[2024-01-24 11:43:25,076] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,080] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,080] [INFO] DQC Reference Directory: /var/lib/cwl/stg59d36b84-8eab-47e5-9a76-7d814f3b9807/dqc_reference
[2024-01-24 11:43:30,058] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,059] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,059] [INFO] Running command: gunzip -c /var/lib/cwl/stg880533d4-8e5a-46ec-af66-2b506b3b5d8f/GCF_020097135.1_ASM2009713v1_genomic.fna.gz | prodigal -d GCF_020097135.1_ASM2009713v1_genomic.fna/cds.fna -a GCF_020097135.1_ASM2009713v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:34,474] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:34,475] [INFO] Task started: HMMsearch
[2024-01-24 11:43:34,475] [INFO] Running command: hmmsearch --tblout GCF_020097135.1_ASM2009713v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59d36b84-8eab-47e5-9a76-7d814f3b9807/dqc_reference/reference_markers.hmm GCF_020097135.1_ASM2009713v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:34,760] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:34,762] [INFO] Found 6/6 markers.
[2024-01-24 11:43:34,792] [INFO] Query marker FASTA was written to GCF_020097135.1_ASM2009713v1_genomic.fna/markers.fasta
[2024-01-24 11:43:34,792] [INFO] Task started: Blastn
[2024-01-24 11:43:34,792] [INFO] Running command: blastn -query GCF_020097135.1_ASM2009713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59d36b84-8eab-47e5-9a76-7d814f3b9807/dqc_reference/reference_markers.fasta -out GCF_020097135.1_ASM2009713v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:35,391] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:35,415] [INFO] Selected 20 target genomes.
[2024-01-24 11:43:35,416] [INFO] Target genome list was writen to GCF_020097135.1_ASM2009713v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:35,433] [INFO] Task started: fastANI
[2024-01-24 11:43:35,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg880533d4-8e5a-46ec-af66-2b506b3b5d8f/GCF_020097135.1_ASM2009713v1_genomic.fna.gz --refList GCF_020097135.1_ASM2009713v1_genomic.fna/target_genomes.txt --output GCF_020097135.1_ASM2009713v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:44,953] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:44,954] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59d36b84-8eab-47e5-9a76-7d814f3b9807/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:44,955] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59d36b84-8eab-47e5-9a76-7d814f3b9807/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:44,968] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:44,969] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:44,969] [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
Macrococcus armenti	strain=JEK37	GCA_020097135.1	2875764	2875764	type	True	100.0	732	734	95	conclusive
Macrococcus caseolyticus subsp. hominis	strain=CCM 7927	GCA_002742395.2	1891096	69966	type	True	83.1359	423	734	95	below_threshold
Macrococcus caseolyticus	strain=FDAARGOS_868	GCA_016028795.1	69966	69966	type	True	83.1299	447	734	95	below_threshold
Macrococcus canis	strain=KM 45013	GCA_002119805.1	1855823	1855823	type	True	83.0565	455	734	95	below_threshold
Macrococcus caseolyticus subsp. caseolyticus	strain=CCM 3540	GCA_003259685.1	2233644	69966	type	True	82.8838	436	734	95	below_threshold
Macrococcus caseolyticus	strain=DSM 20597	GCA_002902665.1	69966	69966	type	True	82.871	427	734	95	below_threshold
Macrococcus epidermidis	strain=01/688	GCA_003259695.1	1902580	1902580	type	True	80.5889	310	734	95	below_threshold
Macrococcus goetzii	strain=CCM 4927	GCA_002742385.2	1891097	1891097	type	True	80.3683	305	734	95	below_threshold
Macrococcus bohemicus	strain=03/115	GCA_003259675.1	1903056	1903056	type	True	80.1597	295	734	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	79.1606	51	734	95	below_threshold
Staphylococcus aureus	strain=PartF-Saureus-RM8376	GCA_022869625.1	1280	1280	type	True	78.7274	93	734	95	below_threshold
Staphylococcus aureus	strain=NCTC 08532	GCA_002902205.1	1280	1280	type	True	77.7536	92	734	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:44,971] [INFO] DFAST Taxonomy check result was written to GCF_020097135.1_ASM2009713v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:44,971] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:44,971] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:44,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59d36b84-8eab-47e5-9a76-7d814f3b9807/dqc_reference/checkm_data
[2024-01-24 11:43:44,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:44,997] [INFO] Task started: CheckM
[2024-01-24 11:43:44,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020097135.1_ASM2009713v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020097135.1_ASM2009713v1_genomic.fna/checkm_input GCF_020097135.1_ASM2009713v1_genomic.fna/checkm_result
[2024-01-24 11:44:05,652] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:05,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:05,672] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:05,672] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:05,673] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020097135.1_ASM2009713v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:05,673] [INFO] Task started: Blastn
[2024-01-24 11:44:05,673] [INFO] Running command: blastn -query GCF_020097135.1_ASM2009713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59d36b84-8eab-47e5-9a76-7d814f3b9807/dqc_reference/reference_markers_gtdb.fasta -out GCF_020097135.1_ASM2009713v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:06,470] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:06,475] [INFO] Selected 21 target genomes.
[2024-01-24 11:44:06,476] [INFO] Target genome list was writen to GCF_020097135.1_ASM2009713v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:06,493] [INFO] Task started: fastANI
[2024-01-24 11:44:06,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg880533d4-8e5a-46ec-af66-2b506b3b5d8f/GCF_020097135.1_ASM2009713v1_genomic.fna.gz --refList GCF_020097135.1_ASM2009713v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020097135.1_ASM2009713v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:15,869] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:15,886] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:44:15,886] [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_002119805.1	s__Macrococcus_B canis	83.0673	455	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.0	96.44	96.14	0.86	0.82	14	-
GCF_002902665.1	s__Macrococcus_B caseolyticus	82.871	427	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.0	98.20	96.60	0.90	0.84	54	-
GCF_003259695.1	s__Macrococcus_B epidermidis	80.5885	310	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.5758	N/A	N/A	N/A	N/A	1	-
GCF_002742385.2	s__Macrococcus_B goetzii	80.3563	305	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.5758	96.60	96.57	0.86	0.86	4	-
GCF_003259675.1	s__Macrococcus_B bohemicus	80.1449	295	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.0	98.03	97.95	0.86	0.85	5	-
GCF_004117835.1	s__Macrococcus_B sp004117835	79.2587	244	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004359615.1	s__Macrococcus brunensis	78.8654	135	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431205.1	s__Staphylococcus sp001431205	78.3125	82	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901825.1	s__Mammaliicoccus sciuri	78.107	134	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	96.65	95.60	0.90	0.84	216	-
GCF_003970495.1	s__Staphylococcus pasteuri	77.6858	94	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.98	98.67	0.95	0.89	34	-
GCF_002732165.1	s__Staphylococcus xylosus	77.4477	91	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.41	97.01	0.95	0.90	48	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:15,888] [INFO] GTDB search result was written to GCF_020097135.1_ASM2009713v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:15,889] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:15,894] [INFO] DFAST_QC result json was written to GCF_020097135.1_ASM2009713v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:15,895] [INFO] DFAST_QC completed!
[2024-01-24 11:44:15,895] [INFO] Total running time: 0h0m51s