[2024-01-24 14:15:02,672] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:02,674] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:02,675] [INFO] DQC Reference Directory: /var/lib/cwl/stg55015146-ed64-49b4-8bc5-31f14a5daa1d/dqc_reference
[2024-01-24 14:15:04,045] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:04,046] [INFO] Task started: Prodigal
[2024-01-24 14:15:04,046] [INFO] Running command: gunzip -c /var/lib/cwl/stg8846514e-94d6-474a-8a34-6378fbc32f11/GCF_004355005.1_ASM435500v1_genomic.fna.gz | prodigal -d GCF_004355005.1_ASM435500v1_genomic.fna/cds.fna -a GCF_004355005.1_ASM435500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:25,528] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:25,528] [INFO] Task started: HMMsearch
[2024-01-24 14:15:25,528] [INFO] Running command: hmmsearch --tblout GCF_004355005.1_ASM435500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55015146-ed64-49b4-8bc5-31f14a5daa1d/dqc_reference/reference_markers.hmm GCF_004355005.1_ASM435500v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:25,938] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:25,939] [INFO] Found 6/6 markers.
[2024-01-24 14:15:26,001] [INFO] Query marker FASTA was written to GCF_004355005.1_ASM435500v1_genomic.fna/markers.fasta
[2024-01-24 14:15:26,001] [INFO] Task started: Blastn
[2024-01-24 14:15:26,001] [INFO] Running command: blastn -query GCF_004355005.1_ASM435500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55015146-ed64-49b4-8bc5-31f14a5daa1d/dqc_reference/reference_markers.fasta -out GCF_004355005.1_ASM435500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:26,927] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:26,930] [INFO] Selected 14 target genomes.
[2024-01-24 14:15:26,931] [INFO] Target genome list was writen to GCF_004355005.1_ASM435500v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:26,939] [INFO] Task started: fastANI
[2024-01-24 14:15:26,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg8846514e-94d6-474a-8a34-6378fbc32f11/GCF_004355005.1_ASM435500v1_genomic.fna.gz --refList GCF_004355005.1_ASM435500v1_genomic.fna/target_genomes.txt --output GCF_004355005.1_ASM435500v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:46,950] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:46,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55015146-ed64-49b4-8bc5-31f14a5daa1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:46,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55015146-ed64-49b4-8bc5-31f14a5daa1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:46,970] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:15:46,970] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:15:46,971] [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
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	81.9885	1209	2417	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	81.9739	1218	2417	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	81.8851	1222	2417	95	below_threshold
Belnapia rosea	strain=CGMCC 1.10758	GCA_900104205.1	938405	938405	type	True	81.854	1203	2417	95	below_threshold
Belnapia rosea	strain=CPCC 100156	GCA_900101615.1	938405	938405	type	True	81.811	1181	2417	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	81.4258	1206	2417	95	below_threshold
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	81.2353	1176	2417	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	79.3844	804	2417	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	79.3686	910	2417	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	79.2388	698	2417	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.5399	740	2417	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.3181	679	2417	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	78.0388	688	2417	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.2722	699	2417	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:46,973] [INFO] DFAST Taxonomy check result was written to GCF_004355005.1_ASM435500v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:46,973] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:46,973] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:46,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55015146-ed64-49b4-8bc5-31f14a5daa1d/dqc_reference/checkm_data
[2024-01-24 14:15:46,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:47,046] [INFO] Task started: CheckM
[2024-01-24 14:15:47,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004355005.1_ASM435500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004355005.1_ASM435500v1_genomic.fna/checkm_input GCF_004355005.1_ASM435500v1_genomic.fna/checkm_result
[2024-01-24 14:16:54,252] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:54,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:54,292] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:54,292] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:54,293] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004355005.1_ASM435500v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:54,293] [INFO] Task started: Blastn
[2024-01-24 14:16:54,293] [INFO] Running command: blastn -query GCF_004355005.1_ASM435500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55015146-ed64-49b4-8bc5-31f14a5daa1d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004355005.1_ASM435500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:56,130] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:56,135] [INFO] Selected 8 target genomes.
[2024-01-24 14:16:56,135] [INFO] Target genome list was writen to GCF_004355005.1_ASM435500v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:56,147] [INFO] Task started: fastANI
[2024-01-24 14:16:56,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg8846514e-94d6-474a-8a34-6378fbc32f11/GCF_004355005.1_ASM435500v1_genomic.fna.gz --refList GCF_004355005.1_ASM435500v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004355005.1_ASM435500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:13,356] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:13,368] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:13,369] [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_004355005.1	s__Paracraurococcus ruber_A	100.0	2408	2417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004343615.1	s__Paracraurococcus sp004343615	84.8384	1314	2417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258945.1	s__Paracraurococcus frigidaeris	84.4997	1387	2417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013112485.1	s__Paracraurococcus sp013112485	84.2104	1398	2417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353985.1	s__Paracraurococcus ruber	84.0835	1372	2417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	99.87	99.87	0.95	0.95	2	-
GCF_014283215.1	s__Siccirubricoccus deserti	81.9729	1218	2417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Siccirubricoccus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016775475.1	s__Belnapia sp016775475	81.8932	1220	2417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084075.1	s__G192 sp019084075	81.2952	1140	2417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__G192	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:17:13,371] [INFO] GTDB search result was written to GCF_004355005.1_ASM435500v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:13,378] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:13,383] [INFO] DFAST_QC result json was written to GCF_004355005.1_ASM435500v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:13,384] [INFO] DFAST_QC completed!
[2024-01-24 14:17:13,384] [INFO] Total running time: 0h2m11s