[2024-01-25 19:32:51,062] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:32:51,064] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:32:51,064] [INFO] DQC Reference Directory: /var/lib/cwl/stg7990092f-6139-4e56-a4d0-b9929d04e168/dqc_reference
[2024-01-25 19:32:52,169] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:32:52,170] [INFO] Task started: Prodigal
[2024-01-25 19:32:52,170] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa651552-6159-4172-8b11-94fdb6fe3e2f/GCF_016862915.1_ASM1686291v1_genomic.fna.gz | prodigal -d GCF_016862915.1_ASM1686291v1_genomic.fna/cds.fna -a GCF_016862915.1_ASM1686291v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:33:19,438] [INFO] Task succeeded: Prodigal
[2024-01-25 19:33:19,439] [INFO] Task started: HMMsearch
[2024-01-25 19:33:19,439] [INFO] Running command: hmmsearch --tblout GCF_016862915.1_ASM1686291v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7990092f-6139-4e56-a4d0-b9929d04e168/dqc_reference/reference_markers.hmm GCF_016862915.1_ASM1686291v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:33:19,794] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:33:19,795] [INFO] Found 6/6 markers.
[2024-01-25 19:33:19,864] [INFO] Query marker FASTA was written to GCF_016862915.1_ASM1686291v1_genomic.fna/markers.fasta
[2024-01-25 19:33:19,864] [INFO] Task started: Blastn
[2024-01-25 19:33:19,864] [INFO] Running command: blastn -query GCF_016862915.1_ASM1686291v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7990092f-6139-4e56-a4d0-b9929d04e168/dqc_reference/reference_markers.fasta -out GCF_016862915.1_ASM1686291v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:21,004] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:21,011] [INFO] Selected 29 target genomes.
[2024-01-25 19:33:21,011] [INFO] Target genome list was writen to GCF_016862915.1_ASM1686291v1_genomic.fna/target_genomes.txt
[2024-01-25 19:33:21,020] [INFO] Task started: fastANI
[2024-01-25 19:33:21,020] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa651552-6159-4172-8b11-94fdb6fe3e2f/GCF_016862915.1_ASM1686291v1_genomic.fna.gz --refList GCF_016862915.1_ASM1686291v1_genomic.fna/target_genomes.txt --output GCF_016862915.1_ASM1686291v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:34:13,032] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:13,033] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7990092f-6139-4e56-a4d0-b9929d04e168/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:34:13,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7990092f-6139-4e56-a4d0-b9929d04e168/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:34:13,049] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:34:13,049] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:34:13,049] [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 phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	81.6486	1015	3187	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	81.5844	1427	3187	95	below_threshold
Micromonospora mirobrigensis	strain=DSM 44830	GCA_900091555.1	262898	262898	type	True	81.2664	1284	3187	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	81.2338	1213	3187	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	81.2318	1259	3187	95	below_threshold
Micromonospora siamensis	strain=DSM 45097	GCA_900090305.1	299152	299152	type	True	81.2255	1277	3187	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	81.1992	1358	3187	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	81.1866	1364	3187	95	below_threshold
Micromonospora craterilacus	strain=NA12	GCA_003236315.1	1655439	1655439	type	True	81.1632	1180	3187	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	81.1444	1229	3187	95	below_threshold
Micromonospora viridifaciens	strain=DSM 43909	GCA_900091545.1	1881	1881	type	True	81.1129	1273	3187	95	below_threshold
Micromonospora rosaria	strain=DSM 803	GCA_001567585.1	47874	47874	type	True	81.0471	1350	3187	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	81.0437	1351	3187	95	below_threshold
Micromonospora carbonacea	strain=DSM 43815	GCA_014205165.1	47853	47853	type	True	81.0365	1396	3187	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	80.9552	1409	3187	95	below_threshold
Micromonospora orduensis	strain=S2509	GCA_006228125.1	1420891	1420891	type	True	80.9276	1239	3187	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	80.9169	1349	3187	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	80.8984	1367	3187	95	below_threshold
Micromonospora pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	80.8019	1120	3187	95	below_threshold
Micromonospora ureilytica	strain=DSM 101692	GCA_015751765.1	709868	709868	type	True	80.7361	1314	3187	95	below_threshold
Micromonospora vinacea	strain=DSM 101695	GCA_015751785.1	709878	709878	type	True	80.7005	1366	3187	95	below_threshold
Micromonospora taraxaci	strain=DSM 45885	GCA_007830095.1	1316803	1316803	type	True	80.6598	1359	3187	95	below_threshold
Micromonospora chokoriensis	strain=DSM 45160	GCA_900091505.1	356851	356851	type	True	80.6028	1317	3187	95	below_threshold
