[2024-01-24 14:05:49,149] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:49,151] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:49,151] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a339fe8-fae5-45d9-9216-415c87e9566e/dqc_reference
[2024-01-24 14:05:50,418] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:50,419] [INFO] Task started: Prodigal
[2024-01-24 14:05:50,419] [INFO] Running command: gunzip -c /var/lib/cwl/stgd07ef162-0268-4a77-927a-c3ec539305ac/GCF_023921125.1_ASM2392112v1_genomic.fna.gz | prodigal -d GCF_023921125.1_ASM2392112v1_genomic.fna/cds.fna -a GCF_023921125.1_ASM2392112v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:02,287] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:02,288] [INFO] Task started: HMMsearch
[2024-01-24 14:06:02,288] [INFO] Running command: hmmsearch --tblout GCF_023921125.1_ASM2392112v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a339fe8-fae5-45d9-9216-415c87e9566e/dqc_reference/reference_markers.hmm GCF_023921125.1_ASM2392112v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:02,602] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:02,604] [INFO] Found 6/6 markers.
[2024-01-24 14:06:02,641] [INFO] Query marker FASTA was written to GCF_023921125.1_ASM2392112v1_genomic.fna/markers.fasta
[2024-01-24 14:06:02,641] [INFO] Task started: Blastn
[2024-01-24 14:06:02,642] [INFO] Running command: blastn -query GCF_023921125.1_ASM2392112v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a339fe8-fae5-45d9-9216-415c87e9566e/dqc_reference/reference_markers.fasta -out GCF_023921125.1_ASM2392112v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:03,797] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:03,801] [INFO] Selected 11 target genomes.
[2024-01-24 14:06:03,801] [INFO] Target genome list was writen to GCF_023921125.1_ASM2392112v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:03,803] [INFO] Task started: fastANI
[2024-01-24 14:06:03,803] [INFO] Running command: fastANI --query /var/lib/cwl/stgd07ef162-0268-4a77-927a-c3ec539305ac/GCF_023921125.1_ASM2392112v1_genomic.fna.gz --refList GCF_023921125.1_ASM2392112v1_genomic.fna/target_genomes.txt --output GCF_023921125.1_ASM2392112v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:12,947] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:12,948] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a339fe8-fae5-45d9-9216-415c87e9566e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:12,948] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a339fe8-fae5-45d9-9216-415c87e9566e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:12,958] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:12,958] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:12,958] [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 citreus	strain=DSM 20133	GCA_009192745.1	1670	1670	type	True	83.7051	876	1309	95	below_threshold
Arthrobacter koreensis	strain=DSM 16760	GCA_009193255.1	199136	199136	type	True	83.0577	812	1309	95	below_threshold
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	82.4024	809	1309	95	below_threshold
Arthrobacter luteolus	strain=DSM 13067	GCA_008973725.1	98672	98672	type	True	82.3484	822	1309	95	below_threshold
Arthrobacter luteolus	strain=NBRC 107841	GCA_001552075.1	98672	98672	type	True	82.2816	817	1309	95	below_threshold
Arthrobacter gallicola	strain=Sa2CUA1	GCA_014836775.1	2762225	2762225	type	True	82.2322	743	1309	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	80.7667	612	1309	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	80.6404	559	1309	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	80.594	611	1309	95	below_threshold
Arthrobacter celericrescens	strain=NEAU-SA2	GCA_003614925.1	2320851	2320851	type	True	78.6675	352	1309	95	below_threshold
Arthrobacter terricola	strain=JH1-1	GCA_004354015.1	2547396	2547396	type	True	78.0252	265	1309	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:12,960] [INFO] DFAST Taxonomy check result was written to GCF_023921125.1_ASM2392112v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:12,960] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:12,960] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:12,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a339fe8-fae5-45d9-9216-415c87e9566e/dqc_reference/checkm_data
[2024-01-24 14:06:12,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:13,006] [INFO] Task started: CheckM
[2024-01-24 14:06:13,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023921125.1_ASM2392112v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023921125.1_ASM2392112v1_genomic.fna/checkm_input GCF_023921125.1_ASM2392112v1_genomic.fna/checkm_result
[2024-01-24 14:06:51,419] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:51,420] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:51,444] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:51,444] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:51,445] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023921125.1_ASM2392112v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:51,445] [INFO] Task started: Blastn
[2024-01-24 14:06:51,445] [INFO] Running command: blastn -query GCF_023921125.1_ASM2392112v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a339fe8-fae5-45d9-9216-415c87e9566e/dqc_reference/reference_markers_gtdb.fasta -out GCF_023921125.1_ASM2392112v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:53,075] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:53,079] [INFO] Selected 10 target genomes.
[2024-01-24 14:06:53,079] [INFO] Target genome list was writen to GCF_023921125.1_ASM2392112v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:53,082] [INFO] Task started: fastANI
[2024-01-24 14:06:53,083] [INFO] Running command: fastANI --query /var/lib/cwl/stgd07ef162-0268-4a77-927a-c3ec539305ac/GCF_023921125.1_ASM2392112v1_genomic.fna.gz --refList GCF_023921125.1_ASM2392112v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023921125.1_ASM2392112v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:01,152] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:01,165] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:07:01,166] [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_009192745.1	s__Arthrobacter_B citreus	83.7091	875	1309	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_015355785.1	s__Arthrobacter_B gandavensis_A	83.2295	791	1309	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	83.1873	853	1309	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_009193255.1	s__Arthrobacter_B koreensis	83.0681	811	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	99.08	99.08	0.97	0.97	2	-
GCF_014836875.1	s__Arthrobacter_B sp014836875	82.4069	809	1309	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_001552075.1	s__Arthrobacter_B luteolus	82.301	815	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014836775.1	s__Arthrobacter_B sp014836775	82.2353	742	1309	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	80.2992	635	1309	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_002892795.1	s__Arthrobacter sp002892795	78.6666	351	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614925.1	s__Arthrobacter_G celericrescens	78.6513	354	1309	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:01,167] [INFO] GTDB search result was written to GCF_023921125.1_ASM2392112v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:01,167] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:01,171] [INFO] DFAST_QC result json was written to GCF_023921125.1_ASM2392112v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:01,171] [INFO] DFAST_QC completed!
[2024-01-24 14:07:01,171] [INFO] Total running time: 0h1m12s