[2024-01-24 13:41:20,611] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:20,620] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:20,621] [INFO] DQC Reference Directory: /var/lib/cwl/stgb611c945-1ea3-4c5e-90b8-412ce56e8a6c/dqc_reference
[2024-01-24 13:41:22,064] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:22,065] [INFO] Task started: Prodigal
[2024-01-24 13:41:22,066] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d99abd9-9e81-459b-ae6a-18db0c796053/GCF_012034245.1_ASM1203424v1_genomic.fna.gz | prodigal -d GCF_012034245.1_ASM1203424v1_genomic.fna/cds.fna -a GCF_012034245.1_ASM1203424v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:40,930] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:40,930] [INFO] Task started: HMMsearch
[2024-01-24 13:41:40,930] [INFO] Running command: hmmsearch --tblout GCF_012034245.1_ASM1203424v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb611c945-1ea3-4c5e-90b8-412ce56e8a6c/dqc_reference/reference_markers.hmm GCF_012034245.1_ASM1203424v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:41,307] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:41,309] [INFO] Found 6/6 markers.
[2024-01-24 13:41:41,363] [INFO] Query marker FASTA was written to GCF_012034245.1_ASM1203424v1_genomic.fna/markers.fasta
[2024-01-24 13:41:41,363] [INFO] Task started: Blastn
[2024-01-24 13:41:41,363] [INFO] Running command: blastn -query GCF_012034245.1_ASM1203424v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb611c945-1ea3-4c5e-90b8-412ce56e8a6c/dqc_reference/reference_markers.fasta -out GCF_012034245.1_ASM1203424v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:42,635] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:42,639] [INFO] Selected 29 target genomes.
[2024-01-24 13:41:42,639] [INFO] Target genome list was writen to GCF_012034245.1_ASM1203424v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:42,651] [INFO] Task started: fastANI
[2024-01-24 13:41:42,651] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d99abd9-9e81-459b-ae6a-18db0c796053/GCF_012034245.1_ASM1203424v1_genomic.fna.gz --refList GCF_012034245.1_ASM1203424v1_genomic.fna/target_genomes.txt --output GCF_012034245.1_ASM1203424v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:28,051] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:28,052] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb611c945-1ea3-4c5e-90b8-412ce56e8a6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:28,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb611c945-1ea3-4c5e-90b8-412ce56e8a6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:28,075] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:42:28,075] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:42:28,075] [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	86.7175	1144	2001	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	86.5308	1204	2001	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	86.4296	1476	2001	95	below_threshold
Micromonospora citrea	strain=DSM 43903	GCA_900090315.1	47855	47855	type	True	86.2064	1393	2001	95	below_threshold
Micromonospora echinofusca	strain=DSM 43913	GCA_900091445.1	47858	47858	type	True	85.9552	1385	2001	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	85.6351	1449	2001	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	85.5801	1415	2001	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	85.5663	1425	2001	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	85.4308	1393	2001	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	85.3594	1272	2001	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	84.8913	1225	2001	95	below_threshold
Micromonospora krabiensis	strain=DSM 45344	GCA_900091425.1	307121	307121	type	True	84.808	1376	2001	95	below_threshold
Micromonospora nigra	strain=DSM 43818	GCA_900091585.1	145857	145857	type	True	84.7562	1229	2001	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	84.6968	1311	2001	95	below_threshold
Micromonospora globbae	strain=WPS1-2	GCA_003610785.1	1894969	1894969	type	True	84.6911	1377	2001	95	below_threshold
Micromonospora carbonacea	strain=DSM 43168	GCA_900091535.1	47853	47853	type	True	84.6191	1311	2001	95	below_threshold
Micromonospora carbonacea	strain=DSM 43815	GCA_014205165.1	47853	47853	type	True	84.5976	1305	2001	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	84.4844	1328	2001	95	below_threshold
Micromonospora marina	strain=DSM 45555	GCA_900091565.1	307120	307120	type	True	84.4321	1249	2001	95	below_threshold
Salinispora arenicola	strain=DSM 44819	GCA_006716065.1	168697	168697	type	True	84.2621	1072	2001	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	84.1725	1273	2001	95	below_threshold
Micromonospora radicis	strain=AZ1-13	GCA_003583405.1	1894971	1894971	type	True	84.1256	1193	2001	95	below_threshold
Salinispora mooreana	strain=CNT-150	GCA_000514435.1	999545	999545	type	True	83.9799	1013	2001	95	below_threshold
