[2024-01-24 13:49:45,295] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:45,297] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:45,297] [INFO] DQC Reference Directory: /var/lib/cwl/stg356db87c-7eaa-4932-ad5e-0b83e0d1e90d/dqc_reference
[2024-01-24 13:49:46,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:46,637] [INFO] Task started: Prodigal
[2024-01-24 13:49:46,637] [INFO] Running command: gunzip -c /var/lib/cwl/stg5023d29f-0199-4be5-b611-867ba5759d17/GCF_024178315.1_ASM2417831v1_genomic.fna.gz | prodigal -d GCF_024178315.1_ASM2417831v1_genomic.fna/cds.fna -a GCF_024178315.1_ASM2417831v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:04,246] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:04,247] [INFO] Task started: HMMsearch
[2024-01-24 13:50:04,247] [INFO] Running command: hmmsearch --tblout GCF_024178315.1_ASM2417831v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg356db87c-7eaa-4932-ad5e-0b83e0d1e90d/dqc_reference/reference_markers.hmm GCF_024178315.1_ASM2417831v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:04,590] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:04,592] [INFO] Found 6/6 markers.
[2024-01-24 13:50:04,643] [INFO] Query marker FASTA was written to GCF_024178315.1_ASM2417831v1_genomic.fna/markers.fasta
[2024-01-24 13:50:04,643] [INFO] Task started: Blastn
[2024-01-24 13:50:04,643] [INFO] Running command: blastn -query GCF_024178315.1_ASM2417831v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg356db87c-7eaa-4932-ad5e-0b83e0d1e90d/dqc_reference/reference_markers.fasta -out GCF_024178315.1_ASM2417831v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:05,589] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:05,592] [INFO] Selected 12 target genomes.
[2024-01-24 13:50:05,592] [INFO] Target genome list was writen to GCF_024178315.1_ASM2417831v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:05,596] [INFO] Task started: fastANI
[2024-01-24 13:50:05,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg5023d29f-0199-4be5-b611-867ba5759d17/GCF_024178315.1_ASM2417831v1_genomic.fna.gz --refList GCF_024178315.1_ASM2417831v1_genomic.fna/target_genomes.txt --output GCF_024178315.1_ASM2417831v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:21,450] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:21,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg356db87c-7eaa-4932-ad5e-0b83e0d1e90d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:21,450] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg356db87c-7eaa-4932-ad5e-0b83e0d1e90d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:21,460] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:21,460] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:21,461] [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	83.6746	1225	1870	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	83.6354	1254	1870	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	82.3163	1134	1870	95	below_threshold
Belnapia rosea	strain=CPCC 100156	GCA_900101615.1	938405	938405	type	True	81.9028	1112	1870	95	below_threshold
Belnapia rosea	strain=CGMCC 1.10758	GCA_900104205.1	938405	938405	type	True	81.8581	1107	1870	95	below_threshold
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	81.5852	1071	1870	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	79.4057	777	1870	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	79.2172	637	1870	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.7709	650	1870	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	78.7269	717	1870	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.721	687	1870	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.0402	640	1870	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:21,462] [INFO] DFAST Taxonomy check result was written to GCF_024178315.1_ASM2417831v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:21,463] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:21,463] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:21,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg356db87c-7eaa-4932-ad5e-0b83e0d1e90d/dqc_reference/checkm_data
[2024-01-24 13:50:21,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:21,521] [INFO] Task started: CheckM
[2024-01-24 13:50:21,521] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024178315.1_ASM2417831v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024178315.1_ASM2417831v1_genomic.fna/checkm_input GCF_024178315.1_ASM2417831v1_genomic.fna/checkm_result
[2024-01-24 13:51:13,553] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:13,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:13,575] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:13,576] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:13,576] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024178315.1_ASM2417831v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:13,577] [INFO] Task started: Blastn
[2024-01-24 13:51:13,577] [INFO] Running command: blastn -query GCF_024178315.1_ASM2417831v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg356db87c-7eaa-4932-ad5e-0b83e0d1e90d/dqc_reference/reference_markers_gtdb.fasta -out GCF_024178315.1_ASM2417831v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:15,331] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:15,335] [INFO] Selected 11 target genomes.
[2024-01-24 13:51:15,336] [INFO] Target genome list was writen to GCF_024178315.1_ASM2417831v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:15,366] [INFO] Task started: fastANI
[2024-01-24 13:51:15,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg5023d29f-0199-4be5-b611-867ba5759d17/GCF_024178315.1_ASM2417831v1_genomic.fna.gz --refList GCF_024178315.1_ASM2417831v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024178315.1_ASM2417831v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:33,866] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:33,881] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:51:33,881] [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_008360935.1	s__Siccirubricoccus phaeus	89.6404	1488	1870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Siccirubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014283215.1	s__Siccirubricoccus deserti	83.6482	1252	1870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Siccirubricoccus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003258945.1	s__Paracraurococcus frigidaeris	82.5963	1146	1870	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	82.4602	1101	1870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	99.87	99.87	0.95	0.95	2	-
GCF_013112485.1	s__Paracraurococcus sp013112485	82.4072	1129	1870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343615.1	s__Paracraurococcus sp004343615	82.3516	1093	1870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016775475.1	s__Belnapia sp016775475	82.3122	1134	1870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004355005.1	s__Paracraurococcus ruber_A	81.7758	1132	1870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084075.1	s__G192 sp019084075	81.6443	1072	1870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__G192	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000802185.1	s__Belnapia sp000802185	81.5025	1068	1870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004761865.1	s__Crenalkalicoccus roseus	81.0773	920	1870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:33,883] [INFO] GTDB search result was written to GCF_024178315.1_ASM2417831v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:33,883] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:33,886] [INFO] DFAST_QC result json was written to GCF_024178315.1_ASM2417831v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:33,887] [INFO] DFAST_QC completed!
[2024-01-24 13:51:33,887] [INFO] Total running time: 0h1m49s