Micromonospora luteifusca	strain=DSM 100204	GCA_016907275.1	709860	709860	type	True	80.557	1279	3187	95	below_threshold
Phytohabitans flavus	strain=NBRC 107702	GCA_011764545.1	1076124	1076124	type	True	79.494	1351	3187	95	below_threshold
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	79.4599	1397	3187	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	79.4271	1436	3187	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	79.0891	1445	3187	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	78.2936	1217	3187	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:34:13,051] [INFO] DFAST Taxonomy check result was written to GCF_016862915.1_ASM1686291v1_genomic.fna/tc_result.tsv
[2024-01-25 19:34:13,051] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:34:13,051] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:34:13,051] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7990092f-6139-4e56-a4d0-b9929d04e168/dqc_reference/checkm_data
[2024-01-25 19:34:13,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:34:13,150] [INFO] Task started: CheckM
[2024-01-25 19:34:13,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862915.1_ASM1686291v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862915.1_ASM1686291v1_genomic.fna/checkm_input GCF_016862915.1_ASM1686291v1_genomic.fna/checkm_result
[2024-01-25 19:35:48,700] [INFO] Task succeeded: CheckM
[2024-01-25 19:35:48,702] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.94%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:35:48,732] [INFO] ===== Completeness check finished =====
[2024-01-25 19:35:48,732] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:35:48,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862915.1_ASM1686291v1_genomic.fna/markers.fasta)
[2024-01-25 19:35:48,733] [INFO] Task started: Blastn
[2024-01-25 19:35:48,733] [INFO] Running command: blastn -query GCF_016862915.1_ASM1686291v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7990092f-6139-4e56-a4d0-b9929d04e168/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862915.1_ASM1686291v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:50,565] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:50,572] [INFO] Selected 13 target genomes.
[2024-01-25 19:35:50,572] [INFO] Target genome list was writen to GCF_016862915.1_ASM1686291v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:35:50,598] [INFO] Task started: fastANI
[2024-01-25 19:35:50,598] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa651552-6159-4172-8b11-94fdb6fe3e2f/GCF_016862915.1_ASM1686291v1_genomic.fna.gz --refList GCF_016862915.1_ASM1686291v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862915.1_ASM1686291v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:21,364] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:21,373] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:21,373] [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_016862915.1	s__Plantactinospora endophytica	100.0	3182	3187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016862935.1	s__Plantactinospora mayteni	90.044	2287	3187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003030345.1	s__Plantactinospora sp003030345	89.76	2193	3187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	98.72	98.72	0.95	0.95	2	-
GCF_002846275.1	s__Plantactinospora sp002846275	88.9346	2034	3187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217235.1	s__Plantactinospora sp004217235	88.4332	1888	3187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014874095.1	s__Plantactinospora soyae	85.8788	2163	3187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015690345.1	s__Plantactinospora sp015690345	85.3262	1806	3187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090235.1	s__Micromonospora echinaurantiaca	81.5168	1442	3187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.93	95.22	0.84	0.83	3	-
GCF_003725545.1	s__Micromonospora sp003725545	81.3562	1189	3187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_900091465.1	s__Micromonospora rhizosphaerae	81.2396	1258	3187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091435.1	s__Micromonospora chaiyaphumensis	81.2032	1357	3187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.16	95.15	0.86	0.86	3	-
GCF_900090295.1	s__Micromonospora coxensis	81.1818	1364	3187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348325.1	s__Micromonospora sp004348325	80.9023	1076	3187	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.89	97.89	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:36:21,376] [INFO] GTDB search result was written to GCF_016862915.1_ASM1686291v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:21,376] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:21,382] [INFO] DFAST_QC result json was written to GCF_016862915.1_ASM1686291v1_genomic.fna/dqc_result.json
[2024-01-25 19:36:21,382] [INFO] DFAST_QC completed!
[2024-01-25 19:36:21,382] [INFO] Total running time: 0h3m30s