[2024-01-24 14:28:16,280] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:16,287] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:16,287] [INFO] DQC Reference Directory: /var/lib/cwl/stg127b45dd-1ad0-4312-b9ef-c6bbd2f714a7/dqc_reference
[2024-01-24 14:28:17,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:17,788] [INFO] Task started: Prodigal
[2024-01-24 14:28:17,788] [INFO] Running command: gunzip -c /var/lib/cwl/stge7dff09f-4779-485b-85c0-722513460a79/GCF_002742385.2_ASM274238v2_genomic.fna.gz | prodigal -d GCF_002742385.2_ASM274238v2_genomic.fna/cds.fna -a GCF_002742385.2_ASM274238v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:23,142] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:23,142] [INFO] Task started: HMMsearch
[2024-01-24 14:28:23,142] [INFO] Running command: hmmsearch --tblout GCF_002742385.2_ASM274238v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg127b45dd-1ad0-4312-b9ef-c6bbd2f714a7/dqc_reference/reference_markers.hmm GCF_002742385.2_ASM274238v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:23,428] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:23,429] [INFO] Found 6/6 markers.
[2024-01-24 14:28:23,468] [INFO] Query marker FASTA was written to GCF_002742385.2_ASM274238v2_genomic.fna/markers.fasta
[2024-01-24 14:28:23,469] [INFO] Task started: Blastn
[2024-01-24 14:28:23,469] [INFO] Running command: blastn -query GCF_002742385.2_ASM274238v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg127b45dd-1ad0-4312-b9ef-c6bbd2f714a7/dqc_reference/reference_markers.fasta -out GCF_002742385.2_ASM274238v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:24,141] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:24,144] [INFO] Selected 18 target genomes.
[2024-01-24 14:28:24,144] [INFO] Target genome list was writen to GCF_002742385.2_ASM274238v2_genomic.fna/target_genomes.txt
[2024-01-24 14:28:24,165] [INFO] Task started: fastANI
[2024-01-24 14:28:24,166] [INFO] Running command: fastANI --query /var/lib/cwl/stge7dff09f-4779-485b-85c0-722513460a79/GCF_002742385.2_ASM274238v2_genomic.fna.gz --refList GCF_002742385.2_ASM274238v2_genomic.fna/target_genomes.txt --output GCF_002742385.2_ASM274238v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:33,231] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:33,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg127b45dd-1ad0-4312-b9ef-c6bbd2f714a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:33,232] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg127b45dd-1ad0-4312-b9ef-c6bbd2f714a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:33,247] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:28:33,247] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:28:33,247] [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 goetzii	strain=CCM 4927	GCA_002742385.2	1891097	1891097	type	True	100.0	851	852	95	inconclusive
Macrococcus epidermidis	strain=01/688	GCA_003259695.1	1902580	1902580	type	True	95.5758	727	852	95	inconclusive
Macrococcus bohemicus	strain=03/115	GCA_003259675.1	1903056	1903056	type	True	92.8172	674	852	95	below_threshold
Macrococcus caseolyticus subsp. hominis	strain=CCM 7927	GCA_002742395.2	1891096	69966	type	True	80.6393	277	852	95	below_threshold
Macrococcus armenti	strain=JEK37	GCA_020097135.1	2875764	2875764	type	True	80.2778	317	852	95	below_threshold
Macrococcus caseolyticus	strain=DSM 20597	GCA_002902665.1	69966	69966	type	True	80.0385	277	852	95	below_threshold
Macrococcus caseolyticus	strain=FDAARGOS_868	GCA_016028795.1	69966	69966	type	True	79.9629	289	852	95	below_threshold
Mammaliicoccus vitulinus	strain=FDAARGOS_1207	GCA_016889245.1	71237	71237	suspected-type	True	78.0543	119	852	95	below_threshold
Mammaliicoccus sciuri	strain=DSM 20345	GCA_001046995.1	1296	1296	type	True	77.9614	141	852	95	below_threshold
Mammaliicoccus vitulinus	strain=DSM 15615	GCA_002902265.1	71237	71237	type	True	77.864	113	852	95	below_threshold
Mammaliicoccus lentus	strain=NCTC12102	GCA_900458735.1	42858	42858	type	True	77.8415	133	852	95	below_threshold
Staphylococcus caprae	strain=NCTC12196	GCA_900458385.1	29380	29380	type	True	77.7631	87	852	95	below_threshold
Mammaliicoccus lentus	strain=NCTC 12102	GCA_002902755.1	42858	42858	type	True	77.7298	130	852	95	below_threshold
