[2024-01-24 13:36:31,402] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:31,406] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:31,406] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9d556d5-5a01-467a-b8da-c28a6c440db2/dqc_reference
[2024-01-24 13:36:32,788] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:32,789] [INFO] Task started: Prodigal
[2024-01-24 13:36:32,789] [INFO] Running command: gunzip -c /var/lib/cwl/stg37395978-0b90-4388-80c8-3931b46e3dad/GCF_017874315.1_ASM1787431v1_genomic.fna.gz | prodigal -d GCF_017874315.1_ASM1787431v1_genomic.fna/cds.fna -a GCF_017874315.1_ASM1787431v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:43,496] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:43,497] [INFO] Task started: HMMsearch
[2024-01-24 13:36:43,497] [INFO] Running command: hmmsearch --tblout GCF_017874315.1_ASM1787431v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9d556d5-5a01-467a-b8da-c28a6c440db2/dqc_reference/reference_markers.hmm GCF_017874315.1_ASM1787431v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:43,751] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:43,752] [INFO] Found 6/6 markers.
[2024-01-24 13:36:43,785] [INFO] Query marker FASTA was written to GCF_017874315.1_ASM1787431v1_genomic.fna/markers.fasta
[2024-01-24 13:36:43,786] [INFO] Task started: Blastn
[2024-01-24 13:36:43,786] [INFO] Running command: blastn -query GCF_017874315.1_ASM1787431v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9d556d5-5a01-467a-b8da-c28a6c440db2/dqc_reference/reference_markers.fasta -out GCF_017874315.1_ASM1787431v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:44,525] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:44,530] [INFO] Selected 22 target genomes.
[2024-01-24 13:36:44,531] [INFO] Target genome list was writen to GCF_017874315.1_ASM1787431v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:44,543] [INFO] Task started: fastANI
[2024-01-24 13:36:44,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg37395978-0b90-4388-80c8-3931b46e3dad/GCF_017874315.1_ASM1787431v1_genomic.fna.gz --refList GCF_017874315.1_ASM1787431v1_genomic.fna/target_genomes.txt --output GCF_017874315.1_ASM1787431v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:00,204] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:00,205] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9d556d5-5a01-467a-b8da-c28a6c440db2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:00,205] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9d556d5-5a01-467a-b8da-c28a6c440db2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:00,216] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:00,217] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:00,217] [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
Symbiobacterium terraclitae	strain=DSM 27138	GCA_017874315.1	557451	557451	type	True	100.0	1259	1261	95	conclusive
Symbiobacterium thermophilum	strain=IAM14863	GCA_000009905.1	2734	2734	type	True	82.6336	834	1261	95	below_threshold
Thermaerobacter marianensis	strain=DSM 12885	GCA_000184705.1	73919	73919	type	True	75.8669	143	1261	95	below_threshold
Adlercreutzia caecimuris	strain=B7	GCA_000403355.2	671266	671266	type	True	75.5328	51	1261	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	75.0275	89	1261	95	below_threshold
Microlunatus kandeliicorticis	strain=DSM 100723	GCA_014137855.1	1759536	1759536	type	True	74.9911	114	1261	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	74.9615	76	1261	95	below_threshold
Nocardioides acrostichi	strain=CBS4Y-1	GCA_015319165.1	2784339	2784339	type	True	74.936	97	1261	95	below_threshold
Roseomonas ludipueritiae	strain=DSM 14915	GCA_014490445.1	198093	198093	type	True	74.9046	104	1261	95	below_threshold
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	74.8831	83	1261	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	74.8527	134	1261	95	below_threshold
Nocardia farcinica	strain=NBRC 15532	GCA_001612925.1	37329	37329	type	True	74.85	135	1261	95	below_threshold
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	74.8459	135	1261	95	below_threshold
Pseudonocardia cypriaca	strain=DSM 45511	GCA_006717045.1	882449	882449	type	True	74.7739	162	1261	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:00,219] [INFO] DFAST Taxonomy check result was written to GCF_017874315.1_ASM1787431v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:00,219] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:00,219] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:00,219] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9d556d5-5a01-467a-b8da-c28a6c440db2/dqc_reference/checkm_data
[2024-01-24 13:37:00,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:00,259] [INFO] Task started: CheckM
[2024-01-24 13:37:00,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874315.1_ASM1787431v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874315.1_ASM1787431v1_genomic.fna/checkm_input GCF_017874315.1_ASM1787431v1_genomic.fna/checkm_result
[2024-01-24 13:37:35,999] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:36,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:36,021] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:36,022] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:36,022] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874315.1_ASM1787431v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:36,023] [INFO] Task started: Blastn
[2024-01-24 13:37:36,023] [INFO] Running command: blastn -query GCF_017874315.1_ASM1787431v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9d556d5-5a01-467a-b8da-c28a6c440db2/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874315.1_ASM1787431v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:37,317] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:37,324] [INFO] Selected 16 target genomes.
[2024-01-24 13:37:37,324] [INFO] Target genome list was writen to GCF_017874315.1_ASM1787431v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:37,370] [INFO] Task started: fastANI
[2024-01-24 13:37:37,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg37395978-0b90-4388-80c8-3931b46e3dad/GCF_017874315.1_ASM1787431v1_genomic.fna.gz --refList GCF_017874315.1_ASM1787431v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874315.1_ASM1787431v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:46,491] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:46,501] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:46,501] [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_017874315.1	s__Symbiobacterium terraclitae	100.0	1259	1261	d__Bacteria;p__Firmicutes_E;c__Symbiobacteriia;o__Symbiobacteriales;f__Symbiobacteriaceae;g__Symbiobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000009905.1	s__Symbiobacterium thermophilum	82.6269	835	1261	d__Bacteria;p__Firmicutes_E;c__Symbiobacteriia;o__Symbiobacteriales;f__Symbiobacteriaceae;g__Symbiobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242675.1	s__Symbiobacterium sp003242675	82.5096	671	1261	d__Bacteria;p__Firmicutes_E;c__Symbiobacteriia;o__Symbiobacteriales;f__Symbiobacteriaceae;g__Symbiobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242505.1	s__ZC4RG38 sp003242505	77.1168	209	1261	d__Bacteria;p__Firmicutes_E;c__Symbiobacteriia;o__Symbiobacteriales;f__ZC4RG38;g__ZC4RG38	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004634385.1	s__Thermaerobacter sp004634385	76.0413	132	1261	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__Thermaerobacteraceae;g__Thermaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000184705.1	s__Thermaerobacter marianensis	75.873	142	1261	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__Thermaerobacteraceae;g__Thermaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765395.1	s__UBA2862 sp902765395	75.7116	75	1261	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA2862	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919045.1	s__CAILLO01 sp903919045	75.1975	61	1261	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__UBA5734;g__CAILLO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011362545.1	s__DSTP01 sp011362545	75.1409	71	1261	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__DSTP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016190985.1	s__Lacunisphaera sp016190985	75.0154	68	1261	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106975.1	s__Pseudomonas_O kuykendallii	74.8831	83	1261	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_O	95.0	96.83	96.68	0.93	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:46,503] [INFO] GTDB search result was written to GCF_017874315.1_ASM1787431v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:46,509] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:46,514] [INFO] DFAST_QC result json was written to GCF_017874315.1_ASM1787431v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:46,515] [INFO] DFAST_QC completed!
[2024-01-24 13:37:46,515] [INFO] Total running time: 0h1m15s