[2024-01-24 13:46:03,873] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:03,875] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:03,875] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f9a0d10-1aa7-4c65-b7c0-c0374ec8ece8/dqc_reference
[2024-01-24 13:46:05,264] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:05,265] [INFO] Task started: Prodigal
[2024-01-24 13:46:05,266] [INFO] Running command: gunzip -c /var/lib/cwl/stg3955174c-efb2-4836-a91a-2eb16c7996aa/GCF_014653785.1_ASM1465378v1_genomic.fna.gz | prodigal -d GCF_014653785.1_ASM1465378v1_genomic.fna/cds.fna -a GCF_014653785.1_ASM1465378v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:21,831] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:21,831] [INFO] Task started: HMMsearch
[2024-01-24 13:46:21,831] [INFO] Running command: hmmsearch --tblout GCF_014653785.1_ASM1465378v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f9a0d10-1aa7-4c65-b7c0-c0374ec8ece8/dqc_reference/reference_markers.hmm GCF_014653785.1_ASM1465378v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:22,176] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:22,177] [INFO] Found 6/6 markers.
[2024-01-24 13:46:22,231] [INFO] Query marker FASTA was written to GCF_014653785.1_ASM1465378v1_genomic.fna/markers.fasta
[2024-01-24 13:46:22,231] [INFO] Task started: Blastn
[2024-01-24 13:46:22,232] [INFO] Running command: blastn -query GCF_014653785.1_ASM1465378v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f9a0d10-1aa7-4c65-b7c0-c0374ec8ece8/dqc_reference/reference_markers.fasta -out GCF_014653785.1_ASM1465378v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:23,528] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:23,532] [INFO] Selected 11 target genomes.
[2024-01-24 13:46:23,532] [INFO] Target genome list was writen to GCF_014653785.1_ASM1465378v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:23,541] [INFO] Task started: fastANI
[2024-01-24 13:46:23,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg3955174c-efb2-4836-a91a-2eb16c7996aa/GCF_014653785.1_ASM1465378v1_genomic.fna.gz --refList GCF_014653785.1_ASM1465378v1_genomic.fna/target_genomes.txt --output GCF_014653785.1_ASM1465378v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:37,185] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:37,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f9a0d10-1aa7-4c65-b7c0-c0374ec8ece8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:37,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f9a0d10-1aa7-4c65-b7c0-c0374ec8ece8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:37,197] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:37,197] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:37,197] [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
Promicromonospora soli	strain=CGMCC 4.7398	GCA_014653785.1	2035533	2035533	type	True	100.0	1780	1781	95	conclusive
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	86.881	1270	1781	95	below_threshold
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	86.753	1280	1781	95	below_threshold
Promicromonospora kroppenstedtii	strain=DSM 19349	GCA_000515355.1	440482	440482	type	True	85.8055	1134	1781	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	84.1881	1012	1781	95	below_threshold
Myceligenerans xiligouense	strain=DSM 15700	GCA_003814695.1	253184	253184	type	True	80.5582	764	1781	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	79.2468	647	1781	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	78.9181	572	1781	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	78.8808	579	1781	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	78.1208	516	1781	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	78.0524	477	1781	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:37,199] [INFO] DFAST Taxonomy check result was written to GCF_014653785.1_ASM1465378v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:37,200] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:37,200] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:37,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f9a0d10-1aa7-4c65-b7c0-c0374ec8ece8/dqc_reference/checkm_data
[2024-01-24 13:46:37,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:37,254] [INFO] Task started: CheckM
[2024-01-24 13:46:37,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014653785.1_ASM1465378v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014653785.1_ASM1465378v1_genomic.fna/checkm_input GCF_014653785.1_ASM1465378v1_genomic.fna/checkm_result
[2024-01-24 13:47:25,956] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:25,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:25,973] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:25,973] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:25,973] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014653785.1_ASM1465378v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:25,973] [INFO] Task started: Blastn
[2024-01-24 13:47:25,974] [INFO] Running command: blastn -query GCF_014653785.1_ASM1465378v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f9a0d10-1aa7-4c65-b7c0-c0374ec8ece8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014653785.1_ASM1465378v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:27,884] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:27,887] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:27,888] [INFO] Target genome list was writen to GCF_014653785.1_ASM1465378v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:27,896] [INFO] Task started: fastANI
[2024-01-24 13:47:27,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg3955174c-efb2-4836-a91a-2eb16c7996aa/GCF_014653785.1_ASM1465378v1_genomic.fna.gz --refList GCF_014653785.1_ASM1465378v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014653785.1_ASM1465378v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:41,780] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:41,789] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:41,789] [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_014653785.1	s__Promicromonospora soli	100.0	1780	1781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003058225.1	s__Promicromonospora sp003058225	89.2299	1418	1781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	98.27	98.27	0.94	0.94	2	-
GCF_900608595.1	s__Promicromonospora panici	88.1429	1409	1781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096495.1	s__Promicromonospora sukumoe_A	87.11	1339	1781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137995.1	s__Promicromonospora sukumoe	86.7201	1284	1781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000385135.1	s__Promicromonospora sukumoe_B	86.282	1325	1781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	95.99	95.99	0.93	0.93	2	-
GCF_003550025.1	s__Promicromonospora thailandica	86.0615	1247	1781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515355.1	s__Promicromonospora kroppenstedtii	85.7872	1134	1781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	97.09	97.09	0.84	0.84	2	-
GCF_003814695.1	s__Myceligenerans xiligouense	80.5761	761	1781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Myceligenerans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010287905.1	s__Cellulosimicrobium fucosivorans	79.362	658	1781	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.84	98.55	0.94	0.90	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:41,791] [INFO] GTDB search result was written to GCF_014653785.1_ASM1465378v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:41,791] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:41,795] [INFO] DFAST_QC result json was written to GCF_014653785.1_ASM1465378v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:41,795] [INFO] DFAST_QC completed!
[2024-01-24 13:47:41,795] [INFO] Total running time: 0h1m38s