[2024-01-24 11:05:34,589] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:34,591] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:34,591] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d149319-3abc-4ffb-9172-9a63a8fb6ab8/dqc_reference
[2024-01-24 11:05:35,793] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:35,794] [INFO] Task started: Prodigal
[2024-01-24 11:05:35,795] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb26892c-0495-4c93-878c-48716b28a4ce/GCF_014645775.1_ASM1464577v1_genomic.fna.gz | prodigal -d GCF_014645775.1_ASM1464577v1_genomic.fna/cds.fna -a GCF_014645775.1_ASM1464577v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:54,604] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:54,605] [INFO] Task started: HMMsearch
[2024-01-24 11:05:54,605] [INFO] Running command: hmmsearch --tblout GCF_014645775.1_ASM1464577v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d149319-3abc-4ffb-9172-9a63a8fb6ab8/dqc_reference/reference_markers.hmm GCF_014645775.1_ASM1464577v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:54,965] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:54,966] [INFO] Found 6/6 markers.
[2024-01-24 11:05:55,019] [INFO] Query marker FASTA was written to GCF_014645775.1_ASM1464577v1_genomic.fna/markers.fasta
[2024-01-24 11:05:55,020] [INFO] Task started: Blastn
[2024-01-24 11:05:55,020] [INFO] Running command: blastn -query GCF_014645775.1_ASM1464577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d149319-3abc-4ffb-9172-9a63a8fb6ab8/dqc_reference/reference_markers.fasta -out GCF_014645775.1_ASM1464577v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:56,210] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:56,214] [INFO] Selected 23 target genomes.
[2024-01-24 11:05:56,214] [INFO] Target genome list was writen to GCF_014645775.1_ASM1464577v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:56,225] [INFO] Task started: fastANI
[2024-01-24 11:05:56,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb26892c-0495-4c93-878c-48716b28a4ce/GCF_014645775.1_ASM1464577v1_genomic.fna.gz --refList GCF_014645775.1_ASM1464577v1_genomic.fna/target_genomes.txt --output GCF_014645775.1_ASM1464577v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:35,192] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:35,193] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d149319-3abc-4ffb-9172-9a63a8fb6ab8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:35,194] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d149319-3abc-4ffb-9172-9a63a8fb6ab8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:35,213] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:06:35,214] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:35,214] [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 yangpuensis	strain=CGMCC 4.5736	GCA_014645775.1	683228	683228	type	True	100.0	2131	2134	95	conclusive
Micromonospora yangpuensis	strain=DSM 45577	GCA_900091615.1	683228	683228	type	True	99.9992	2134	2134	95	conclusive
Micromonospora rosaria	strain=DSM 803	GCA_001567585.1	47874	47874	type	True	86.5473	1445	2134	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	84.4464	962	2134	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	84.3576	1240	2134	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	84.2747	1270	2134	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	84.264	1393	2134	95	below_threshold
Micromonospora inositola	strain=DSM 43819	GCA_900090285.1	47865	47865	type	True	84.2472	1177	2134	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	84.179	1235	2134	95	below_threshold
Micromonospora carbonacea	strain=DSM 43815	GCA_014205165.1	47853	47853	type	True	84.1505	1409	2134	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	84.1406	1289	2134	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	84.1194	1404	2134	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	84.054	1030	2134	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	83.7947	1092	2134	95	below_threshold
Micromonospora maritima		GCA_902825405.1	986711	986711	type	True	83.7499	952	2134	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	83.7119	1167	2134	95	below_threshold
Micromonospora humi	strain=DSM 45647	GCA_900090105.1	745366	745366	type	True	83.4745	1275	2134	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	83.3532	1265	2134	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.3452	1292	2134	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.0684	1246	2134	95	below_threshold
Micromonospora taraxaci	strain=DSM 45885	GCA_007830095.1	1316803	1316803	type	True	83.0275	1233	2134	95	below_threshold
Micromonospora violae	strain=DSM 45888	GCA_004217135.1	1278207	1278207	type	True	83.0218	1252	2134	95	below_threshold