Salinispora mooreana	strain=DSM 45549	GCA_000379065.1	999545	999545	type	True	83.9799	1017	2001	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.9521	1249	2001	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	83.9067	1216	2001	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	83.8757	1210	2001	95	below_threshold
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	83.8131	1234	2001	95	below_threshold
Salinispora fenicalii	strain=CNT-569	GCA_000514815.1	1137263	1137263	type	True	83.6479	1018	2001	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:28,077] [INFO] DFAST Taxonomy check result was written to GCF_012034245.1_ASM1203424v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:28,077] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:28,077] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:28,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb611c945-1ea3-4c5e-90b8-412ce56e8a6c/dqc_reference/checkm_data
[2024-01-24 13:42:28,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:28,136] [INFO] Task started: CheckM
[2024-01-24 13:42:28,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012034245.1_ASM1203424v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012034245.1_ASM1203424v1_genomic.fna/checkm_input GCF_012034245.1_ASM1203424v1_genomic.fna/checkm_result
[2024-01-24 13:43:26,541] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:26,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:26,570] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:26,571] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:26,571] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012034245.1_ASM1203424v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:26,572] [INFO] Task started: Blastn
[2024-01-24 13:43:26,572] [INFO] Running command: blastn -query GCF_012034245.1_ASM1203424v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb611c945-1ea3-4c5e-90b8-412ce56e8a6c/dqc_reference/reference_markers_gtdb.fasta -out GCF_012034245.1_ASM1203424v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:28,343] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:28,348] [INFO] Selected 16 target genomes.
[2024-01-24 13:43:28,348] [INFO] Target genome list was writen to GCF_012034245.1_ASM1203424v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:28,371] [INFO] Task started: fastANI
[2024-01-24 13:43:28,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d99abd9-9e81-459b-ae6a-18db0c796053/GCF_012034245.1_ASM1203424v1_genomic.fna.gz --refList GCF_012034245.1_ASM1203424v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012034245.1_ASM1203424v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:56,819] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:56,836] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:56,836] [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_012034245.1	s__Micromonospora sp012034245	100.0	1998	2001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009707425.1	s__Micromonospora sp009707425	93.6059	1597	2001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217535.1	s__Micromonospora sp004217535	88.8439	1502	2001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236335.1	s__Micromonospora deserti	86.5096	1206	2001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090235.1	s__Micromonospora echinaurantiaca	86.461	1471	2001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.93	95.22	0.84	0.83	3	-
GCF_018070575.1	s__Micromonospora sp018070575	85.8081	1338	2001	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	85.5426	1429	2001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.27	95.68	0.85	0.81	4	-
GCF_004217615.1	s__Micromonospora kangleipakensis	85.5426	1420	2001	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	85.4453	1219	2001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_900090295.1	s__Micromonospora coxensis	85.4226	1395	2001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610785.1	s__Micromonospora globbae	84.7122	1374	2001	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	84.6067	1304	2001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_003583405.1	s__Micromonospora radicis	84.0625	1203	2001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379065.1	s__Micromonospora mooreana	83.9478	1020	2001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.98	95.97	0.92	0.83	3	-
GCF_010560025.1	s__Micromonospora sp010560025	83.9149	1227	2001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.75	99.70	1.00	1.00	3	-
GCF_016863495.1	s__Micromonospora andamanensis	83.7835	1234	2001	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.71	95.67	0.86	0.84	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:56,838] [INFO] GTDB search result was written to GCF_012034245.1_ASM1203424v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:56,838] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:56,843] [INFO] DFAST_QC result json was written to GCF_012034245.1_ASM1203424v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:56,843] [INFO] DFAST_QC completed!
[2024-01-24 13:43:56,843] [INFO] Total running time: 0h2m36s