[2024-01-24 13:22:16,237] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:16,239] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:16,239] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bf7c83d-d020-4014-ac80-02fdd681fccc/dqc_reference
[2024-01-24 13:22:17,570] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:17,571] [INFO] Task started: Prodigal
[2024-01-24 13:22:17,571] [INFO] Running command: gunzip -c /var/lib/cwl/stg5135511f-4bd7-45b4-9c06-7266d5b408e8/GCF_003626595.1_ASM362659v1_genomic.fna.gz | prodigal -d GCF_003626595.1_ASM362659v1_genomic.fna/cds.fna -a GCF_003626595.1_ASM362659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:37,865] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:37,866] [INFO] Task started: HMMsearch
[2024-01-24 13:22:37,866] [INFO] Running command: hmmsearch --tblout GCF_003626595.1_ASM362659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bf7c83d-d020-4014-ac80-02fdd681fccc/dqc_reference/reference_markers.hmm GCF_003626595.1_ASM362659v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:38,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:38,403] [INFO] Found 6/6 markers.
[2024-01-24 13:22:38,459] [INFO] Query marker FASTA was written to GCF_003626595.1_ASM362659v1_genomic.fna/markers.fasta
[2024-01-24 13:22:38,459] [INFO] Task started: Blastn
[2024-01-24 13:22:38,459] [INFO] Running command: blastn -query GCF_003626595.1_ASM362659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bf7c83d-d020-4014-ac80-02fdd681fccc/dqc_reference/reference_markers.fasta -out GCF_003626595.1_ASM362659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:39,738] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:39,756] [INFO] Selected 22 target genomes.
[2024-01-24 13:22:39,757] [INFO] Target genome list was writen to GCF_003626595.1_ASM362659v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:39,768] [INFO] Task started: fastANI
[2024-01-24 13:22:39,769] [INFO] Running command: fastANI --query /var/lib/cwl/stg5135511f-4bd7-45b4-9c06-7266d5b408e8/GCF_003626595.1_ASM362659v1_genomic.fna.gz --refList GCF_003626595.1_ASM362659v1_genomic.fna/target_genomes.txt --output GCF_003626595.1_ASM362659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:21,934] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:21,935] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bf7c83d-d020-4014-ac80-02fdd681fccc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:21,935] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bf7c83d-d020-4014-ac80-02fdd681fccc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:21,951] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:23:21,951] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:21,952] [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=JCM 12677	GCA_003626595.1	230091	230091	type	True	100.0	2304	2304	95	conclusive
Micromonospora endolithica	strain=DSM 44398	GCA_007994185.1	230091	230091	type	True	99.9962	2304	2304	95	conclusive
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	86.6113	1153	2304	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	86.0967	1512	2304	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	85.9545	1210	2304	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	85.6404	1454	2304	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	85.4862	1496	2304	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	85.4374	1445	2304	95	below_threshold
Micromonospora inositola	strain=DSM 43819	GCA_900090285.1	47865	47865	type	True	85.3661	1355	2304	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	85.167	1298	2304	95	below_threshold
Micromonospora veneta	strain=CAP181	GCA_016598485.1	2796464	2796464	type	True	85.15	1363	2304	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	84.8071	1311	2304	95	below_threshold
Micromonospora globispora	strain=S2901	GCA_003857015.1	1450148	1450148	type	True	84.8042	1105	2304	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	84.7564	1455	2304	95	below_threshold
Micromonospora haikouensis	strain=DSM 45626	GCA_900091595.1	686309	686309	type	True	84.6101	1416	2304	95	below_threshold
Micromonospora carbonacea	strain=DSM 43168	GCA_900091535.1	47853	47853	type	True	84.6046	1424	2304	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	84.5924	1385	2304	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	84.5746	1445	2304	95	below_threshold
Micromonospora craterilacus	strain=NA12	GCA_003236315.1	1655439	1655439	type	True	84.558	1244	2304	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	84.3906	1263	2304	95	below_threshold
Micromonospora luteifusca	strain=DSM 100204	GCA_016907275.1	709860	709860	type	True	84.3373	1393	2304	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	84.2871	1402	2304	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:21,953] [INFO] DFAST Taxonomy check result was written to GCF_003626595.1_ASM362659v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:21,954] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:21,954] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:21,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bf7c83d-d020-4014-ac80-02fdd681fccc/dqc_reference/checkm_data
[2024-01-24 13:23:21,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:22,024] [INFO] Task started: CheckM
[2024-01-24 13:23:22,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003626595.1_ASM362659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003626595.1_ASM362659v1_genomic.fna/checkm_input GCF_003626595.1_ASM362659v1_genomic.fna/checkm_result
[2024-01-24 13:24:32,158] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:32,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:32,182] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:32,182] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:32,183] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003626595.1_ASM362659v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:32,183] [INFO] Task started: Blastn
[2024-01-24 13:24:32,183] [INFO] Running command: blastn -query GCF_003626595.1_ASM362659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bf7c83d-d020-4014-ac80-02fdd681fccc/dqc_reference/reference_markers_gtdb.fasta -out GCF_003626595.1_ASM362659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:34,025] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:34,030] [INFO] Selected 20 target genomes.
[2024-01-24 13:24:34,030] [INFO] Target genome list was writen to GCF_003626595.1_ASM362659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:34,073] [INFO] Task started: fastANI
[2024-01-24 13:24:34,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg5135511f-4bd7-45b4-9c06-7266d5b408e8/GCF_003626595.1_ASM362659v1_genomic.fna.gz --refList GCF_003626595.1_ASM362659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003626595.1_ASM362659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:10,252] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:10,272] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:10,272] [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	100.0	2304	2304	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	86.08	1515	2304	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	85.9349	1212	2304	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	85.53	1489	2304	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	85.416	1449	2304	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	85.3653	1354	2304	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	85.2522	1410	2304	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	85.1648	1361	2304	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	85.1567	1287	2304	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	84.9853	1370	2304	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	84.7838	1108	2304	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	84.7622	1317	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091595.1	s__Micromonospora haikouensis	84.562	1423	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	-
GCF_014205165.1	s__Micromonospora carbonacea	84.5614	1454	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_018070325.1	s__Micromonospora sp018070325	84.5124	1427	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.6333	N/A	N/A	N/A	N/A	1	-
GCF_003236315.1	s__Micromonospora craterilacus	84.512	1250	2304	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	84.4736	1405	2304	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158815.1	s__Micromonospora sp000158815	84.4336	1343	2304	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	84.3501	1269	2304	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	84.3223	1397	2304	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 13:25:10,274] [INFO] GTDB search result was written to GCF_003626595.1_ASM362659v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:10,274] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:10,278] [INFO] DFAST_QC result json was written to GCF_003626595.1_ASM362659v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:10,278] [INFO] DFAST_QC completed!
[2024-01-24 13:25:10,278] [INFO] Total running time: 0h2m54s