Micromonospora avicenniae	strain=DSM 45758	GCA_900156065.1	1198245	1198245	type	True	82.5987	1186	2134	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:35,215] [INFO] DFAST Taxonomy check result was written to GCF_014645775.1_ASM1464577v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:35,216] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:35,216] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:35,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d149319-3abc-4ffb-9172-9a63a8fb6ab8/dqc_reference/checkm_data
[2024-01-24 11:06:35,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:35,280] [INFO] Task started: CheckM
[2024-01-24 11:06:35,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645775.1_ASM1464577v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645775.1_ASM1464577v1_genomic.fna/checkm_input GCF_014645775.1_ASM1464577v1_genomic.fna/checkm_result
[2024-01-24 11:07:41,441] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:41,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:41,471] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:41,471] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:41,471] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645775.1_ASM1464577v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:41,472] [INFO] Task started: Blastn
[2024-01-24 11:07:41,472] [INFO] Running command: blastn -query GCF_014645775.1_ASM1464577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d149319-3abc-4ffb-9172-9a63a8fb6ab8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645775.1_ASM1464577v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:43,245] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:43,250] [INFO] Selected 21 target genomes.
[2024-01-24 11:07:43,250] [INFO] Target genome list was writen to GCF_014645775.1_ASM1464577v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:43,288] [INFO] Task started: fastANI
[2024-01-24 11:07:43,288] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb26892c-0495-4c93-878c-48716b28a4ce/GCF_014645775.1_ASM1464577v1_genomic.fna.gz --refList GCF_014645775.1_ASM1464577v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645775.1_ASM1464577v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:08:18,939] [INFO] Task succeeded: fastANI
[2024-01-24 11:08:18,961] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:08:18,961] [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_900091615.1	s__Micromonospora yangpuensis	99.9992	2134	2134	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_001567585.1	s__Micromonospora rosaria	86.528	1447	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210435.1	s__Micromonospora wenchangensis	84.3652	1363	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.84	95.43	0.85	0.83	5	-
GCF_900090245.1	s__Micromonospora halophytica	84.3431	1244	2134	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	84.2626	1273	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090285.1	s__Micromonospora inositola	84.26	1176	2134	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	84.2373	1206	2134	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	84.1793	1235	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.27	95.68	0.85	0.81	4	-
GCF_900090235.1	s__Micromonospora echinaurantiaca	84.1654	1283	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.93	95.22	0.84	0.83	3	-
GCF_014205165.1	s__Micromonospora carbonacea	84.1527	1410	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_003236335.1	s__Micromonospora deserti	84.0384	1032	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091525.1	s__Micromonospora matsumotoense	83.9484	1409	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725545.1	s__Micromonospora sp003725545	83.9184	1127	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_007830265.1	s__Micromonospora olivasterospora	83.6936	1170	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003027925.1	s__Micromonospora sp003027925	83.5527	1278	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090105.1	s__Micromonospora humi	83.4598	1276	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803395.1	s__Micromonospora sp016803395	83.1933	1124	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217135.1	s__Micromonospora violae	83.0578	1247	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863495.1	s__Micromonospora andamanensis	82.8844	1257	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.71	95.67	0.86	0.84	3	-
GCF_003626635.1	s__Micromonospora musae	82.8393	1196	2134	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.26	97.34	0.95	0.93	3	-
GCF_900156065.1	s__Micromonospora avicenniae	82.6052	1186	2134	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 11:08:18,963] [INFO] GTDB search result was written to GCF_014645775.1_ASM1464577v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:08:18,964] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:08:18,970] [INFO] DFAST_QC result json was written to GCF_014645775.1_ASM1464577v1_genomic.fna/dqc_result.json
[2024-01-24 11:08:18,970] [INFO] DFAST_QC completed!
[2024-01-24 11:08:18,970] [INFO] Total running time: 0h2m44s