[2024-01-24 10:47:11,668] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:11,670] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:11,670] [INFO] DQC Reference Directory: /var/lib/cwl/stg95b6aa04-dce9-4887-979c-ded8c6df8296/dqc_reference
[2024-01-24 10:47:16,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:16,945] [INFO] Task started: Prodigal
[2024-01-24 10:47:16,945] [INFO] Running command: gunzip -c /var/lib/cwl/stg04e97b0a-d97b-4fce-8236-d06f73dc4a89/GCF_016863515.1_ASM1686351v1_genomic.fna.gz | prodigal -d GCF_016863515.1_ASM1686351v1_genomic.fna/cds.fna -a GCF_016863515.1_ASM1686351v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:39,810] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:39,810] [INFO] Task started: HMMsearch
[2024-01-24 10:47:39,810] [INFO] Running command: hmmsearch --tblout GCF_016863515.1_ASM1686351v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95b6aa04-dce9-4887-979c-ded8c6df8296/dqc_reference/reference_markers.hmm GCF_016863515.1_ASM1686351v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:40,145] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:40,147] [INFO] Found 6/6 markers.
[2024-01-24 10:47:40,210] [INFO] Query marker FASTA was written to GCF_016863515.1_ASM1686351v1_genomic.fna/markers.fasta
[2024-01-24 10:47:40,210] [INFO] Task started: Blastn
[2024-01-24 10:47:40,210] [INFO] Running command: blastn -query GCF_016863515.1_ASM1686351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95b6aa04-dce9-4887-979c-ded8c6df8296/dqc_reference/reference_markers.fasta -out GCF_016863515.1_ASM1686351v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:41,333] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:41,337] [INFO] Selected 16 target genomes.
[2024-01-24 10:47:41,338] [INFO] Target genome list was writen to GCF_016863515.1_ASM1686351v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:41,345] [INFO] Task started: fastANI
[2024-01-24 10:47:41,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg04e97b0a-d97b-4fce-8236-d06f73dc4a89/GCF_016863515.1_ASM1686351v1_genomic.fna.gz --refList GCF_016863515.1_ASM1686351v1_genomic.fna/target_genomes.txt --output GCF_016863515.1_ASM1686351v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:09,761] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:09,762] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95b6aa04-dce9-4887-979c-ded8c6df8296/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:09,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95b6aa04-dce9-4887-979c-ded8c6df8296/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:09,776] [INFO] Found 16 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 10:48:09,776] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:48:09,777] [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 gifhornensis	strain=NBRC 16317	GCA_016863515.1	84594	84594	type	True	100.0	2208	2214	95	inconclusive
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	96.3427	1928	2214	95	inconclusive
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	96.3209	1938	2214	95	inconclusive
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	95.9008	1926	2214	95	inconclusive
Micromonospora zingiberis	strain=PLAI 1-1	GCA_004331455.1	2053011	2053011	type	True	89.4233	1540	2214	95	below_threshold
Micromonospora radicis	strain=AZ1-13	GCA_003583405.1	1894971	1894971	type	True	87.9229	1492	2214	95	below_threshold
Micromonospora craterilacus	strain=NA12	GCA_003236315.1	1655439	1655439	type	True	87.0208	1355	2214	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	86.1815	1491	2214	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	84.1983	995	2214	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	84.0202	1284	2214	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	83.6959	1236	2214	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	83.5573	1133	2214	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	83.393	1325	2214	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	83.3183	1332	2214	95	below_threshold
Micromonospora viridifaciens	strain=DSM 43909	GCA_900091545.1	1881	1881	type	True	83.2724	1187	2214	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.1715	1268	2214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:09,778] [INFO] DFAST Taxonomy check result was written to GCF_016863515.1_ASM1686351v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:09,779] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:09,779] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:09,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95b6aa04-dce9-4887-979c-ded8c6df8296/dqc_reference/checkm_data
[2024-01-24 10:48:09,780] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:09,843] [INFO] Task started: CheckM
[2024-01-24 10:48:09,844] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863515.1_ASM1686351v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863515.1_ASM1686351v1_genomic.fna/checkm_input GCF_016863515.1_ASM1686351v1_genomic.fna/checkm_result
[2024-01-24 10:49:18,648] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:18,649] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:18,673] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:18,673] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:18,674] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863515.1_ASM1686351v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:18,674] [INFO] Task started: Blastn
[2024-01-24 10:49:18,674] [INFO] Running command: blastn -query GCF_016863515.1_ASM1686351v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95b6aa04-dce9-4887-979c-ded8c6df8296/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863515.1_ASM1686351v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:20,380] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:20,384] [INFO] Selected 11 target genomes.
[2024-01-24 10:49:20,384] [INFO] Target genome list was writen to GCF_016863515.1_ASM1686351v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:20,394] [INFO] Task started: fastANI
[2024-01-24 10:49:20,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg04e97b0a-d97b-4fce-8236-d06f73dc4a89/GCF_016863515.1_ASM1686351v1_genomic.fna.gz --refList GCF_016863515.1_ASM1686351v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863515.1_ASM1686351v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:39,242] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:39,259] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:39,259] [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	100.0	2208	2214	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	89.4366	1539	2214	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	87.9265	1491	2214	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	87.0768	1349	2214	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	86.8405	1482	2214	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	86.6157	1414	2214	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	86.5682	1278	2214	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	86.3198	1377	2214	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	86.1192	1513	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.04	99.04	0.94	0.94	2	-
GCF_018070465.1	s__Micromonospora sp018070465	85.8724	1422	2214	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	85.8504	1465	2214	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.06	96.13	0.95	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:39,262] [INFO] GTDB search result was written to GCF_016863515.1_ASM1686351v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:39,263] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:39,266] [INFO] DFAST_QC result json was written to GCF_016863515.1_ASM1686351v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:39,267] [INFO] DFAST_QC completed!
[2024-01-24 10:49:39,267] [INFO] Total running time: 0h2m28s