[2024-01-24 12:13:28,550] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:28,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:28,552] [INFO] DQC Reference Directory: /var/lib/cwl/stgd39f908e-df27-4054-85d6-31e80140482f/dqc_reference
[2024-01-24 12:13:29,982] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:29,983] [INFO] Task started: Prodigal
[2024-01-24 12:13:29,983] [INFO] Running command: gunzip -c /var/lib/cwl/stg04d9fc16-333c-4a00-91de-e64ab74436fa/GCF_010499455.1_ASM1049945v1_genomic.fna.gz | prodigal -d GCF_010499455.1_ASM1049945v1_genomic.fna/cds.fna -a GCF_010499455.1_ASM1049945v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:48,391] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:48,391] [INFO] Task started: HMMsearch
[2024-01-24 12:13:48,391] [INFO] Running command: hmmsearch --tblout GCF_010499455.1_ASM1049945v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd39f908e-df27-4054-85d6-31e80140482f/dqc_reference/reference_markers.hmm GCF_010499455.1_ASM1049945v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:48,746] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:48,747] [INFO] Found 6/6 markers.
[2024-01-24 12:13:48,803] [INFO] Query marker FASTA was written to GCF_010499455.1_ASM1049945v1_genomic.fna/markers.fasta
[2024-01-24 12:13:48,803] [INFO] Task started: Blastn
[2024-01-24 12:13:48,803] [INFO] Running command: blastn -query GCF_010499455.1_ASM1049945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd39f908e-df27-4054-85d6-31e80140482f/dqc_reference/reference_markers.fasta -out GCF_010499455.1_ASM1049945v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:49,864] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:49,868] [INFO] Selected 15 target genomes.
[2024-01-24 12:13:49,868] [INFO] Target genome list was writen to GCF_010499455.1_ASM1049945v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:49,877] [INFO] Task started: fastANI
[2024-01-24 12:13:49,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg04d9fc16-333c-4a00-91de-e64ab74436fa/GCF_010499455.1_ASM1049945v1_genomic.fna.gz --refList GCF_010499455.1_ASM1049945v1_genomic.fna/target_genomes.txt --output GCF_010499455.1_ASM1049945v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:06,981] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:06,982] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd39f908e-df27-4054-85d6-31e80140482f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:06,982] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd39f908e-df27-4054-85d6-31e80140482f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:06,998] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:06,999] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:06,999] [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
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	100.0	1701	1702	95	conclusive
Ideonella dechloratans	strain=CCUG 30977	GCA_008801845.1	36863	36863	type	True	81.409	732	1702	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	81.402	763	1702	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	81.2229	721	1702	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	80.6965	684	1702	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	80.5396	753	1702	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	80.5189	591	1702	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	79.6844	774	1702	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	79.6679	774	1702	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	79.4912	792	1702	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	79.3813	597	1702	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	79.3611	592	1702	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	79.3572	589	1702	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	78.8347	539	1702	95	below_threshold
Inhella proteolytica	strain=1Y17	GCA_016093275.1	2795029	2795029	type	True	78.5642	612	1702	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:07,000] [INFO] DFAST Taxonomy check result was written to GCF_010499455.1_ASM1049945v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:07,001] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:07,001] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:07,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd39f908e-df27-4054-85d6-31e80140482f/dqc_reference/checkm_data
[2024-01-24 12:14:07,002] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:07,051] [INFO] Task started: CheckM
[2024-01-24 12:14:07,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010499455.1_ASM1049945v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010499455.1_ASM1049945v1_genomic.fna/checkm_input GCF_010499455.1_ASM1049945v1_genomic.fna/checkm_result
[2024-01-24 12:15:59,721] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:59,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:59,741] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:59,742] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:59,742] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010499455.1_ASM1049945v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:59,743] [INFO] Task started: Blastn
[2024-01-24 12:15:59,743] [INFO] Running command: blastn -query GCF_010499455.1_ASM1049945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd39f908e-df27-4054-85d6-31e80140482f/dqc_reference/reference_markers_gtdb.fasta -out GCF_010499455.1_ASM1049945v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:01,947] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:01,951] [INFO] Selected 11 target genomes.
[2024-01-24 12:16:01,951] [INFO] Target genome list was writen to GCF_010499455.1_ASM1049945v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:01,961] [INFO] Task started: fastANI
[2024-01-24 12:16:01,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg04d9fc16-333c-4a00-91de-e64ab74436fa/GCF_010499455.1_ASM1049945v1_genomic.fna.gz --refList GCF_010499455.1_ASM1049945v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010499455.1_ASM1049945v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:14,697] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:14,707] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:14,707] [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_010499455.1	s__Ideonella sp010499455	100.0	1701	1702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017302485.1	s__Ideonella sp017302485	81.9372	524	1702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069875.1	s__Ideonella sp018069875	81.501	874	1702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCF_018069755.1	s__Ideonella sp018069755	81.4714	849	1702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008801845.1	s__Ideonella dechloratans	81.417	731	1702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333615.1	s__Ideonella sp000333615	81.2629	677	1702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201595.1	s__Sphaerotilus hippei	80.5785	749	1702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213265.1	s__Ideonella sp016213265	80.4326	686	1702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927045.1	s__Azohydromonas caseinilytica	79.744	765	1702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571085.1	s__Azohydromonas lata	79.6384	729	1702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213205.1	s__Aquabacterium_A sp016213205	79.3129	732	1702	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:14,710] [INFO] GTDB search result was written to GCF_010499455.1_ASM1049945v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:14,711] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:14,716] [INFO] DFAST_QC result json was written to GCF_010499455.1_ASM1049945v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:14,717] [INFO] DFAST_QC completed!
[2024-01-24 12:16:14,717] [INFO] Total running time: 0h2m46s