[2024-01-24 11:26:12,989] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:12,992] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:12,993] [INFO] DQC Reference Directory: /var/lib/cwl/stg4dba8e22-f7a3-494b-8f85-c58be6056568/dqc_reference
[2024-01-24 11:26:14,348] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:14,349] [INFO] Task started: Prodigal
[2024-01-24 11:26:14,349] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d43af32-9838-4164-9092-e58efce7c868/GCF_014874095.1_ASM1487409v1_genomic.fna.gz | prodigal -d GCF_014874095.1_ASM1487409v1_genomic.fna/cds.fna -a GCF_014874095.1_ASM1487409v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:44,726] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:44,726] [INFO] Task started: HMMsearch
[2024-01-24 11:26:44,727] [INFO] Running command: hmmsearch --tblout GCF_014874095.1_ASM1487409v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4dba8e22-f7a3-494b-8f85-c58be6056568/dqc_reference/reference_markers.hmm GCF_014874095.1_ASM1487409v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:45,208] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:45,211] [INFO] Found 6/6 markers.
[2024-01-24 11:26:45,294] [INFO] Query marker FASTA was written to GCF_014874095.1_ASM1487409v1_genomic.fna/markers.fasta
[2024-01-24 11:26:45,295] [INFO] Task started: Blastn
[2024-01-24 11:26:45,295] [INFO] Running command: blastn -query GCF_014874095.1_ASM1487409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4dba8e22-f7a3-494b-8f85-c58be6056568/dqc_reference/reference_markers.fasta -out GCF_014874095.1_ASM1487409v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:46,515] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:46,520] [INFO] Selected 32 target genomes.
[2024-01-24 11:26:46,521] [INFO] Target genome list was writen to GCF_014874095.1_ASM1487409v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:46,531] [INFO] Task started: fastANI
[2024-01-24 11:26:46,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d43af32-9838-4164-9092-e58efce7c868/GCF_014874095.1_ASM1487409v1_genomic.fna.gz --refList GCF_014874095.1_ASM1487409v1_genomic.fna/target_genomes.txt --output GCF_014874095.1_ASM1487409v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:39,688] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:39,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4dba8e22-f7a3-494b-8f85-c58be6056568/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:39,689] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4dba8e22-f7a3-494b-8f85-c58be6056568/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:39,718] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:39,719] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:39,719] [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 echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	81.3023	1364	3238	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	81.2693	1012	3238	95	below_threshold
Micromonospora inositola	strain=DSM 43819	GCA_900090285.1	47865	47865	type	True	81.1303	1231	3238	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	81.0164	1311	3238	95	below_threshold
Micromonospora globispora	strain=S2901	GCA_003857015.1	1450148	1450148	type	True	81.0125	973	3238	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	80.9715	1127	3238	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	80.95	1175	3238	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	80.9385	1272	3238	95	below_threshold
Micromonospora veneta	strain=CAP181	GCA_016598485.1	2796464	2796464	type	True	80.9196	1221	3238	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	80.9047	1307	3238	95	below_threshold
Micromonospora coriariae	strain=DSM 44875	GCA_900091455.1	285665	285665	type	True	80.8981	1310	3238	95	below_threshold
Micromonospora mirobrigensis	strain=DSM 44830	GCA_900091555.1	262898	262898	type	True	80.8958	1194	3238	95	below_threshold
Micromonospora polyrhachis	strain=DSM 45886	GCA_014203835.1	1282883	1282883	type	True	80.8564	1178	3238	95	below_threshold
Micromonospora craterilacus	strain=NA12	GCA_003236315.1	1655439	1655439	type	True	80.8214	1160	3238	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	80.7817	1294	3238	95	below_threshold
Micromonospora inyonensis	strain=DSM 46123	GCA_900091415.1	47866	47866	type	True	80.651	1156	3238	95	below_threshold
Micromonospora parathelypteridis	strain=DSM 103125	GCA_014201145.1	1839617	1839617	type	True	80.6398	1298	3238	95	below_threshold
Micromonospora vinacea	strain=DSM 101695	GCA_015751785.1	709878	709878	type	True	80.6325	1305	3238	95	below_threshold
Micromonospora orduensis	strain=S2509	GCA_006228125.1	1420891	1420891	type	True	80.6318	1177	3238	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	80.589	1289	3238	95	below_threshold
Micromonospora rubida	strain=NEAU-HG-1	GCA_009908295.1	2697657	2697657	type	True	80.5481	1254	3238	95	below_threshold
Micromonospora pallida	strain=DSM 43817	GCA_900090325.1	145854	145854	type	True	80.5265	1234	3238	95	below_threshold
Micromonospora parathelypteridis	strain=CGMCC 4.7347	GCA_014646315.1	1839617	1839617	type	True	80.5067	1306	3238	95	below_threshold
