[2024-01-24 13:49:27,471] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:27,473] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:27,473] [INFO] DQC Reference Directory: /var/lib/cwl/stg9416dbf2-fb5c-40f7-9d01-cfe0e8238d6e/dqc_reference
[2024-01-24 13:49:28,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:28,832] [INFO] Task started: Prodigal
[2024-01-24 13:49:28,833] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2811285-b877-416e-88ee-2bda162049d3/GCF_016127935.1_ASM1612793v1_genomic.fna.gz | prodigal -d GCF_016127935.1_ASM1612793v1_genomic.fna/cds.fna -a GCF_016127935.1_ASM1612793v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:34,148] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:34,149] [INFO] Task started: HMMsearch
[2024-01-24 13:49:34,149] [INFO] Running command: hmmsearch --tblout GCF_016127935.1_ASM1612793v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9416dbf2-fb5c-40f7-9d01-cfe0e8238d6e/dqc_reference/reference_markers.hmm GCF_016127935.1_ASM1612793v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:34,416] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:34,418] [INFO] Found 6/6 markers.
[2024-01-24 13:49:34,455] [INFO] Query marker FASTA was written to GCF_016127935.1_ASM1612793v1_genomic.fna/markers.fasta
[2024-01-24 13:49:34,456] [INFO] Task started: Blastn
[2024-01-24 13:49:34,456] [INFO] Running command: blastn -query GCF_016127935.1_ASM1612793v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9416dbf2-fb5c-40f7-9d01-cfe0e8238d6e/dqc_reference/reference_markers.fasta -out GCF_016127935.1_ASM1612793v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:35,157] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:35,161] [INFO] Selected 22 target genomes.
[2024-01-24 13:49:35,161] [INFO] Target genome list was writen to GCF_016127935.1_ASM1612793v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:35,172] [INFO] Task started: fastANI
[2024-01-24 13:49:35,172] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2811285-b877-416e-88ee-2bda162049d3/GCF_016127935.1_ASM1612793v1_genomic.fna.gz --refList GCF_016127935.1_ASM1612793v1_genomic.fna/target_genomes.txt --output GCF_016127935.1_ASM1612793v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:46,335] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:46,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9416dbf2-fb5c-40f7-9d01-cfe0e8238d6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:46,336] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9416dbf2-fb5c-40f7-9d01-cfe0e8238d6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:46,348] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:46,349] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:46,349] [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 pettenkoferi	strain=FDAARGOS_1071	GCA_016127935.1	170573	170573	type	True	100.0	829	830	95	conclusive
Staphylococcus pettenkoferi	strain=CCUG 51270	GCA_002902685.1	170573	170573	type	True	99.9191	759	830	95	conclusive
Staphylococcus argensis	strain=DSM 29875	GCA_002902305.1	1607738	1607738	type	True	92.3353	758	830	95	below_threshold
Macrococcus armenti	strain=JEK37	GCA_020097135.1	2875764	2875764	type	True	79.7785	63	830	95	below_threshold
Staphylococcus petrasii	strain=NCTC13835	GCA_900458665.1	1276936	1276936	type	True	79.5136	191	830	95	below_threshold
Staphylococcus durrellii	strain=27_4_6_LY	GCA_015594545.1	2781773	2781773	type	True	79.418	172	830	95	below_threshold
Staphylococcus schleiferi	strain=NCTC12218	GCA_900458895.2	1295	1295	type	True	78.8537	128	830	95	below_threshold
Staphylococcus gallinarum	strain=NCTC 12195	GCA_003968815.1	1293	1293	type	True	78.7422	168	830	95	below_threshold
Staphylococcus petrasii	strain=CCUG 62727	GCA_002902565.1	1276936	1276936	type	True	78.6427	185	830	95	below_threshold
Staphylococcus caeli	strain=82B	GCA_900097965.1	2201815	2201815	type	True	78.5011	182	830	95	below_threshold
Staphylococcus succinus subsp. succinus	strain=DSM 14617	GCA_001006765.1	224030	61015	type	True	78.4787	174	830	95	below_threshold
Staphylococcus intermedius	strain=NCTC 11048	GCA_002902385.1	1285	1285	type	True	78.0648	135	830	95	below_threshold
Staphylococcus pasteuri	strain=DSM 10656	GCA_003970495.1	45972	45972	type	True	77.9202	183	830	95	below_threshold
Staphylococcus intermedius	strain=NCTC 11048	GCA_000308095.1	1285	1285	type	True	77.6492	130	830	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:46,351] [INFO] DFAST Taxonomy check result was written to GCF_016127935.1_ASM1612793v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:46,351] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:46,351] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:46,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9416dbf2-fb5c-40f7-9d01-cfe0e8238d6e/dqc_reference/checkm_data
