[2024-01-24 10:57:23,115] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:23,118] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:23,118] [INFO] DQC Reference Directory: /var/lib/cwl/stg5503f15f-89d5-44b1-abb8-b7f726907af1/dqc_reference
[2024-01-24 10:57:24,340] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:24,341] [INFO] Task started: Prodigal
[2024-01-24 10:57:24,341] [INFO] Running command: gunzip -c /var/lib/cwl/stg841ee248-26b7-4359-8a52-55a46748e49b/GCF_024171995.1_ASM2417199v1_genomic.fna.gz | prodigal -d GCF_024171995.1_ASM2417199v1_genomic.fna/cds.fna -a GCF_024171995.1_ASM2417199v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:43,423] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:43,424] [INFO] Task started: HMMsearch
[2024-01-24 10:57:43,424] [INFO] Running command: hmmsearch --tblout GCF_024171995.1_ASM2417199v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5503f15f-89d5-44b1-abb8-b7f726907af1/dqc_reference/reference_markers.hmm GCF_024171995.1_ASM2417199v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:43,787] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:43,788] [INFO] Found 6/6 markers.
[2024-01-24 10:57:43,841] [INFO] Query marker FASTA was written to GCF_024171995.1_ASM2417199v1_genomic.fna/markers.fasta
[2024-01-24 10:57:43,842] [INFO] Task started: Blastn
[2024-01-24 10:57:43,842] [INFO] Running command: blastn -query GCF_024171995.1_ASM2417199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5503f15f-89d5-44b1-abb8-b7f726907af1/dqc_reference/reference_markers.fasta -out GCF_024171995.1_ASM2417199v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:45,128] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:45,132] [INFO] Selected 10 target genomes.
[2024-01-24 10:57:45,132] [INFO] Target genome list was writen to GCF_024171995.1_ASM2417199v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:45,135] [INFO] Task started: fastANI
[2024-01-24 10:57:45,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg841ee248-26b7-4359-8a52-55a46748e49b/GCF_024171995.1_ASM2417199v1_genomic.fna.gz --refList GCF_024171995.1_ASM2417199v1_genomic.fna/target_genomes.txt --output GCF_024171995.1_ASM2417199v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:58,085] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:58,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5503f15f-89d5-44b1-abb8-b7f726907af1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:58,086] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5503f15f-89d5-44b1-abb8-b7f726907af1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:58,108] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:58,109] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:58,109] [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 umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	99.9894	2160	2169	95	conclusive
Promicromonospora soli	strain=CGMCC 4.7398	GCA_014653785.1	2035533	2035533	type	True	86.7102	1274	2169	95	below_threshold
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	85.5154	1422	2169	95	below_threshold
Promicromonospora kroppenstedtii	strain=DSM 19349	GCA_000515355.1	440482	440482	type	True	85.1149	1242	2169	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	84.0768	1130	2169	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	83.9535	1239	2169	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	78.6239	588	2169	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.8125	558	2169	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	77.73	486	2169	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	77.6318	544	2169	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:58,111] [INFO] DFAST Taxonomy check result was written to GCF_024171995.1_ASM2417199v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:58,112] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:58,112] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:58,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5503f15f-89d5-44b1-abb8-b7f726907af1/dqc_reference/checkm_data
[2024-01-24 10:57:58,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:58,176] [INFO] Task started: CheckM
[2024-01-24 10:57:58,176] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024171995.1_ASM2417199v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024171995.1_ASM2417199v1_genomic.fna/checkm_input GCF_024171995.1_ASM2417199v1_genomic.fna/checkm_result
[2024-01-24 10:58:59,397] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:59,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:59,417] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:59,417] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:59,418] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024171995.1_ASM2417199v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:59,418] [INFO] Task started: Blastn
[2024-01-24 10:58:59,418] [INFO] Running command: blastn -query GCF_024171995.1_ASM2417199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5503f15f-89d5-44b1-abb8-b7f726907af1/dqc_reference/reference_markers_gtdb.fasta -out GCF_024171995.1_ASM2417199v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:01,266] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:01,268] [INFO] Selected 8 target genomes.
[2024-01-24 10:59:01,269] [INFO] Target genome list was writen to GCF_024171995.1_ASM2417199v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:01,296] [INFO] Task started: fastANI
[2024-01-24 10:59:01,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg841ee248-26b7-4359-8a52-55a46748e49b/GCF_024171995.1_ASM2417199v1_genomic.fna.gz --refList GCF_024171995.1_ASM2417199v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024171995.1_ASM2417199v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:13,694] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:13,702] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:59:13,702] [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_003096495.1	s__Promicromonospora sukumoe_A	87.2384	1470	2169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900608595.1	s__Promicromonospora panici	87.1357	1413	2169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058225.1	s__Promicromonospora sp003058225	87.0235	1440	2169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	98.27	98.27	0.94	0.94	2	-
GCF_014653785.1	s__Promicromonospora soli	86.71	1274	2169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550025.1	s__Promicromonospora thailandica	85.6247	1422	2169	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	85.5316	1420	2169	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	85.5281	1429	2169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	95.99	95.99	0.93	0.93	2	-
GCF_000515355.1	s__Promicromonospora kroppenstedtii	85.1485	1237	2169	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	97.09	97.09	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:13,703] [INFO] GTDB search result was written to GCF_024171995.1_ASM2417199v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:13,704] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:13,706] [INFO] DFAST_QC result json was written to GCF_024171995.1_ASM2417199v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:13,707] [INFO] DFAST_QC completed!
[2024-01-24 10:59:13,707] [INFO] Total running time: 0h1m51s