[2024-01-24 12:44:41,971] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:41,973] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:41,973] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e78dedb-fda5-4d45-811e-e51a473dbde1/dqc_reference
[2024-01-24 12:44:43,361] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:43,362] [INFO] Task started: Prodigal
[2024-01-24 12:44:43,363] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d5008f4-f7cb-4bb6-ae7f-ffef0328089d/GCF_017599305.1_ASM1759930v1_genomic.fna.gz | prodigal -d GCF_017599305.1_ASM1759930v1_genomic.fna/cds.fna -a GCF_017599305.1_ASM1759930v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:09,385] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:09,386] [INFO] Task started: HMMsearch
[2024-01-24 12:45:09,386] [INFO] Running command: hmmsearch --tblout GCF_017599305.1_ASM1759930v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e78dedb-fda5-4d45-811e-e51a473dbde1/dqc_reference/reference_markers.hmm GCF_017599305.1_ASM1759930v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:09,784] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:09,785] [INFO] Found 6/6 markers.
[2024-01-24 12:45:09,843] [INFO] Query marker FASTA was written to GCF_017599305.1_ASM1759930v1_genomic.fna/markers.fasta
[2024-01-24 12:45:09,843] [INFO] Task started: Blastn
[2024-01-24 12:45:09,844] [INFO] Running command: blastn -query GCF_017599305.1_ASM1759930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e78dedb-fda5-4d45-811e-e51a473dbde1/dqc_reference/reference_markers.fasta -out GCF_017599305.1_ASM1759930v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:11,160] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:11,163] [INFO] Selected 10 target genomes.
[2024-01-24 12:45:11,164] [INFO] Target genome list was writen to GCF_017599305.1_ASM1759930v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:11,169] [INFO] Task started: fastANI
[2024-01-24 12:45:11,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d5008f4-f7cb-4bb6-ae7f-ffef0328089d/GCF_017599305.1_ASM1759930v1_genomic.fna.gz --refList GCF_017599305.1_ASM1759930v1_genomic.fna/target_genomes.txt --output GCF_017599305.1_ASM1759930v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:32,657] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:32,658] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e78dedb-fda5-4d45-811e-e51a473dbde1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:32,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e78dedb-fda5-4d45-811e-e51a473dbde1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:32,667] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:32,667] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:32,667] [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 matsumotoense	strain=DSM 44100	GCA_900091525.1	121616	121616	type	True	93.2497	1999	2484	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	93.2017	2080	2484	95	below_threshold
Micromonospora wenchangensis	strain=CCTCC AA 2012002	GCA_002210435.1	1185415	1185415	type	True	92.8601	2002	2484	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	91.772	1909	2484	95	below_threshold
Micromonospora rifamycinica	strain=AM105	GCA_001542325.1	291594	291594	type	True	91.7562	1721	2484	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	86.0586	1445	2484	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	84.9034	1045	2484	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	84.5409	1479	2484	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	84.3326	1241	2484	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.1508	1311	2484	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:32,669] [INFO] DFAST Taxonomy check result was written to GCF_017599305.1_ASM1759930v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:32,670] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:32,670] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:32,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e78dedb-fda5-4d45-811e-e51a473dbde1/dqc_reference/checkm_data
[2024-01-24 12:45:32,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:32,743] [INFO] Task started: CheckM
[2024-01-24 12:45:32,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017599305.1_ASM1759930v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017599305.1_ASM1759930v1_genomic.fna/checkm_input GCF_017599305.1_ASM1759930v1_genomic.fna/checkm_result
[2024-01-24 12:47:10,615] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:10,616] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:10,655] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:10,656] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:10,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017599305.1_ASM1759930v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:10,657] [INFO] Task started: Blastn
[2024-01-24 12:47:10,657] [INFO] Running command: blastn -query GCF_017599305.1_ASM1759930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e78dedb-fda5-4d45-811e-e51a473dbde1/dqc_reference/reference_markers_gtdb.fasta -out GCF_017599305.1_ASM1759930v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:12,608] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:12,615] [INFO] Selected 9 target genomes.
[2024-01-24 12:47:12,616] [INFO] Target genome list was writen to GCF_017599305.1_ASM1759930v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:12,623] [INFO] Task started: fastANI
[2024-01-24 12:47:12,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d5008f4-f7cb-4bb6-ae7f-ffef0328089d/GCF_017599305.1_ASM1759930v1_genomic.fna.gz --refList GCF_017599305.1_ASM1759930v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017599305.1_ASM1759930v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:33,798] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:33,807] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:33,807] [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_017599305.1	s__Micromonospora sp017599305	100.0	2479	2484	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_900091525.1	s__Micromonospora matsumotoense	93.2592	1998	2484	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	92.868	2001	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.84	95.43	0.85	0.83	5	-
GCF_900090265.1	s__Micromonospora rifamycinica	91.7988	1906	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900090295.1	s__Micromonospora coxensis	86.1247	1530	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090245.1	s__Micromonospora halophytica	86.0427	1448	2484	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	85.2888	1639	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_900091555.1	s__Micromonospora mirobrigensis	85.0315	1384	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091475.1	s__Micromonospora chersina	84.7252	1424	2484	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.87	95.82	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:33,809] [INFO] GTDB search result was written to GCF_017599305.1_ASM1759930v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:33,810] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:33,813] [INFO] DFAST_QC result json was written to GCF_017599305.1_ASM1759930v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:33,813] [INFO] DFAST_QC completed!
[2024-01-24 12:47:33,814] [INFO] Total running time: 0h2m52s