46-bfb0-e145c97bc725/GCF_014635045.1_ASM1463504v1_genomic.fna.gz | prodigal -d GCF_014635045.1_ASM1463504v1_genomic.fna/cds.fna -a GCF_014635045.1_ASM1463504v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:38,487] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:38,487] [INFO] Task started: HMMsearch
[2024-01-24 13:27:38,487] [INFO] Running command: hmmsearch --tblout GCF_014635045.1_ASM1463504v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6dcf16bb-efb8-4726-9534-3e3c1a165f4d/dqc_reference/reference_markers.hmm GCF_014635045.1_ASM1463504v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:38,768] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:38,769] [INFO] Found 6/6 markers.
[2024-01-24 13:27:38,794] [INFO] Query marker FASTA was written to GCF_014635045.1_ASM1463504v1_genomic.fna/markers.fasta
[2024-01-24 13:27:38,795] [INFO] Task started: Blastn
[2024-01-24 13:27:38,795] [INFO] Running command: blastn -query GCF_014635045.1_ASM1463504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dcf16bb-efb8-4726-9534-3e3c1a165f4d/dqc_reference/reference_markers.fasta -out GCF_014635045.1_ASM1463504v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:39,454] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:39,458] [INFO] Selected 12 target genomes.
[2024-01-24 13:27:39,458] [INFO] Target genome list was writen to GCF_014635045.1_ASM1463504v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:39,483] [INFO] Task started: fastANI
[2024-01-24 13:27:39,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg85311e1d-00e1-4a46-bfb0-e145c97bc725/GCF_014635045.1_ASM1463504v1_genomic.fna.gz --refList GCF_014635045.1_ASM1463504v1_genomic.fna/target_genomes.txt --output GCF_014635045.1_ASM1463504v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:27:45,561] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:45,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6dcf16bb-efb8-4726-9534-3e3c1a165f4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:27:45,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6dcf16bb-efb8-4726-9534-3e3c1a165f4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:27:45,573] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:27:45,573] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:27:45,574] [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=CCM 7045	GCA_014635045.1	214473	214473	type	True	100.0	936	936	95	conclusive
Staphylococcus nepalensis	strain=NCTC13834	GCA_900458695.1	214473	214473	type	True	99.999	935	936	95	conclusive
Staphylococcus nepalensis	strain=DSM 15150	GCA_002902745.1	214473	214473	type	True	99.7119	756	936	95	conclusive
Staphylococcus cohnii subsp. barensis	strain=SC5	GCA_014180735.1	2834574	29382	type	True	83.5668	701	936	95	below_threshold
Staphylococcus cohnii	strain=NCTC11041	GCA_900458255.1	29382	29382	type	True	83.3868	694	936	95	below_threshold
Staphylococcus cohnii subsp. cohnii	strain=NCTC 11041	GCA_002902365.1	74704	29382	suspected-type	True	83.3559	680	936	95	below_threshold
Staphylococcus ureilyticus	strain=DSM 6718	GCA_002902235.1	94138	94138	type	True	83.3082	655	936	95	below_threshold
Staphylococcus shinii	strain=K22-5M	GCA_017583065.1	2912228	2912228	type	True	80.9105	527	936	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:27:45,575] [INFO] DFAST Taxonomy check result was written to GCF_014635045.1_ASM1463504v1_genomic.fna/tc_result.tsv
[2024-01-24 13:27:45,575] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:27:45,576] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:27:45,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6dcf16bb-efb8-4726-9534-3e3c1a165f4d/dqc_reference/checkm_data
[2024-01-24 13:27:45,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:27:45,605] [INFO] Task started: CheckM
[2024-01-24 13:27:45,605] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635045.1_ASM1463504v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635045.1_ASM1463504v1_genomic.fna/checkm_input GCF_014635045.1_ASM1463504v1_genomic.fna/checkm_result
[2024-01-24 13:28:08,974] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:08,976] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:08,998] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:08,998] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:08,998] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635045.1_ASM1463504v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:08,999] [INFO] Task started: Blastn
[2024-01-24 13:28:08,999] [INFO] Running command: blastn -query GCF_014635045.1_ASM1463504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dcf16bb-efb8-4726-9534-3e3c1a165f4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635045.1_ASM1463504v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:09,727] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:09,731] [INFO] Selected 14 target genomes.
[2024-01-24 13:28:09,731] [INFO] Target genome list was writen to GCF_014635045.1_ASM1463504v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:09,756] [INFO] Task started: fastANI
[2024-01-24 13:28:09,757] [INFO] Running command: fastANI --query /var/lib/cwl/stg85311e1d-00e1-4a46-bfb0-e145c97bc725/GCF_014635045.1_ASM1463504v1_genomic.fna.gz --refList GCF_014635045.1_ASM1463504v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635045.1_ASM1463504v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:17,796] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:17,809] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:17,809] [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	100.0	936	936	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	83.3435	681	936	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	83.3154	654	936	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	81.0177	537	936	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.34	99.08	0.95	0.91	11	-
GCF_900458565.1	s__Staphylococcus equorum	80.5354	533	936	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.19	97.35	0.94	0.89	49	-
GCF_001747895.1	s__Staphylococcus equorum_A	80.4681	515	936	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	80.2924	525	936	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	80.283	544	936	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.09	97.23	0.94	0.90	8	-
GCF_013391405.1	s__Staphylococcus sp013391405	80.1636	501	936	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002732165.1	s__Staphylococcus xylosus	80.121	511	936	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.41	97.01	0.95	0.90	48	-
GCF_001431205.1	s__Staphylococcus sp001431205	80.11	532	936	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	80.1095	480	936	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.99	95.53	0.94	0.89	24	-
GCF_900097965.1	s__Staphylococcus caeli	80.0383	449	936	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004785665.1	s__Staphylococcus pragensis	78.5085	245	936	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.69	99.09	0.98	0.94	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:17,812] [INFO] GTDB search result was written to GCF_014635045.1_ASM1463504v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:17,813] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:17,816] [INFO] DFAST_QC result json was written to GCF_014635045.1_ASM1463504v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:17,816] [INFO] DFAST_QC completed!
[2024-01-24 13:28:17,816] [INFO] Total running time: 0h0m46s