[2024-01-24 11:51:23,909] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:23,912] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:23,912] [INFO] DQC Reference Directory: /var/lib/cwl/stg72791f57-d002-4699-88e3-7266941e9a36/dqc_reference
[2024-01-24 11:51:25,309] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:25,311] [INFO] Task started: Prodigal
[2024-01-24 11:51:25,311] [INFO] Running command: gunzip -c /var/lib/cwl/stga1491b1b-1a45-4499-b903-b65abc178b71/GCF_003149495.1_ASM314949v1_genomic.fna.gz | prodigal -d GCF_003149495.1_ASM314949v1_genomic.fna/cds.fna -a GCF_003149495.1_ASM314949v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:55,013] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:55,014] [INFO] Task started: HMMsearch
[2024-01-24 11:51:55,014] [INFO] Running command: hmmsearch --tblout GCF_003149495.1_ASM314949v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72791f57-d002-4699-88e3-7266941e9a36/dqc_reference/reference_markers.hmm GCF_003149495.1_ASM314949v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:55,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:55,404] [INFO] Found 6/6 markers.
[2024-01-24 11:51:55,473] [INFO] Query marker FASTA was written to GCF_003149495.1_ASM314949v1_genomic.fna/markers.fasta
[2024-01-24 11:51:55,473] [INFO] Task started: Blastn
[2024-01-24 11:51:55,474] [INFO] Running command: blastn -query GCF_003149495.1_ASM314949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72791f57-d002-4699-88e3-7266941e9a36/dqc_reference/reference_markers.fasta -out GCF_003149495.1_ASM314949v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:56,153] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:56,157] [INFO] Selected 15 target genomes.
[2024-01-24 11:51:56,158] [INFO] Target genome list was writen to GCF_003149495.1_ASM314949v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:56,164] [INFO] Task started: fastANI
[2024-01-24 11:51:56,164] [INFO] Running command: fastANI --query /var/lib/cwl/stga1491b1b-1a45-4499-b903-b65abc178b71/GCF_003149495.1_ASM314949v1_genomic.fna.gz --refList GCF_003149495.1_ASM314949v1_genomic.fna/target_genomes.txt --output GCF_003149495.1_ASM314949v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:23,917] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:23,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72791f57-d002-4699-88e3-7266941e9a36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:23,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72791f57-d002-4699-88e3-7266941e9a36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:23,935] [INFO] Found 15 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:52:23,935] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:23,935] [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
Gemmata obscuriglobus	strain=DSM 5831	GCA_003149495.1	114	114	type	True	100.0	2999	2999	95	conclusive
Gemmata obscuriglobus	strain=DSM 5831	GCA_008065095.1	114	114	type	True	99.9975	2998	2999	95	conclusive
Gemmata obscuriglobus		GCA_901538385.1	114	114	type	True	99.9972	2998	2999	95	conclusive
Gemmata obscuriglobus	strain=UQM 2246	GCA_000171775.1	114	114	type	True	99.7807	2610	2999	95	conclusive
Urbifossiella limnaea	strain=ETA_A1	GCA_007747215.1	2528023	2528023	type	True	78.0291	982	2999	95	below_threshold
Fimbriiglobus ruber	strain=SP5	GCA_002197845.1	1908690	1908690	type	True	76.6449	635	2999	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	74.8623	100	2999	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	74.8613	196	2999	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	74.8478	179	2999	95	below_threshold
Phytoactinopolyspora halophila	strain=YIM 96934	GCA_003287285.1	1981511	1981511	type	True	74.8027	78	2999	95	below_threshold
Dietzia timorensis	strain=ID05-A0528	GCA_001651825.1	499555	499555	type	True	74.8006	50	2999	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	74.7814	109	2999	95	below_threshold
Dietzia timorensis	strain=ID05-A0528	GCA_001659785.1	499555	499555	type	True	74.7752	58	2999	95	below_threshold
Brachybacterium muris	strain=DSM 15460	GCA_016907455.1	219301	219301	type	True	74.7426	65	2999	95	below_threshold
Nakamurella deserti	strain=12Sc4-1	GCA_003260015.1	2164074	2164074	type	True	74.6602	181	2999	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:23,937] [INFO] DFAST Taxonomy check result was written to GCF_003149495.1_ASM314949v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:23,938] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:23,938] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:23,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72791f57-d002-4699-88e3-7266941e9a36/dqc_reference/checkm_data
[2024-01-24 11:52:23,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:24,025] [INFO] Task started: CheckM
[2024-01-24 11:52:24,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003149495.1_ASM314949v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003149495.1_ASM314949v1_genomic.fna/checkm_input GCF_003149495.1_ASM314949v1_genomic.fna/checkm_result
[2024-01-24 11:53:46,267] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:46,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:46,300] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:46,301] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:46,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003149495.1_ASM314949v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:46,301] [INFO] Task started: Blastn
[2024-01-24 11:53:46,302] [INFO] Running command: blastn -query GCF_003149495.1_ASM314949v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72791f57-d002-4699-88e3-7266941e9a36/dqc_reference/reference_markers_gtdb.fasta -out GCF_003149495.1_ASM314949v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:47,184] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:47,188] [INFO] Selected 11 target genomes.
[2024-01-24 11:53:47,189] [INFO] Target genome list was writen to GCF_003149495.1_ASM314949v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:47,196] [INFO] Task started: fastANI
[2024-01-24 11:53:47,197] [INFO] Running command: fastANI --query /var/lib/cwl/stga1491b1b-1a45-4499-b903-b65abc178b71/GCF_003149495.1_ASM314949v1_genomic.fna.gz --refList GCF_003149495.1_ASM314949v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003149495.1_ASM314949v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:54:11,424] [INFO] Task succeeded: fastANI
[2024-01-24 11:54:11,444] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:54:11,445] [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_008065095.1	s__Gemmata obscuriglobus	99.9975	2998	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	99.98	99.95	1.00	1.00	4	conclusive
GCF_017939745.1	s__Gemmata sp017939745	80.0202	1498	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306025.1	s__Gemmata sp017306025	79.9858	1023	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013128195.2	s__Gemmata tundricola	79.8736	1365	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000531095.1	s__Gemmata massiliana	79.7696	1414	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	97.81	97.81	0.89	0.89	2	-
GCF_901538265.1	s__Gemmata massiliana_A	79.7561	1435	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872595.1	s__Gemmata sp016872595	79.5039	1083	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901538445.1	s__Gemmata sp901538445	79.1682	1124	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005772955.1	s__Gemmata sp005772955	79.042	960	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	99.91	99.90	0.94	0.93	4	-
GCA_005773755.1	s__Gemmata sp005773755	78.877	784	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747215.1	s__Urbifossiella limnaea	78.0394	976	2999	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:54:11,447] [INFO] GTDB search result was written to GCF_003149495.1_ASM314949v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:54:11,448] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:54:11,451] [INFO] DFAST_QC result json was written to GCF_003149495.1_ASM314949v1_genomic.fna/dqc_result.json
[2024-01-24 11:54:11,451] [INFO] DFAST_QC completed!
[2024-01-24 11:54:11,451] [INFO] Total running time: 0h2m48s