Micromonospora ureilytica	strain=DSM 101692	GCA_015751765.1	709868	709868	type	True	80.5048	1294	3238	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	80.4903	1297	3238	95	below_threshold
Micromonospora pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	80.4658	1075	3238	95	below_threshold
Micromonospora chalcea	strain=DSM 43026	GCA_002926165.1	1874	1874	type	True	80.4235	1238	3238	95	below_threshold
Micromonospora luteifusca	strain=DSM 100204	GCA_016907275.1	709860	709860	type	True	80.3783	1259	3238	95	below_threshold
Phytohabitans flavus	strain=NBRC 107702	GCA_011764545.1	1076124	1076124	type	True	79.1761	1264	3238	95	below_threshold
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	79.0332	1322	3238	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	78.9202	1315	3238	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	78.0641	1154	3238	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:39,721] [INFO] DFAST Taxonomy check result was written to GCF_014874095.1_ASM1487409v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:39,721] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:39,721] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:39,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4dba8e22-f7a3-494b-8f85-c58be6056568/dqc_reference/checkm_data
[2024-01-24 11:27:39,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:39,810] [INFO] Task started: CheckM
[2024-01-24 11:27:39,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014874095.1_ASM1487409v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014874095.1_ASM1487409v1_genomic.fna/checkm_input GCF_014874095.1_ASM1487409v1_genomic.fna/checkm_result
[2024-01-24 11:29:22,070] [INFO] Task succeeded: CheckM
[2024-01-24 11:29:22,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.94%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:29:22,100] [INFO] ===== Completeness check finished =====
[2024-01-24 11:29:22,100] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:29:22,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014874095.1_ASM1487409v1_genomic.fna/markers.fasta)
[2024-01-24 11:29:22,101] [INFO] Task started: Blastn
[2024-01-24 11:29:22,101] [INFO] Running command: blastn -query GCF_014874095.1_ASM1487409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4dba8e22-f7a3-494b-8f85-c58be6056568/dqc_reference/reference_markers_gtdb.fasta -out GCF_014874095.1_ASM1487409v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:29:23,884] [INFO] Task succeeded: Blastn
[2024-01-24 11:29:23,888] [INFO] Selected 13 target genomes.
[2024-01-24 11:29:23,888] [INFO] Target genome list was writen to GCF_014874095.1_ASM1487409v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:29:23,898] [INFO] Task started: fastANI
[2024-01-24 11:29:23,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d43af32-9838-4164-9092-e58efce7c868/GCF_014874095.1_ASM1487409v1_genomic.fna.gz --refList GCF_014874095.1_ASM1487409v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014874095.1_ASM1487409v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:29:52,490] [INFO] Task succeeded: fastANI
[2024-01-24 11:29:52,504] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:29:52,504] [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_014874095.1	s__Plantactinospora soyae	100.0	3237	3238	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_015690345.1	s__Plantactinospora sp015690345	90.3831	2012	3238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862935.1	s__Plantactinospora mayteni	86.0616	2102	3238	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	86.0411	2085	3238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	98.72	98.72	0.95	0.95	2	-
GCF_016862915.1	s__Plantactinospora endophytica	86.0256	2150	3238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846275.1	s__Plantactinospora sp002846275	85.2575	1926	3238	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	85.2074	1795	3238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003762835.1	s__Plantactinospora sp003762835	83.1843	1469	3238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633685.1	s__Micromonospora_G pisi	81.346	1501	3238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667505.1	s__Micromonospora sp003667505	80.9149	1215	3238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.83	98.83	0.94	0.94	2	-
GCF_003236315.1	s__Micromonospora craterilacus	80.8911	1147	3238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003434305.1	s__Micromonospora sp003434305	80.8159	1262	3238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018324255.1	s__Polymorphospora rubra	80.219	1321	3238	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Polymorphospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:29:52,506] [INFO] GTDB search result was written to GCF_014874095.1_ASM1487409v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:29:52,507] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:29:52,511] [INFO] DFAST_QC result json was written to GCF_014874095.1_ASM1487409v1_genomic.fna/dqc_result.json
[2024-01-24 11:29:52,511] [INFO] DFAST_QC completed!
[2024-01-24 11:29:52,511] [INFO] Total running time: 0h3m40s