[2024-01-24 14:19:00,282] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:00,289] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:00,289] [INFO] DQC Reference Directory: /var/lib/cwl/stgd499c8cc-d56e-4152-9456-989ea519a53b/dqc_reference
[2024-01-24 14:19:01,665] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:01,666] [INFO] Task started: Prodigal
[2024-01-24 14:19:01,666] [INFO] Running command: gunzip -c /var/lib/cwl/stgb574eb17-2e77-43c3-91c3-3f4a70a8ae75/GCF_011492965.1_ASM1149296v1_genomic.fna.gz | prodigal -d GCF_011492965.1_ASM1149296v1_genomic.fna/cds.fna -a GCF_011492965.1_ASM1149296v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:13,015] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:13,016] [INFO] Task started: HMMsearch
[2024-01-24 14:19:13,016] [INFO] Running command: hmmsearch --tblout GCF_011492965.1_ASM1149296v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd499c8cc-d56e-4152-9456-989ea519a53b/dqc_reference/reference_markers.hmm GCF_011492965.1_ASM1149296v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:13,283] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:13,285] [INFO] Found 6/6 markers.
[2024-01-24 14:19:13,329] [INFO] Query marker FASTA was written to GCF_011492965.1_ASM1149296v1_genomic.fna/markers.fasta
[2024-01-24 14:19:13,329] [INFO] Task started: Blastn
[2024-01-24 14:19:13,329] [INFO] Running command: blastn -query GCF_011492965.1_ASM1149296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd499c8cc-d56e-4152-9456-989ea519a53b/dqc_reference/reference_markers.fasta -out GCF_011492965.1_ASM1149296v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:14,112] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:14,116] [INFO] Selected 17 target genomes.
[2024-01-24 14:19:14,116] [INFO] Target genome list was writen to GCF_011492965.1_ASM1149296v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:14,123] [INFO] Task started: fastANI
[2024-01-24 14:19:14,123] [INFO] Running command: fastANI --query /var/lib/cwl/stgb574eb17-2e77-43c3-91c3-3f4a70a8ae75/GCF_011492965.1_ASM1149296v1_genomic.fna.gz --refList GCF_011492965.1_ASM1149296v1_genomic.fna/target_genomes.txt --output GCF_011492965.1_ASM1149296v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:28,562] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:28,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd499c8cc-d56e-4152-9456-989ea519a53b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:28,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd499c8cc-d56e-4152-9456-989ea519a53b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:28,576] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:28,576] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:28,577] [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
Rubrobacter marinus	strain=SCSIO 52915	GCA_011492965.1	2653852	2653852	type	True	100.0	1471	1472	95	conclusive
Rubrobacter tropicus	strain=SCSIO 52909	GCA_011492945.1	2653851	2653851	type	True	78.8914	577	1472	95	below_threshold
Rubrobacter radiotolerans	strain=DSM 5868	GCA_900175965.1	42256	42256	type	True	77.9336	410	1472	95	below_threshold
Rubrobacter aplysinae	strain=RV113	GCA_001029505.1	909625	909625	type	True	77.7785	328	1472	95	below_threshold
Rubrobacter indicoceani	strain=SCSIO 08198	GCA_003568865.1	2051957	2051957	type	True	77.3941	283	1472	95	below_threshold
Humibacter ginsenosidimutans	strain=WJ7-1	GCA_007859675.1	2599293	2599293	type	True	75.1294	75	1472	95	below_threshold
Lysobacter xinjiangensis	strain=KCTC 22558	GCA_014651995.1	546892	546892	type	True	75.1078	60	1472	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	75.079	104	1472	95	below_threshold
Glycomyces dulcitolivorans	strain=SJ-25	GCA_003265355.1	2200759	2200759	type	True	75.0432	138	1472	95	below_threshold
Glycomyces artemisiae	strain=CGMCC 4.7067	GCA_003002955.1	1076443	1076443	type	True	75.0034	171	1472	95	below_threshold
Kibdelosporangium aridum	strain=DSM 43828	GCA_900176515.1	2030	2030	type	True	74.9857	98	1472	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	74.9257	79	1472	95	below_threshold
Lysobacter terrigena	strain=17J7-1	GCA_004361065.1	2488749	2488749	type	True	74.8907	51	1472	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	74.7792	159	1472	95	below_threshold
Methylobacterium platani	strain=PMB02	GCA_001653715.1	427683	427683	type	True	74.7402	153	1472	95	below_threshold
Methylobacterium platani	strain=JCM 14648	GCA_001043885.1	427683	427683	type	True	74.7378	138	1472	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:28,579] [INFO] DFAST Taxonomy check result was written to GCF_011492965.1_ASM1149296v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:28,579] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:28,580] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:28,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd499c8cc-d56e-4152-9456-989ea519a53b/dqc_reference/checkm_data
[2024-01-24 14:19:28,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:28,632] [INFO] Task started: CheckM
[2024-01-24 14:19:28,632] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011492965.1_ASM1149296v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011492965.1_ASM1149296v1_genomic.fna/checkm_input GCF_011492965.1_ASM1149296v1_genomic.fna/checkm_result
[2024-01-24 14:20:04,833] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:04,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:04,857] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:04,858] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:04,858] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011492965.1_ASM1149296v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:04,858] [INFO] Task started: Blastn
[2024-01-24 14:20:04,859] [INFO] Running command: blastn -query GCF_011492965.1_ASM1149296v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd499c8cc-d56e-4152-9456-989ea519a53b/dqc_reference/reference_markers_gtdb.fasta -out GCF_011492965.1_ASM1149296v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:06,073] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:06,077] [INFO] Selected 14 target genomes.
[2024-01-24 14:20:06,077] [INFO] Target genome list was writen to GCF_011492965.1_ASM1149296v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:06,114] [INFO] Task started: fastANI
[2024-01-24 14:20:06,115] [INFO] Running command: fastANI --query /var/lib/cwl/stgb574eb17-2e77-43c3-91c3-3f4a70a8ae75/GCF_011492965.1_ASM1149296v1_genomic.fna.gz --refList GCF_011492965.1_ASM1149296v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011492965.1_ASM1149296v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:16,236] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:16,251] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:16,251] [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_011492965.1	s__SCSIO-52915 sp011492965	100.0	1471	1472	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52915	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016781775.1	s__SCSIO-52915 sp016781775	86.6796	646	1472	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806105.1	s__SCSIO-52915 sp902806105	85.7344	746	1472	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781635.1	s__SCSIO-52915 sp016781635	85.1297	543	1472	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781705.1	s__SCSIO-52915 sp016781705	80.2807	428	1472	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781885.1	s__SCSIO-52915 sp016781885	79.3667	309	1472	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806075.1	s__SCSIO-52915 sp902806075	79.3366	364	1472	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52915	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011492945.1	s__SCSIO-52909 sp011492945	78.9377	571	1472	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806055.1	s__SCSIO-52915 sp902806055	78.7749	387	1472	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013815575.1	s__SCSIO-52909 sp013815575	78.6728	279	1472	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	97.69	97.69	0.64	0.64	2	-
GCA_016779205.1	s__GCA-2862085 sp016779205	74.6373	72	1472	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:16,253] [INFO] GTDB search result was written to GCF_011492965.1_ASM1149296v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:16,254] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:16,257] [INFO] DFAST_QC result json was written to GCF_011492965.1_ASM1149296v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:16,257] [INFO] DFAST_QC completed!
[2024-01-24 14:20:16,257] [INFO] Total running time: 0h1m16s