[2024-01-24 13:40:46,134] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:46,138] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:46,139] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf779570-0399-46a0-a2ef-3b42cb224d03/dqc_reference
[2024-01-24 13:40:47,462] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:47,462] [INFO] Task started: Prodigal
[2024-01-24 13:40:47,463] [INFO] Running command: gunzip -c /var/lib/cwl/stg760a0c07-a6ad-4ae7-9397-7fa1dc9b332b/GCF_002926165.1_ASM292616v1_genomic.fna.gz | prodigal -d GCF_002926165.1_ASM292616v1_genomic.fna/cds.fna -a GCF_002926165.1_ASM292616v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:05,954] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:05,954] [INFO] Task started: HMMsearch
[2024-01-24 13:41:05,954] [INFO] Running command: hmmsearch --tblout GCF_002926165.1_ASM292616v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf779570-0399-46a0-a2ef-3b42cb224d03/dqc_reference/reference_markers.hmm GCF_002926165.1_ASM292616v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:06,288] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:06,290] [INFO] Found 6/6 markers.
[2024-01-24 13:41:06,351] [INFO] Query marker FASTA was written to GCF_002926165.1_ASM292616v1_genomic.fna/markers.fasta
[2024-01-24 13:41:06,351] [INFO] Task started: Blastn
[2024-01-24 13:41:06,352] [INFO] Running command: blastn -query GCF_002926165.1_ASM292616v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf779570-0399-46a0-a2ef-3b42cb224d03/dqc_reference/reference_markers.fasta -out GCF_002926165.1_ASM292616v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:07,559] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:07,563] [INFO] Selected 16 target genomes.
[2024-01-24 13:41:07,563] [INFO] Target genome list was writen to GCF_002926165.1_ASM292616v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:07,622] [INFO] Task started: fastANI
[2024-01-24 13:41:07,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg760a0c07-a6ad-4ae7-9397-7fa1dc9b332b/GCF_002926165.1_ASM292616v1_genomic.fna.gz --refList GCF_002926165.1_ASM292616v1_genomic.fna/target_genomes.txt --output GCF_002926165.1_ASM292616v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:39,901] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:39,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf779570-0399-46a0-a2ef-3b42cb224d03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:39,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf779570-0399-46a0-a2ef-3b42cb224d03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:39,915] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:39,915] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:39,915] [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 chalcea	strain=DSM 43026	GCA_002926165.1	1874	1874	type	True	100.0	2227	2248	95	conclusive
Micromonospora aurantiaca	strain=ATCC 27029	GCA_003721415.1	47850	47850	type	True	93.8226	1823	2248	95	below_threshold
Micromonospora aurantiaca	strain=ATCC 27029	GCA_000145235.1	47850	47850	type	True	93.76	1841	2248	95	below_threshold
Micromonospora tulbaghiae	strain=DSM 45142	GCA_900091605.1	479978	479978	type	True	93.6512	1794	2248	95	below_threshold
Micromonospora marina	strain=DSM 45555	GCA_900091565.1	307120	307120	type	True	92.7861	1604	2248	95	below_threshold
Micromonospora sediminicola	strain=DSM 45794	GCA_900089585.1	946078	946078	type	True	89.7806	1622	2248	95	below_threshold
Micromonospora maritima		GCA_902825405.1	986711	986711	type	True	89.4451	1187	2248	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	89.3979	1612	2248	95	below_threshold
Micromonospora humi	strain=DSM 45647	GCA_900090105.1	745366	745366	type	True	89.354	1604	2248	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	87.8359	1526	2248	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	87.8317	1508	2248	95	below_threshold
Micromonospora mirobrigensis	strain=DSM 44830	GCA_900091555.1	262898	262898	type	True	85.4161	1399	2248	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	84.6824	1428	2248	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	84.4492	1233	2248	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	76.3692	665	2248	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	76.2886	663	2248	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:39,917] [INFO] DFAST Taxonomy check result was written to GCF_002926165.1_ASM292616v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:39,918] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:39,918] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:39,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf779570-0399-46a0-a2ef-3b42cb224d03/dqc_reference/checkm_data
[2024-01-24 13:41:39,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:39,983] [INFO] Task started: CheckM
[2024-01-24 13:41:39,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002926165.1_ASM292616v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002926165.1_ASM292616v1_genomic.fna/checkm_input GCF_002926165.1_ASM292616v1_genomic.fna/checkm_result
[2024-01-24 13:42:45,272] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:45,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:45,300] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:45,300] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:45,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002926165.1_ASM292616v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:45,301] [INFO] Task started: Blastn
[2024-01-24 13:42:45,301] [INFO] Running command: blastn -query GCF_002926165.1_ASM292616v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf779570-0399-46a0-a2ef-3b42cb224d03/dqc_reference/reference_markers_gtdb.fasta -out GCF_002926165.1_ASM292616v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:47,108] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:47,113] [INFO] Selected 14 target genomes.
[2024-01-24 13:42:47,113] [INFO] Target genome list was writen to GCF_002926165.1_ASM292616v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:47,255] [INFO] Task started: fastANI
[2024-01-24 13:42:47,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg760a0c07-a6ad-4ae7-9397-7fa1dc9b332b/GCF_002926165.1_ASM292616v1_genomic.fna.gz --refList GCF_002926165.1_ASM292616v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002926165.1_ASM292616v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:17,225] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:17,239] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:17,239] [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_002926165.1	s__Micromonospora chalcea	100.0	2219	2248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	95.31	0.89	0.84	18	conclusive
GCF_000145235.1	s__Micromonospora aurantiaca	93.7599	1841	2248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.1942	98.37	95.58	0.90	0.84	15	-
GCF_900091605.1	s__Micromonospora tulbaghiae	93.6508	1794	2248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.1942	97.73	96.20	0.92	0.87	5	-
GCF_900091565.1	s__Micromonospora marina	92.7861	1604	2248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.54	95.96	0.90	0.86	3	-
GCF_900089585.1	s__Micromonospora sediminicola	89.7552	1625	2248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.55	97.81	0.94	0.92	3	-
GCF_902825405.1	s__Micromonospora maritima	89.4068	1190	2248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013694245.1	s__Micromonospora sp013694245	89.345	1618	2248	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	89.3251	1607	2248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002140155.1	s__Micromonospora sp002140155	88.8061	1559	2248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648395.1	s__Micromonospora fulviviridis	87.8492	1525	2248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_900091475.1	s__Micromonospora chersina	87.7716	1516	2248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.87	95.82	0.87	0.87	3	-
GCF_900089595.1	s__Micromonospora auratinigra	87.05	1501	2248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091555.1	s__Micromonospora mirobrigensis	85.4683	1392	2248	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009908295.1	s__Micromonospora rubida	84.9237	1392	2248	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 13:43:17,241] [INFO] GTDB search result was written to GCF_002926165.1_ASM292616v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:17,241] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:17,245] [INFO] DFAST_QC result json was written to GCF_002926165.1_ASM292616v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:17,245] [INFO] DFAST_QC completed!
[2024-01-24 13:43:17,245] [INFO] Total running time: 0h2m31s