[2024-01-24 11:52:49,010] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:49,012] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:49,012] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ebd04e3-cdeb-4291-8882-c2fadbe5f282/dqc_reference
[2024-01-24 11:52:50,208] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:50,208] [INFO] Task started: Prodigal
[2024-01-24 11:52:50,209] [INFO] Running command: gunzip -c /var/lib/cwl/stg4fd552a5-f582-45ae-818f-5f0def2da5e7/GCF_028617085.1_ASM2861708v1_genomic.fna.gz | prodigal -d GCF_028617085.1_ASM2861708v1_genomic.fna/cds.fna -a GCF_028617085.1_ASM2861708v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:57,596] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:57,596] [INFO] Task started: HMMsearch
[2024-01-24 11:52:57,597] [INFO] Running command: hmmsearch --tblout GCF_028617085.1_ASM2861708v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ebd04e3-cdeb-4291-8882-c2fadbe5f282/dqc_reference/reference_markers.hmm GCF_028617085.1_ASM2861708v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:57,831] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:57,833] [INFO] Found 6/6 markers.
[2024-01-24 11:52:57,863] [INFO] Query marker FASTA was written to GCF_028617085.1_ASM2861708v1_genomic.fna/markers.fasta
[2024-01-24 11:52:57,863] [INFO] Task started: Blastn
[2024-01-24 11:52:57,863] [INFO] Running command: blastn -query GCF_028617085.1_ASM2861708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ebd04e3-cdeb-4291-8882-c2fadbe5f282/dqc_reference/reference_markers.fasta -out GCF_028617085.1_ASM2861708v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:58,545] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:58,550] [INFO] Selected 14 target genomes.
[2024-01-24 11:52:58,550] [INFO] Target genome list was writen to GCF_028617085.1_ASM2861708v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:58,556] [INFO] Task started: fastANI
[2024-01-24 11:52:58,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fd552a5-f582-45ae-818f-5f0def2da5e7/GCF_028617085.1_ASM2861708v1_genomic.fna.gz --refList GCF_028617085.1_ASM2861708v1_genomic.fna/target_genomes.txt --output GCF_028617085.1_ASM2861708v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:53:07,659] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:07,659] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ebd04e3-cdeb-4291-8882-c2fadbe5f282/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:53:07,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ebd04e3-cdeb-4291-8882-c2fadbe5f282/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:53:07,671] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:53:07,671] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:53:07,671] [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	78.0119	315	966	95	below_threshold
Rubrobacter aplysinae	strain=RV113	GCA_001029505.1	909625	909625	type	True	77.5425	235	966	95	below_threshold
Rubrobacter radiotolerans	strain=DSM 5868	GCA_900175965.1	42256	42256	type	True	77.5128	264	966	95	below_threshold
Rubrobacter tropicus	strain=SCSIO 52909	GCA_011492945.1	2653851	2653851	type	True	77.4288	295	966	95	below_threshold
Rubrobacter indicoceani	strain=SCSIO 08198	GCA_003568865.1	2051957	2051957	type	True	77.0108	174	966	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	75.4116	108	966	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	75.0985	85	966	95	below_threshold
Pseudonocardia kujensis	strain=KCTC 29062	GCA_021283305.1	1128675	1128675	type	True	75.083	115	966	95	below_threshold
Pseudonocardia oroxyli	strain=CGMCC 4.3143	GCA_900102195.1	366584	366584	type	True	74.7411	83	966	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:53:07,673] [INFO] DFAST Taxonomy check result was written to GCF_028617085.1_ASM2861708v1_genomic.fna/tc_result.tsv
[2024-01-24 11:53:07,673] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:53:07,673] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:53:07,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ebd04e3-cdeb-4291-8882-c2fadbe5f282/dqc_reference/checkm_data
[2024-01-24 11:53:07,674] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:53:07,709] [INFO] Task started: CheckM
[2024-01-24 11:53:07,709] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028617085.1_ASM2861708v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028617085.1_ASM2861708v1_genomic.fna/checkm_input GCF_028617085.1_ASM2861708v1_genomic.fna/checkm_result
[2024-01-24 11:53:33,675] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:33,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:33,696] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:33,696] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:33,696] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028617085.1_ASM2861708v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:33,697] [INFO] Task started: Blastn
[2024-01-24 11:53:33,697] [INFO] Running command: blastn -query GCF_028617085.1_ASM2861708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ebd04e3-cdeb-4291-8882-c2fadbe5f282/dqc_reference/reference_markers_gtdb.fasta -out GCF_028617085.1_ASM2861708v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:34,702] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:34,706] [INFO] Selected 19 target genomes.
[2024-01-24 11:53:34,706] [INFO] Target genome list was writen to GCF_028617085.1_ASM2861708v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:34,776] [INFO] Task started: fastANI
[2024-01-24 11:53:34,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fd552a5-f582-45ae-818f-5f0def2da5e7/GCF_028617085.1_ASM2861708v1_genomic.fna.gz --refList GCF_028617085.1_ASM2861708v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028617085.1_ASM2861708v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:46,076] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:46,103] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:53:46,104] [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_007164525.1	s__Rubrobacter_B xylanophilus_A	81.5847	453	966	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014185.1	s__Rubrobacter_B xylanophilus	79.7763	479	966	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902810695.1	s__CADDYV01 sp902810695	78.9759	420	966	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__CADDYV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004337705.1	s__Rubrobacter_C taiwanensis	78.5807	296	966	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004563715.1	s__SIRX01 sp004563715	78.1043	307	966	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011492965.1	s__SCSIO-52915 sp011492965	78.0311	314	966	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_016781725.1	s__SCSIO-52909 sp016781725	77.8942	226	966	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	98.84	98.84	0.72	0.72	2	-
GCA_902812425.1	s__SCSIO-52909 sp902812425	77.6584	251	966	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_016781705.1	s__SCSIO-52915 sp016781705	77.646	208	966	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	77.6067	167	966	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_902806085.1	s__SCSIO-52909 sp902806085	77.5397	299	966	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900175965.1	s__Rubrobacter radiotolerans	77.5128	264	966	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_011492945.1	s__SCSIO-52909 sp011492945	77.4387	294	966	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_016781775.1	s__SCSIO-52915 sp016781775	77.4298	212	966	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_013695915.1	s__Rubrobacter_A sp013695915	77.4081	221	966	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805985.1	s__SCSIO-52909 sp902805985	77.3639	216	966	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_013815575.1	s__SCSIO-52909 sp013815575	77.1636	150	966	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_016781885.1	s__SCSIO-52915 sp016781885	77.0051	145	966	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_013817025.1	s__JACDDK01 sp013817025	76.8592	73	966	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__JACDDK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:46,106] [INFO] GTDB search result was written to GCF_028617085.1_ASM2861708v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:46,106] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:46,110] [INFO] DFAST_QC result json was written to GCF_028617085.1_ASM2861708v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:46,111] [INFO] DFAST_QC completed!
[2024-01-24 11:53:46,111] [INFO] Total running time: 0h0m57s