[2024-01-24 13:57:41,833] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:41,835] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:41,835] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d21bcd3-ae0c-49c6-a61f-37009ffd1a33/dqc_reference
[2024-01-24 13:57:43,233] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:43,234] [INFO] Task started: Prodigal
[2024-01-24 13:57:43,235] [INFO] Running command: gunzip -c /var/lib/cwl/stg4462b308-36ce-4511-8b5e-cb2eb1ba3a5d/GCF_007994185.1_ASM799418v1_genomic.fna.gz | prodigal -d GCF_007994185.1_ASM799418v1_genomic.fna/cds.fna -a GCF_007994185.1_ASM799418v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:05,381] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:05,381] [INFO] Task started: HMMsearch
[2024-01-24 13:58:05,381] [INFO] Running command: hmmsearch --tblout GCF_007994185.1_ASM799418v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d21bcd3-ae0c-49c6-a61f-37009ffd1a33/dqc_reference/reference_markers.hmm GCF_007994185.1_ASM799418v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:05,751] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:05,752] [INFO] Found 6/6 markers.
[2024-01-24 13:58:05,810] [INFO] Query marker FASTA was written to GCF_007994185.1_ASM799418v1_genomic.fna/markers.fasta
[2024-01-24 13:58:05,811] [INFO] Task started: Blastn
[2024-01-24 13:58:05,811] [INFO] Running command: blastn -query GCF_007994185.1_ASM799418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d21bcd3-ae0c-49c6-a61f-37009ffd1a33/dqc_reference/reference_markers.fasta -out GCF_007994185.1_ASM799418v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:07,091] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:07,095] [INFO] Selected 22 target genomes.
[2024-01-24 13:58:07,095] [INFO] Target genome list was writen to GCF_007994185.1_ASM799418v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:07,105] [INFO] Task started: fastANI
[2024-01-24 13:58:07,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg4462b308-36ce-4511-8b5e-cb2eb1ba3a5d/GCF_007994185.1_ASM799418v1_genomic.fna.gz --refList GCF_007994185.1_ASM799418v1_genomic.fna/target_genomes.txt --output GCF_007994185.1_ASM799418v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:53,382] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:53,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d21bcd3-ae0c-49c6-a61f-37009ffd1a33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:53,383] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d21bcd3-ae0c-49c6-a61f-37009ffd1a33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:53,402] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:53,402] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:53,402] [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 endolithica	strain=DSM 44398	GCA_007994185.1	230091	230091	type	True	100.0	2341	2342	95	conclusive
Micromonospora endolithica	strain=JCM 12677	GCA_003626595.1	230091	230091	type	True	99.9878	2295	2342	95	conclusive
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	86.6645	1131	2342	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	86.1107	1526	2342	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	85.9127	1211	2342	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	85.5799	1473	2342	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	85.5443	1509	2342	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	85.4879	1457	2342	95	below_threshold
Micromonospora inositola	strain=DSM 43819	GCA_900090285.1	47865	47865	type	True	85.3394	1370	2342	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	85.2495	1291	2342	95	below_threshold
Micromonospora veneta	strain=CAP181	GCA_016598485.1	2796464	2796464	type	True	85.0535	1367	2342	95	below_threshold
Micromonospora globispora	strain=S2901	GCA_003857015.1	1450148	1450148	type	True	84.9057	1100	2342	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	84.7413	1307	2342	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	84.7129	1486	2342	95	below_threshold
Micromonospora craterilacus	strain=NA12	GCA_003236315.1	1655439	1655439	type	True	84.6286	1242	2342	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	84.5995	1440	2342	95	below_threshold
Micromonospora carbonacea	strain=DSM 43168	GCA_900091535.1	47853	47853	type	True	84.5821	1428	2342	95	below_threshold
Micromonospora haikouensis	strain=DSM 45626	GCA_900091595.1	686309	686309	type	True	84.518	1439	2342	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	84.49	1272	2342	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	84.4058	1432	2342	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	84.2558	1387	2342	95	below_threshold
