[2024-01-24 13:58:55,862] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:55,868] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:55,868] [INFO] DQC Reference Directory: /var/lib/cwl/stg76294fb3-938c-4094-b2fd-87cb3794d1d2/dqc_reference
[2024-01-24 13:58:57,212] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:57,213] [INFO] Task started: Prodigal
[2024-01-24 13:58:57,214] [INFO] Running command: gunzip -c /var/lib/cwl/stgadcf5bed-0073-4d34-8b61-b21284770054/GCF_010560025.1_ASM1056002v1_genomic.fna.gz | prodigal -d GCF_010560025.1_ASM1056002v1_genomic.fna/cds.fna -a GCF_010560025.1_ASM1056002v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:17,504] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:17,505] [INFO] Task started: HMMsearch
[2024-01-24 13:59:17,505] [INFO] Running command: hmmsearch --tblout GCF_010560025.1_ASM1056002v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76294fb3-938c-4094-b2fd-87cb3794d1d2/dqc_reference/reference_markers.hmm GCF_010560025.1_ASM1056002v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:17,913] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:17,914] [INFO] Found 6/6 markers.
[2024-01-24 13:59:17,968] [INFO] Query marker FASTA was written to GCF_010560025.1_ASM1056002v1_genomic.fna/markers.fasta
[2024-01-24 13:59:17,969] [INFO] Task started: Blastn
[2024-01-24 13:59:17,969] [INFO] Running command: blastn -query GCF_010560025.1_ASM1056002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76294fb3-938c-4094-b2fd-87cb3794d1d2/dqc_reference/reference_markers.fasta -out GCF_010560025.1_ASM1056002v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:19,163] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:19,166] [INFO] Selected 17 target genomes.
[2024-01-24 13:59:19,167] [INFO] Target genome list was writen to GCF_010560025.1_ASM1056002v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:19,189] [INFO] Task started: fastANI
[2024-01-24 13:59:19,189] [INFO] Running command: fastANI --query /var/lib/cwl/stgadcf5bed-0073-4d34-8b61-b21284770054/GCF_010560025.1_ASM1056002v1_genomic.fna.gz --refList GCF_010560025.1_ASM1056002v1_genomic.fna/target_genomes.txt --output GCF_010560025.1_ASM1056002v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:45,854] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:45,854] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76294fb3-938c-4094-b2fd-87cb3794d1d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:45,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76294fb3-938c-4094-b2fd-87cb3794d1d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:45,871] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:59:45,871] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:59:45,872] [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
Micromonospora tarapacensis	strain=Llam7	GCA_019697375.1	2835305	2835305	type	True	88.202	1546	2108	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	88.0709	1549	2108	95	below_threshold
Micromonospora phaseoli	strain=DSM 45730	GCA_003253475.1	1144548	1144548	type	True	87.9851	1596	2108	95	below_threshold
Micromonospora phaseoli	strain=CGMCC 4.7038	GCA_900109115.1	1144548	1144548	type	True	87.9588	1613	2108	95	below_threshold
Micromonospora craterilacus	strain=NA12	GCA_003236315.1	1655439	1655439	type	True	87.3327	1285	2108	95	below_threshold
Micromonospora radicis	strain=AZ1-13	GCA_003583405.1	1894971	1894971	type	True	86.6441	1385	2108	95	below_threshold
Micromonospora zingiberis	strain=PLAI 1-1	GCA_004331455.1	2053011	2053011	type	True	86.6273	1431	2108	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_003419945.1	2294034	2294034	type	True	86.1981	1328	2108	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	86.065	1491	2108	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	86.0445	1493	2108	95	below_threshold
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	86.0434	1478	2108	95	below_threshold
Micromonospora gifhornensis	strain=NBRC 16317	GCA_016863515.1	84594	84594	type	True	86.0141	1454	2108	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	84.5035	1004	2108	95	below_threshold
Micromonospora nigra	strain=DSM 43818	GCA_900091585.1	145857	145857	type	True	84.4528	1301	2108	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	83.6276	1165	2108	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.3445	1285	2108	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	83.3225	1338	2108	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:45,873] [INFO] DFAST Taxonomy check result was written to GCF_010560025.1_ASM1056002v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:45,874] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:45,874] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:45,874] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76294fb3-938c-4094-b2fd-87cb3794d1d2/dqc_reference/checkm_data
[2024-01-24 13:59:45,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:45,944] [INFO] Task started: CheckM
[2024-01-24 13:59:45,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010560025.1_ASM1056002v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010560025.1_ASM1056002v1_genomic.fna/checkm_input GCF_010560025.1_ASM1056002v1_genomic.fna/checkm_result
[2024-01-24 14:00:53,381] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:53,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:53,409] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:53,409] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:53,409] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010560025.1_ASM1056002v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:53,410] [INFO] Task started: Blastn
[2024-01-24 14:00:53,410] [INFO] Running command: blastn -query GCF_010560025.1_ASM1056002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76294fb3-938c-4094-b2fd-87cb3794d1d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_010560025.1_ASM1056002v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:55,117] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:55,122] [INFO] Selected 11 target genomes.
[2024-01-24 14:00:55,122] [INFO] Target genome list was writen to GCF_010560025.1_ASM1056002v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:55,131] [INFO] Task started: fastANI
[2024-01-24 14:00:55,131] [INFO] Running command: fastANI --query /var/lib/cwl/stgadcf5bed-0073-4d34-8b61-b21284770054/GCF_010560025.1_ASM1056002v1_genomic.fna.gz --refList GCF_010560025.1_ASM1056002v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010560025.1_ASM1056002v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:13,147] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:13,163] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:13,163] [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_010560025.1	s__Micromonospora sp010560025	100.0	2107	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.75	99.70	1.00	1.00	3	conclusive
GCF_018070465.1	s__Micromonospora sp018070465	93.9217	1699	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112325.1	s__Micromonospora sediminimaris	92.4465	1701	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.06	96.13	0.95	0.90	3	-
GCF_016863495.1	s__Micromonospora andamanensis	91.1715	1675	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.71	95.67	0.86	0.84	3	-
GCF_016863535.1	s__Micromonospora lutea	90.1711	1554	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009712475.1	s__Micromonospora sp009712475	89.8293	1492	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012726175.1	s__Micromonospora sp012726175	89.163	1276	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331455.1	s__Micromonospora zingiberis	86.6165	1432	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646235.1	s__Micromonospora sonchi	86.5373	1382	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091625.1	s__Micromonospora peucetia	83.924	1288	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725545.1	s__Micromonospora sp003725545	83.6499	1149	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:01:13,165] [INFO] GTDB search result was written to GCF_010560025.1_ASM1056002v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:13,166] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:13,170] [INFO] DFAST_QC result json was written to GCF_010560025.1_ASM1056002v1_genomic.fna/dqc_result.json
[2024-01-24 14:01:13,170] [INFO] DFAST_QC completed!
[2024-01-24 14:01:13,170] [INFO] Total running time: 0h2m17s