[2024-01-24 11:43:37,672] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:37,677] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:37,677] [INFO] DQC Reference Directory: /var/lib/cwl/stg55b04334-4555-4e23-8904-d2a34af91927/dqc_reference
[2024-01-24 11:43:38,969] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:38,970] [INFO] Task started: Prodigal
[2024-01-24 11:43:38,971] [INFO] Running command: gunzip -c /var/lib/cwl/stg990796a1-96a1-4060-b495-463b7d20799a/GCF_014646235.1_ASM1464623v1_genomic.fna.gz | prodigal -d GCF_014646235.1_ASM1464623v1_genomic.fna/cds.fna -a GCF_014646235.1_ASM1464623v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:58,112] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:58,113] [INFO] Task started: HMMsearch
[2024-01-24 11:43:58,113] [INFO] Running command: hmmsearch --tblout GCF_014646235.1_ASM1464623v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55b04334-4555-4e23-8904-d2a34af91927/dqc_reference/reference_markers.hmm GCF_014646235.1_ASM1464623v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:58,594] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:58,595] [INFO] Found 6/6 markers.
[2024-01-24 11:43:58,654] [INFO] Query marker FASTA was written to GCF_014646235.1_ASM1464623v1_genomic.fna/markers.fasta
[2024-01-24 11:43:58,655] [INFO] Task started: Blastn
[2024-01-24 11:43:58,655] [INFO] Running command: blastn -query GCF_014646235.1_ASM1464623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55b04334-4555-4e23-8904-d2a34af91927/dqc_reference/reference_markers.fasta -out GCF_014646235.1_ASM1464623v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:59,810] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:59,816] [INFO] Selected 20 target genomes.
[2024-01-24 11:43:59,817] [INFO] Target genome list was writen to GCF_014646235.1_ASM1464623v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:59,845] [INFO] Task started: fastANI
[2024-01-24 11:43:59,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg990796a1-96a1-4060-b495-463b7d20799a/GCF_014646235.1_ASM1464623v1_genomic.fna.gz --refList GCF_014646235.1_ASM1464623v1_genomic.fna/target_genomes.txt --output GCF_014646235.1_ASM1464623v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:32,565] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:32,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55b04334-4555-4e23-8904-d2a34af91927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:32,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55b04334-4555-4e23-8904-d2a34af91927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:32,581] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:32,581] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:32,582] [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 craterilacus	strain=NA12	GCA_003236315.1	1655439	1655439	type	True	87.9966	1325	2145	95	below_threshold
Micromonospora zingiberis	strain=PLAI 1-1	GCA_004331455.1	2053011	2053011	type	True	87.4905	1392	2145	95	below_threshold
Micromonospora radicis	strain=AZ1-13	GCA_003583405.1	1894971	1894971	type	True	87.3105	1352	2145	95	below_threshold
Micromonospora tarapacensis	strain=Llam7	GCA_019697375.1	2835305	2835305	type	True	87.0374	1397	2145	95	below_threshold
Micromonospora phaseoli	strain=CGMCC 4.7038	GCA_900109115.1	1144548	1144548	type	True	86.9798	1428	2145	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	86.9672	1399	2145	95	below_threshold
Micromonospora phaseoli	strain=DSM 45730	GCA_003253475.1	1144548	1144548	type	True	86.8669	1447	2145	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	86.8028	1450	2145	95	below_threshold
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	86.8008	1456	2145	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	86.743	1450	2145	95	below_threshold
Micromonospora gifhornensis	strain=NBRC 16317	GCA_016863515.1	84594	84594	type	True	86.6935	1425	2145	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_003419945.1	2294034	2294034	type	True	86.3946	1308	2145	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_014764405.1	2294034	2294034	type	True	86.2051	1345	2145	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	84.4736	985	2145	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	84.4429	1084	2145	95	below_threshold
Micromonospora nigra	strain=DSM 43818	GCA_900091585.1	145857	145857	type	True	84.2673	1218	2145	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	83.6491	1100	2145	95	below_threshold
Micromonospora mirobrigensis	strain=DSM 44830	GCA_900091555.1	262898	262898	type	True	83.5297	1198	2145	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.4283	1227	2145	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	83.3939	1256	2145	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:32,583] [INFO] DFAST Taxonomy check result was written to GCF_014646235.1_ASM1464623v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:32,584] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:32,584] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:32,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55b04334-4555-4e23-8904-d2a34af91927/dqc_reference/checkm_data
[2024-01-24 11:44:32,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:32,650] [INFO] Task started: CheckM
[2024-01-24 11:44:32,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646235.1_ASM1464623v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646235.1_ASM1464623v1_genomic.fna/checkm_input GCF_014646235.1_ASM1464623v1_genomic.fna/checkm_result
[2024-01-24 11:45:32,936] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:32,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:32,967] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:32,968] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:32,968] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646235.1_ASM1464623v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:32,969] [INFO] Task started: Blastn
[2024-01-24 11:45:32,969] [INFO] Running command: blastn -query GCF_014646235.1_ASM1464623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55b04334-4555-4e23-8904-d2a34af91927/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646235.1_ASM1464623v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:34,624] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:34,628] [INFO] Selected 15 target genomes.
[2024-01-24 11:45:34,628] [INFO] Target genome list was writen to GCF_014646235.1_ASM1464623v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:34,641] [INFO] Task started: fastANI
[2024-01-24 11:45:34,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg990796a1-96a1-4060-b495-463b7d20799a/GCF_014646235.1_ASM1464623v1_genomic.fna.gz --refList GCF_014646235.1_ASM1464623v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646235.1_ASM1464623v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:59,749] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:59,772] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:59,772] [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_014646235.1	s__Micromonospora sonchi	100.0	2145	2145	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_016863555.1	s__Micromonospora qiuiae	93.1609	1603	2145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236305.1	s__Micromonospora endophytica	88.547	1288	2145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.96	99.96	0.99	0.98	3	-
GCF_003236315.1	s__Micromonospora craterilacus	88.007	1324	2145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005402585.1	s__Micromonospora sp005402585	87.8703	1430	2145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331455.1	s__Micromonospora zingiberis	87.4379	1398	2145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583405.1	s__Micromonospora radicis	87.3389	1349	2145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863515.1	s__Micromonospora gifhornensis	86.7027	1423	2145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.77	95.90	0.88	0.87	6	-
GCF_010560025.1	s__Micromonospora sp010560025	86.4683	1387	2145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.75	99.70	1.00	1.00	3	-
GCF_900112325.1	s__Micromonospora sediminimaris	86.451	1441	2145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.06	96.13	0.95	0.90	3	-
GCF_013364215.1	s__Micromonospora sp004307965	86.3033	1407	2145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.04	99.04	0.94	0.94	2	-
GCF_014764405.1	s__Micromonospora craniellae	86.2086	1345	2145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.95	99.95	0.98	0.98	2	-
GCF_016863495.1	s__Micromonospora andamanensis	86.2079	1414	2145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.71	95.67	0.86	0.84	3	-
GCF_012726175.1	s__Micromonospora sp012726175	84.7778	1109	2145	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	83.7268	1140	2145	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:59,774] [INFO] GTDB search result was written to GCF_014646235.1_ASM1464623v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:59,775] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:59,778] [INFO] DFAST_QC result json was written to GCF_014646235.1_ASM1464623v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:59,778] [INFO] DFAST_QC completed!
[2024-01-24 11:45:59,779] [INFO] Total running time: 0h2m22s