[2024-01-25 18:12:05,541] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:12:05,543] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:12:05,543] [INFO] DQC Reference Directory: /var/lib/cwl/stg01c9ddc8-9faf-424b-810b-2f4f64f6fa6b/dqc_reference
[2024-01-25 18:12:06,698] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:12:06,699] [INFO] Task started: Prodigal
[2024-01-25 18:12:06,699] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0887e61-e263-4fb8-a63f-4f0efc845010/GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna.gz | prodigal -d GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/cds.fna -a GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:12:21,877] [INFO] Task succeeded: Prodigal
[2024-01-25 18:12:21,877] [INFO] Task started: HMMsearch
[2024-01-25 18:12:21,878] [INFO] Running command: hmmsearch --tblout GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01c9ddc8-9faf-424b-810b-2f4f64f6fa6b/dqc_reference/reference_markers.hmm GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:12:22,164] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:12:22,165] [INFO] Found 6/6 markers.
[2024-01-25 18:12:22,215] [INFO] Query marker FASTA was written to GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/markers.fasta
[2024-01-25 18:12:22,215] [INFO] Task started: Blastn
[2024-01-25 18:12:22,215] [INFO] Running command: blastn -query GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/markers.fasta -db /var/lib/cwl/stg01c9ddc8-9faf-424b-810b-2f4f64f6fa6b/dqc_reference/reference_markers.fasta -out GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:23,337] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:23,340] [INFO] Selected 18 target genomes.
[2024-01-25 18:12:23,341] [INFO] Target genome list was writen to GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/target_genomes.txt
[2024-01-25 18:12:23,360] [INFO] Task started: fastANI
[2024-01-25 18:12:23,360] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0887e61-e263-4fb8-a63f-4f0efc845010/GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna.gz --refList GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/target_genomes.txt --output GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:53,757] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:53,758] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01c9ddc8-9faf-424b-810b-2f4f64f6fa6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:53,758] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01c9ddc8-9faf-424b-810b-2f4f64f6fa6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:53,769] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:12:53,769] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:53,770] [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 radicis	strain=AZ1-13	GCA_003583405.1	1894971	1894971	type	True	100.0	1953	1956	95	conclusive
Micromonospora zingiberis	strain=PLAI 1-1	GCA_004331455.1	2053011	2053011	type	True	89.1462	1547	1956	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	88.1116	1460	1956	95	below_threshold
Micromonospora fiedleri	strain=MG-37	GCA_016774385.1	1157498	1157498	type	True	88.0229	1502	1956	95	below_threshold
Micromonospora gifhornensis	strain=NBRC 16317	GCA_016863515.1	84594	84594	type	True	88.0133	1478	1956	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	88.0001	1473	1956	95	below_threshold
Micromonospora craterilacus	strain=NA12	GCA_003236315.1	1655439	1655439	type	True	87.9551	1320	1956	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	87.0623	1420	1956	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_003419945.1	2294034	2294034	type	True	87.0212	1335	1956	95	below_threshold
Micromonospora craniellae	strain=LHW63014	GCA_014764405.1	2294034	2294034	type	True	86.9318	1356	1956	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	84.9243	979	1956	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	84.6258	1084	1956	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	84.0844	1099	1956	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	83.9435	1311	1956	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	83.8638	1293	1956	95	below_threshold
Micromonospora viridifaciens	strain=DSM 43909	GCA_900091545.1	1881	1881	type	True	83.8056	1156	1956	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.7229	1242	1956	95	below_threshold
Micromonospora inaquosa	strain=LB39	GCA_003857055.1	2203716	2203716	type	True	83.5075	1141	1956	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:53,771] [INFO] DFAST Taxonomy check result was written to GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/tc_result.tsv
[2024-01-25 18:12:53,771] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:53,772] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:53,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01c9ddc8-9faf-424b-810b-2f4f64f6fa6b/dqc_reference/checkm_data
[2024-01-25 18:12:53,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:53,828] [INFO] Task started: CheckM
[2024-01-25 18:12:53,828] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/checkm_input GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/checkm_result
[2024-01-25 18:13:48,034] [INFO] Task succeeded: CheckM
[2024-01-25 18:13:48,035] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:13:48,055] [INFO] ===== Completeness check finished =====
[2024-01-25 18:13:48,056] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:13:48,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/markers.fasta)
[2024-01-25 18:13:48,057] [INFO] Task started: Blastn
[2024-01-25 18:13:48,057] [INFO] Running command: blastn -query GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/markers.fasta -db /var/lib/cwl/stg01c9ddc8-9faf-424b-810b-2f4f64f6fa6b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:49,768] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:49,771] [INFO] Selected 13 target genomes.
[2024-01-25 18:13:49,771] [INFO] Target genome list was writen to GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:13:49,785] [INFO] Task started: fastANI
[2024-01-25 18:13:49,785] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0887e61-e263-4fb8-a63f-4f0efc845010/GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna.gz --refList GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/target_genomes_gtdb.txt --output GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:11,902] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:11,911] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:14:11,912] [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_003583405.1	s__Micromonospora radicis	100.0	1953	1956	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_004331455.1	s__Micromonospora zingiberis	89.1599	1545	1956	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	88.0372	1475	1956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.77	95.90	0.88	0.87	6	-
GCF_003236315.1	s__Micromonospora craterilacus	87.9321	1322	1956	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	87.7573	1453	1956	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	87.2487	1270	1956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.96	99.96	0.99	0.98	3	-
GCF_014646235.1	s__Micromonospora sonchi	87.2411	1367	1956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364215.1	s__Micromonospora sp004307965	86.9582	1495	1956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.04	99.04	0.94	0.94	2	-
GCF_016863555.1	s__Micromonospora qiuiae	86.9506	1336	1956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014764405.1	s__Micromonospora craniellae	86.9316	1356	1956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.95	99.95	0.98	0.98	2	-
GCF_010560025.1	s__Micromonospora sp010560025	86.6156	1393	1956	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	86.3646	1404	1956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.06	96.13	0.95	0.90	3	-
GCF_003664255.1	s__Micromonospora sp003664255	84.3578	1298	1956	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:11,913] [INFO] GTDB search result was written to GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:11,913] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:11,917] [INFO] DFAST_QC result json was written to GCF_003583405.1_CHULA_Jazt_1.1_for_version_1.1_of_the_Jishengella_sp._nov._AZ1-13_genome_from_a_lab_in_CHULA_genomic.fna/dqc_result.json
[2024-01-25 18:14:11,917] [INFO] DFAST_QC completed!
[2024-01-25 18:14:11,917] [INFO] Total running time: 0h2m6s