Micromonospora luteifusca	strain=DSM 100204	GCA_016907275.1	709860	709860	type	True	84.2395	1431	2342	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:53,404] [INFO] DFAST Taxonomy check result was written to GCF_007994185.1_ASM799418v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:53,405] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:53,405] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:53,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d21bcd3-ae0c-49c6-a61f-37009ffd1a33/dqc_reference/checkm_data
[2024-01-24 13:58:53,407] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:53,479] [INFO] Task started: CheckM
[2024-01-24 13:58:53,479] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007994185.1_ASM799418v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007994185.1_ASM799418v1_genomic.fna/checkm_input GCF_007994185.1_ASM799418v1_genomic.fna/checkm_result
[2024-01-24 14:00:19,004] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:19,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:19,033] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:19,033] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:19,033] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007994185.1_ASM799418v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:19,034] [INFO] Task started: Blastn
[2024-01-24 14:00:19,034] [INFO] Running command: blastn -query GCF_007994185.1_ASM799418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d21bcd3-ae0c-49c6-a61f-37009ffd1a33/dqc_reference/reference_markers_gtdb.fasta -out GCF_007994185.1_ASM799418v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:20,869] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:20,873] [INFO] Selected 20 target genomes.
[2024-01-24 14:00:20,873] [INFO] Target genome list was writen to GCF_007994185.1_ASM799418v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:20,893] [INFO] Task started: fastANI
[2024-01-24 14:00:20,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg4462b308-36ce-4511-8b5e-cb2eb1ba3a5d/GCF_007994185.1_ASM799418v1_genomic.fna.gz --refList GCF_007994185.1_ASM799418v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007994185.1_ASM799418v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:57,309] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:57,330] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:57,331] [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_003626595.1	s__Micromonospora endolithica	99.9878	2295	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900090235.1	s__Micromonospora echinaurantiaca	86.1043	1529	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.93	95.22	0.84	0.83	3	-
GCF_003236335.1	s__Micromonospora deserti	85.8715	1216	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090295.1	s__Micromonospora coxensis	85.5189	1512	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091515.1	s__Micromonospora purpureochromogenes	85.4897	1456	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.27	95.68	0.85	0.81	4	-
GCF_900090285.1	s__Micromonospora inositola	85.3513	1371	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217615.1	s__Micromonospora kangleipakensis	85.2989	1424	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003172935.1	s__Micromonospora sp003172935	85.1799	1293	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.27	99.27	0.87	0.87	2	-
GCF_003434305.1	s__Micromonospora sp003434305	85.1436	1331	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598485.1	s__Micromonospora veneta	85.0687	1365	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003857015.1	s__Micromonospora globispora	84.9558	1095	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.52	99.52	0.89	0.89	2	-
GCF_900091465.1	s__Micromonospora rhizosphaerae	84.7844	1301	2342	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	84.6467	1239	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205165.1	s__Micromonospora carbonacea	84.6282	1437	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_900091595.1	s__Micromonospora haikouensis	84.5804	1430	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	-
GCF_018070325.1	s__Micromonospora sp018070325	84.527	1444	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.6333	N/A	N/A	N/A	N/A	1	-
GCF_000158815.1	s__Micromonospora sp000158815	84.4408	1360	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.02	97.02	0.80	0.80	2	-
GCF_007830265.1	s__Micromonospora olivasterospora	84.418	1282	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718555.1	s__Micromonospora chokoriensis_B	84.3831	1408	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907275.1	s__Micromonospora luteifusca	84.255	1427	2342	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:57,332] [INFO] GTDB search result was written to GCF_007994185.1_ASM799418v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:57,333] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:57,338] [INFO] DFAST_QC result json was written to GCF_007994185.1_ASM799418v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:57,338] [INFO] DFAST_QC completed!
[2024-01-24 14:00:57,338] [INFO] Total running time: 0h3m16s