[2024-01-24 12:57:50,401] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:57:50,403] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:57:50,403] [INFO] DQC Reference Directory: /var/lib/cwl/stg813fbf7f-70bc-49fd-aa90-023c810e349d/dqc_reference
[2024-01-24 12:57:51,542] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:57:51,543] [INFO] Task started: Prodigal
[2024-01-24 12:57:51,543] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc3e364b-42b5-40ef-b7a5-5d858afb4412/GCF_023022985.1_ASM2302298v1_genomic.fna.gz | prodigal -d GCF_023022985.1_ASM2302298v1_genomic.fna/cds.fna -a GCF_023022985.1_ASM2302298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:58:02,907] [INFO] Task succeeded: Prodigal
[2024-01-24 12:58:02,908] [INFO] Task started: HMMsearch
[2024-01-24 12:58:02,908] [INFO] Running command: hmmsearch --tblout GCF_023022985.1_ASM2302298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg813fbf7f-70bc-49fd-aa90-023c810e349d/dqc_reference/reference_markers.hmm GCF_023022985.1_ASM2302298v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:58:03,102] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:58:03,104] [INFO] Found 6/6 markers.
[2024-01-24 12:58:03,135] [INFO] Query marker FASTA was written to GCF_023022985.1_ASM2302298v1_genomic.fna/markers.fasta
[2024-01-24 12:58:03,136] [INFO] Task started: Blastn
[2024-01-24 12:58:03,136] [INFO] Running command: blastn -query GCF_023022985.1_ASM2302298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg813fbf7f-70bc-49fd-aa90-023c810e349d/dqc_reference/reference_markers.fasta -out GCF_023022985.1_ASM2302298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:58:04,104] [INFO] Task succeeded: Blastn
[2024-01-24 12:58:04,107] [INFO] Selected 7 target genomes.
[2024-01-24 12:58:04,107] [INFO] Target genome list was writen to GCF_023022985.1_ASM2302298v1_genomic.fna/target_genomes.txt
[2024-01-24 12:58:04,111] [INFO] Task started: fastANI
[2024-01-24 12:58:04,111] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc3e364b-42b5-40ef-b7a5-5d858afb4412/GCF_023022985.1_ASM2302298v1_genomic.fna.gz --refList GCF_023022985.1_ASM2302298v1_genomic.fna/target_genomes.txt --output GCF_023022985.1_ASM2302298v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:58:09,519] [INFO] Task succeeded: fastANI
[2024-01-24 12:58:09,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg813fbf7f-70bc-49fd-aa90-023c810e349d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:58:09,520] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg813fbf7f-70bc-49fd-aa90-023c810e349d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:58:09,527] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:58:09,528] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:58:09,528] [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
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	89.3623	1000	1230	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_017353495.1	2816859	2816859	type	True	89.3218	1001	1230	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	83.7591	857	1230	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	83.5512	844	1230	95	below_threshold
Arthrobacter gandavensis	strain=JCM 13316	GCA_009192735.1	169960	169960	type	True	83.5247	814	1230	95	below_threshold
Arthrobacter citreus	strain=DSM 20133	GCA_009192745.1	1670	1670	type	True	80.5182	564	1230	95	below_threshold
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	80.3279	572	1230	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:58:09,529] [INFO] DFAST Taxonomy check result was written to GCF_023022985.1_ASM2302298v1_genomic.fna/tc_result.tsv
[2024-01-24 12:58:09,530] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:58:09,530] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:58:09,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg813fbf7f-70bc-49fd-aa90-023c810e349d/dqc_reference/checkm_data
[2024-01-24 12:58:09,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:58:09,567] [INFO] Task started: CheckM
[2024-01-24 12:58:09,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023022985.1_ASM2302298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023022985.1_ASM2302298v1_genomic.fna/checkm_input GCF_023022985.1_ASM2302298v1_genomic.fna/checkm_result
[2024-01-24 12:58:44,600] [INFO] Task succeeded: CheckM
[2024-01-24 12:58:44,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:58:44,622] [INFO] ===== Completeness check finished =====
[2024-01-24 12:58:44,622] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:58:44,623] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023022985.1_ASM2302298v1_genomic.fna/markers.fasta)
[2024-01-24 12:58:44,623] [INFO] Task started: Blastn
[2024-01-24 12:58:44,623] [INFO] Running command: blastn -query GCF_023022985.1_ASM2302298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg813fbf7f-70bc-49fd-aa90-023c810e349d/dqc_reference/reference_markers_gtdb.fasta -out GCF_023022985.1_ASM2302298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:58:46,104] [INFO] Task succeeded: Blastn
[2024-01-24 12:58:46,108] [INFO] Selected 10 target genomes.
[2024-01-24 12:58:46,108] [INFO] Target genome list was writen to GCF_023022985.1_ASM2302298v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:58:46,133] [INFO] Task started: fastANI
[2024-01-24 12:58:46,134] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc3e364b-42b5-40ef-b7a5-5d858afb4412/GCF_023022985.1_ASM2302298v1_genomic.fna.gz --refList GCF_023022985.1_ASM2302298v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023022985.1_ASM2302298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:58:54,015] [INFO] Task succeeded: fastANI
[2024-01-24 12:58:54,025] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:58:54,026] [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_018866305.1	s__Arthrobacter_B sp002929435	89.3616	1000	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	98.36	96.67	0.94	0.92	8	-
GCF_018622995.1	s__Arthrobacter_B sp018622995	83.7679	857	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	99.13	98.27	0.96	0.92	3	-
GCF_009192735.1	s__Arthrobacter_B gandavensis	83.517	815	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009192775.1	s__Arthrobacter_B yangruifuii	81.3582	645	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	97.52	97.52	0.93	0.93	2	-
GCF_009192745.1	s__Arthrobacter_B citreus	80.5182	564	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307035.1	s__Arthrobacter_B sp001307035	80.3896	553	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	98.39	98.39	0.92	0.92	2	-
GCF_014836875.1	s__Arthrobacter_B sp014836875	80.3216	573	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	80.2056	617	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099975.1	s__Arthrobacter_G cupressi	78.7512	335	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015751665.1	s__Arthrobacter_D sp015751665	77.9962	308	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:58:54,031] [INFO] GTDB search result was written to GCF_023022985.1_ASM2302298v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:58:54,032] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:58:54,035] [INFO] DFAST_QC result json was written to GCF_023022985.1_ASM2302298v1_genomic.fna/dqc_result.json
[2024-01-24 12:58:54,035] [INFO] DFAST_QC completed!
[2024-01-24 12:58:54,035] [INFO] Total running time: 0h1m4s