[2024-01-24 13:49:46,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:46,389] [INFO] Task started: CheckM
[2024-01-24 13:49:46,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016127935.1_ASM1612793v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016127935.1_ASM1612793v1_genomic.fna/checkm_input GCF_016127935.1_ASM1612793v1_genomic.fna/checkm_result
[2024-01-24 13:50:10,392] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:10,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:10,422] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:10,422] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:10,423] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016127935.1_ASM1612793v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:10,423] [INFO] Task started: Blastn
[2024-01-24 13:50:10,424] [INFO] Running command: blastn -query GCF_016127935.1_ASM1612793v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9416dbf2-fb5c-40f7-9d01-cfe0e8238d6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_016127935.1_ASM1612793v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:11,260] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:11,265] [INFO] Selected 23 target genomes.
[2024-01-24 13:50:11,265] [INFO] Target genome list was writen to GCF_016127935.1_ASM1612793v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:11,288] [INFO] Task started: fastANI
[2024-01-24 13:50:11,288] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2811285-b877-416e-88ee-2bda162049d3/GCF_016127935.1_ASM1612793v1_genomic.fna.gz --refList GCF_016127935.1_ASM1612793v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016127935.1_ASM1612793v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:22,653] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:22,673] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:22,673] [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_002902685.1	s__Staphylococcus pettenkoferi	99.9191	759	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.48	96.01	0.95	0.89	21	conclusive
GCF_002902305.1	s__Staphylococcus argensis	92.3353	758	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.94	99.94	1.00	1.00	8	-
GCF_015594545.1	s__Staphylococcus durrellii	79.4755	174	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015775975.1	s__Staphylococcus lloydii	79.2966	199	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.39	98.19	0.98	0.95	4	-
GCF_010365305.1	s__Staphylococcus sp010365305	79.1443	133	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003491325.1	s__Staphylococcus warneri_A	79.1249	182	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.32	98.95	0.94	0.90	22	-
GCF_900458435.1	s__Staphylococcus carnosus	78.8899	164	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.71	99.56	0.96	0.93	12	-
GCF_002902565.1	s__Staphylococcus petrasii	78.6427	185	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.66	97.62	0.95	0.85	8	-
GCF_002902325.1	s__Staphylococcus capitis	78.6402	157	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.07	96.40	0.94	0.88	151	-
GCF_000875895.1	s__Staphylococcus gallinarum	78.572	187	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.63	98.14	0.94	0.91	25	-
GCF_002902725.1	s__Staphylococcus caprae	78.5358	184	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.57	98.10	0.94	0.91	18	-
GCF_900097965.1	s__Staphylococcus caeli	78.4838	182	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001006765.1	s__Staphylococcus succinus	78.4572	173	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	97.99	95.53	0.94	0.89	24	-
GCA_002902575.1	s__Staphylococcus croceilyticus	78.3426	188	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.95	99.95	1.00	1.00	2	-
GCF_002902235.1	s__Staphylococcus ureilyticus	78.2446	170	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.76	98.26	0.93	0.88	107	-
GCF_002902385.1	s__Staphylococcus intermedius	78.0717	134	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	99.80	99.54	0.96	0.94	8	-
GCF_003970495.1	s__Staphylococcus pasteuri	77.9259	182	830	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	98.67	0.95	0.89	34	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:22,675] [INFO] GTDB search result was written to GCF_016127935.1_ASM1612793v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:22,676] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:22,681] [INFO] DFAST_QC result json was written to GCF_016127935.1_ASM1612793v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:22,681] [INFO] DFAST_QC completed!
[2024-01-24 13:50:22,681] [INFO] Total running time: 0h0m55s