Staphylococcus caprae	strain=NCTC 12196	GCA_002902725.1	29380	29380	type	True	77.529	86	852	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:33,249] [INFO] DFAST Taxonomy check result was written to GCF_002742385.2_ASM274238v2_genomic.fna/tc_result.tsv
[2024-01-24 14:28:33,250] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:33,250] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:33,251] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg127b45dd-1ad0-4312-b9ef-c6bbd2f714a7/dqc_reference/checkm_data
[2024-01-24 14:28:33,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:33,283] [INFO] Task started: CheckM
[2024-01-24 14:28:33,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002742385.2_ASM274238v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002742385.2_ASM274238v2_genomic.fna/checkm_input GCF_002742385.2_ASM274238v2_genomic.fna/checkm_result
[2024-01-24 14:28:56,199] [INFO] Task succeeded: CheckM
[2024-01-24 14:28:56,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:28:56,218] [INFO] ===== Completeness check finished =====
[2024-01-24 14:28:56,218] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:28:56,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002742385.2_ASM274238v2_genomic.fna/markers.fasta)
[2024-01-24 14:28:56,219] [INFO] Task started: Blastn
[2024-01-24 14:28:56,219] [INFO] Running command: blastn -query GCF_002742385.2_ASM274238v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg127b45dd-1ad0-4312-b9ef-c6bbd2f714a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002742385.2_ASM274238v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:57,009] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:57,012] [INFO] Selected 15 target genomes.
[2024-01-24 14:28:57,012] [INFO] Target genome list was writen to GCF_002742385.2_ASM274238v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:28:57,034] [INFO] Task started: fastANI
[2024-01-24 14:28:57,035] [INFO] Running command: fastANI --query /var/lib/cwl/stge7dff09f-4779-485b-85c0-722513460a79/GCF_002742385.2_ASM274238v2_genomic.fna.gz --refList GCF_002742385.2_ASM274238v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002742385.2_ASM274238v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:04,135] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:04,151] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:04,151] [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_002742385.2	s__Macrococcus_B goetzii	100.0	851	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.5758	96.60	96.57	0.86	0.86	4	conclusive
GCF_003259695.1	s__Macrococcus_B epidermidis	95.5758	727	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Macrococcus_B	95.5758	N/A	N/A	N/A	N/A	1	conclusive
GCF_003259675.1	s__Macrococcus_B bohemicus	92.8172	674	852	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_002119805.1	s__Macrococcus_B canis	81.3464	302	852	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	80.0184	278	852	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_004117835.1	s__Macrococcus_B sp004117835	79.7547	263	852	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_002901825.1	s__Mammaliicoccus sciuri	77.9152	136	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	96.65	95.60	0.90	0.84	216	-
GCF_002902265.1	s__Mammaliicoccus vitulinus	77.8738	112	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	98.82	98.52	0.92	0.85	19	-
GCF_002902755.1	s__Mammaliicoccus lentus	77.7354	129	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Mammaliicoccus	95.0	99.03	97.66	0.94	0.90	21	-
GCF_002902725.1	s__Staphylococcus caprae	77.5651	85	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	98.57	98.10	0.94	0.91	18	-
GCF_015594545.1	s__Staphylococcus durrellii	77.3832	83	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010365305.1	s__Staphylococcus sp010365305	77.3431	91	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:04,153] [INFO] GTDB search result was written to GCF_002742385.2_ASM274238v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:04,153] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:04,157] [INFO] DFAST_QC result json was written to GCF_002742385.2_ASM274238v2_genomic.fna/dqc_result.json
[2024-01-24 14:29:04,157] [INFO] DFAST_QC completed!
[2024-01-24 14:29:04,157] [INFO] Total running time: 0h0m48s