[2024-01-24 14:22:01,737] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,740] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,740] [INFO] DQC Reference Directory: /var/lib/cwl/stg0580b9f9-f31a-4813-ad4f-0b3a9c401f2d/dqc_reference
[2024-01-24 14:22:02,957] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:02,960] [INFO] Task started: Prodigal
[2024-01-24 14:22:02,960] [INFO] Running command: gunzip -c /var/lib/cwl/stg39ed3dfe-13ab-4bf3-94c5-1b1d5a40401a/GCF_009828595.1_ASM982859v1_genomic.fna.gz | prodigal -d GCF_009828595.1_ASM982859v1_genomic.fna/cds.fna -a GCF_009828595.1_ASM982859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:13,808] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:13,808] [INFO] Task started: HMMsearch
[2024-01-24 14:22:13,809] [INFO] Running command: hmmsearch --tblout GCF_009828595.1_ASM982859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0580b9f9-f31a-4813-ad4f-0b3a9c401f2d/dqc_reference/reference_markers.hmm GCF_009828595.1_ASM982859v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:14,076] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:14,077] [INFO] Found 6/6 markers.
[2024-01-24 14:22:14,113] [INFO] Query marker FASTA was written to GCF_009828595.1_ASM982859v1_genomic.fna/markers.fasta
[2024-01-24 14:22:14,113] [INFO] Task started: Blastn
[2024-01-24 14:22:14,113] [INFO] Running command: blastn -query GCF_009828595.1_ASM982859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0580b9f9-f31a-4813-ad4f-0b3a9c401f2d/dqc_reference/reference_markers.fasta -out GCF_009828595.1_ASM982859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:15,317] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:15,320] [INFO] Selected 11 target genomes.
[2024-01-24 14:22:15,320] [INFO] Target genome list was writen to GCF_009828595.1_ASM982859v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:15,325] [INFO] Task started: fastANI
[2024-01-24 14:22:15,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg39ed3dfe-13ab-4bf3-94c5-1b1d5a40401a/GCF_009828595.1_ASM982859v1_genomic.fna.gz --refList GCF_009828595.1_ASM982859v1_genomic.fna/target_genomes.txt --output GCF_009828595.1_ASM982859v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:23,909] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:23,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0580b9f9-f31a-4813-ad4f-0b3a9c401f2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:23,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0580b9f9-f31a-4813-ad4f-0b3a9c401f2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:23,921] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:23,921] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:23,922] [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 zhaoguopingii	strain=J391	GCA_009828595.1	2681491	2681491	type	True	100.0	1261	1280	95	conclusive
Arthrobacter crusticola	strain=SLN-3	GCA_004357995.1	2547960	2547960	type	True	92.5706	1031	1280	95	below_threshold
Arthrobacter pityocampae	strain=Tp2	GCA_002927275.1	547334	547334	type	True	80.354	561	1280	95	below_threshold
Arthrobacter ruber	strain=MDB1-42	GCA_002954225.1	1258893	1258893	type	True	80.2717	559	1280	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	80.193	541	1280	95	below_threshold
Arthrobacter bussei	strain=KR32	GCA_009377195.2	2594179	2594179	type	True	80.0496	524	1280	95	below_threshold
Arthrobacter agilis	strain=DSM 20550	GCA_006494655.1	37921	37921	type	True	79.7366	509	1280	95	below_threshold
Arthrobacter cheniae	strain=Hz2	GCA_003602275.1	1258888	1258888	type	True	79.7165	513	1280	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	79.0446	380	1280	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	78.9478	388	1280	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.7224	401	1280	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:23,923] [INFO] DFAST Taxonomy check result was written to GCF_009828595.1_ASM982859v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:23,924] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:23,924] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:23,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0580b9f9-f31a-4813-ad4f-0b3a9c401f2d/dqc_reference/checkm_data
[2024-01-24 14:22:23,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:23,967] [INFO] Task started: CheckM
[2024-01-24 14:22:23,968] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009828595.1_ASM982859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009828595.1_ASM982859v1_genomic.fna/checkm_input GCF_009828595.1_ASM982859v1_genomic.fna/checkm_result
[2024-01-24 14:23:00,291] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:00,292] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:00,310] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:00,310] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:00,311] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009828595.1_ASM982859v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:00,311] [INFO] Task started: Blastn
[2024-01-24 14:23:00,311] [INFO] Running command: blastn -query GCF_009828595.1_ASM982859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0580b9f9-f31a-4813-ad4f-0b3a9c401f2d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009828595.1_ASM982859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:02,112] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:02,115] [INFO] Selected 8 target genomes.
[2024-01-24 14:23:02,115] [INFO] Target genome list was writen to GCF_009828595.1_ASM982859v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:02,123] [INFO] Task started: fastANI
[2024-01-24 14:23:02,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg39ed3dfe-13ab-4bf3-94c5-1b1d5a40401a/GCF_009828595.1_ASM982859v1_genomic.fna.gz --refList GCF_009828595.1_ASM982859v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009828595.1_ASM982859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:10,181] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:10,189] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:10,190] [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_009828595.1	s__Arthrobacter_D zhaoguopingii	100.0	1256	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	99.04	99.04	0.92	0.92	2	conclusive
GCF_016405885.1	s__Arthrobacter_D sp016405885	93.8269	1065	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602285.1	s__Arthrobacter_D sp003602285	93.111	1058	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	95.90	95.90	0.84	0.84	2	-
GCF_004357995.1	s__Arthrobacter_D crusticola	92.5706	1031	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929295.1	s__Arthrobacter_D sp002929295	80.4174	564	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929375.1	s__Arthrobacter_D sp002929375	80.3743	572	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002953615.1	s__Arthrobacter_D agilis_B	80.2491	506	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009377195.2	s__Arthrobacter_D bussei	80.0527	523	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.3875	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:10,192] [INFO] GTDB search result was written to GCF_009828595.1_ASM982859v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:10,192] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:10,196] [INFO] DFAST_QC result json was written to GCF_009828595.1_ASM982859v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:10,196] [INFO] DFAST_QC completed!
[2024-01-24 14:23:10,196] [INFO] Total running time: 0h1m8s