[2024-01-24 12:43:54,227] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:43:54,360] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:43:54,360] [INFO] DQC Reference Directory: /var/lib/cwl/stg7137e67f-8d27-4cb2-a70a-55976690ba20/dqc_reference
[2024-01-24 12:43:59,335] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:43:59,336] [INFO] Task started: Prodigal
[2024-01-24 12:43:59,336] [INFO] Running command: gunzip -c /var/lib/cwl/stg41a9b9ba-65c8-4b71-96ed-a1656988390c/GCF_016774385.1_ASM1677438v1_genomic.fna.gz | prodigal -d GCF_016774385.1_ASM1677438v1_genomic.fna/cds.fna -a GCF_016774385.1_ASM1677438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:19,275] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:19,275] [INFO] Task started: HMMsearch
[2024-01-24 12:44:19,275] [INFO] Running command: hmmsearch --tblout GCF_016774385.1_ASM1677438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7137e67f-8d27-4cb2-a70a-55976690ba20/dqc_reference/reference_markers.hmm GCF_016774385.1_ASM1677438v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:19,587] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:19,589] [INFO] Found 6/6 markers.
[2024-01-24 12:44:19,646] [INFO] Query marker FASTA was written to GCF_016774385.1_ASM1677438v1_genomic.fna/markers.fasta
[2024-01-24 12:44:19,647] [INFO] Task started: Blastn
[2024-01-24 12:44:19,647] [INFO] Running command: blastn -query GCF_016774385.1_ASM1677438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7137e67f-8d27-4cb2-a70a-55976690ba20/dqc_reference/reference_markers.fasta -out GCF_016774385.1_ASM1677438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:20,856] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:20,861] [INFO] Selected 17 target genomes.
[2024-01-24 12:44:20,862] [INFO] Target genome list was writen to GCF_016774385.1_ASM1677438v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:20,891] [INFO] Task started: fastANI
[2024-01-24 12:44:20,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg41a9b9ba-65c8-4b71-96ed-a1656988390c/GCF_016774385.1_ASM1677438v1_genomic.fna.gz --refList GCF_016774385.1_ASM1677438v1_genomic.fna/target_genomes.txt --output GCF_016774385.1_ASM1677438v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:49,814] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:49,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7137e67f-8d27-4cb2-a70a-55976690ba20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:49,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7137e67f-8d27-4cb2-a70a-55976690ba20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:49,831] [INFO] Found 17 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:44:49,831] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:44:49,831] [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 fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	100.0	2233	2237	95	inconclusive
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	96.8399	2006	2237	95	inconclusive
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	96.7969	2015	2237	95	inconclusive
Micromonospora gifhornensis	strain=NBRC 16317	GCA_016863515.1	84594	84594	type	True	95.8713	1929	2237	95	inconclusive
Micromonospora zingiberis	strain=PLAI 1-1	GCA_004331455.1	2053011	2053011	type	True	89.7211	1570	2237	95	below_threshold
Micromonospora radicis	strain=AZ1-13	GCA_003583405.1	1894971	1894971	type	True	88.0705	1484	2237	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	86.3084	1537	2237	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_003419945.1	2294034	2294034	type	True	86.2998	1365	2237	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	84.356	1017	2237	95	below_threshold
Micromonospora nigra	strain=DSM 43818	GCA_900091585.1	145857	145857	type	True	84.1335	1307	2237	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	84.0502	1263	2237	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	83.8523	1275	2237	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	83.6273	1331	2237	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	83.6207	1147	2237	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	83.5277	1358	2237	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	83.4491	1346	2237	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.3098	1306	2237	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:49,833] [INFO] DFAST Taxonomy check result was written to GCF_016774385.1_ASM1677438v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:49,834] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:49,834] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:49,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7137e67f-8d27-4cb2-a70a-55976690ba20/dqc_reference/checkm_data
[2024-01-24 12:44:49,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:49,910] [INFO] Task started: CheckM
[2024-01-24 12:44:49,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016774385.1_ASM1677438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016774385.1_ASM1677438v1_genomic.fna/checkm_input GCF_016774385.1_ASM1677438v1_genomic.fna/checkm_result
[2024-01-24 12:45:58,646] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:58,648] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:58,673] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:58,674] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:58,674] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016774385.1_ASM1677438v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:58,675] [INFO] Task started: Blastn
[2024-01-24 12:45:58,675] [INFO] Running command: blastn -query GCF_016774385.1_ASM1677438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7137e67f-8d27-4cb2-a70a-55976690ba20/dqc_reference/reference_markers_gtdb.fasta -out GCF_016774385.1_ASM1677438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:00,450] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:00,455] [INFO] Selected 16 target genomes.
[2024-01-24 12:46:00,456] [INFO] Target genome list was writen to GCF_016774385.1_ASM1677438v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:00,468] [INFO] Task started: fastANI
[2024-01-24 12:46:00,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg41a9b9ba-65c8-4b71-96ed-a1656988390c/GCF_016774385.1_ASM1677438v1_genomic.fna.gz --refList GCF_016774385.1_ASM1677438v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016774385.1_ASM1677438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:26,806] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:26,830] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:26,830] [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_016863515.1	s__Micromonospora gifhornensis	95.8824	1928	2237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.77	95.90	0.88	0.87	6	conclusive
GCF_004331455.1	s__Micromonospora zingiberis	89.7054	1573	2237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583405.1	s__Micromonospora radicis	88.0563	1486	2237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236315.1	s__Micromonospora craterilacus	87.1572	1394	2237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005402585.1	s__Micromonospora sp005402585	86.9037	1556	2237	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	86.7978	1452	2237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236305.1	s__Micromonospora endophytica	86.6504	1329	2237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.96	99.96	0.99	0.98	3	-
GCF_016863555.1	s__Micromonospora qiuiae	86.6045	1397	2237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364215.1	s__Micromonospora sp004307965	86.2243	1580	2237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.04	99.04	0.94	0.94	2	-
GCF_010560025.1	s__Micromonospora sp010560025	86.033	1488	2237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.75	99.70	1.00	1.00	3	-
GCF_018070465.1	s__Micromonospora sp018070465	86.0314	1455	2237	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	86.0028	1477	2237	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	85.9278	1507	2237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.71	95.67	0.86	0.84	3	-
GCF_012726175.1	s__Micromonospora sp012726175	84.5693	1182	2237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070575.1	s__Micromonospora sp018070575	84.1034	1294	2237	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	83.8508	1180	2237	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 12:46:26,832] [INFO] GTDB search result was written to GCF_016774385.1_ASM1677438v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:26,833] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:26,837] [INFO] DFAST_QC result json was written to GCF_016774385.1_ASM1677438v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:26,838] [INFO] DFAST_QC completed!
[2024-01-24 12:46:26,838] [INFO] Total running time: 0h2m33s