[2024-01-24 10:47:06,599] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,602] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,602] [INFO] DQC Reference Directory: /var/lib/cwl/stg815b3f1b-ba97-4d93-96be-4d0a8f8580e2/dqc_reference
[2024-01-24 10:47:12,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,802] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,802] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f994478-a9dd-410f-b268-7fe2dbb59b80/GCF_021049305.1_ASM2104930v1_genomic.fna.gz | prodigal -d GCF_021049305.1_ASM2104930v1_genomic.fna/cds.fna -a GCF_021049305.1_ASM2104930v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:27,746] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:27,747] [INFO] Task started: HMMsearch
[2024-01-24 10:47:27,747] [INFO] Running command: hmmsearch --tblout GCF_021049305.1_ASM2104930v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg815b3f1b-ba97-4d93-96be-4d0a8f8580e2/dqc_reference/reference_markers.hmm GCF_021049305.1_ASM2104930v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:28,047] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:28,049] [INFO] Found 6/6 markers.
[2024-01-24 10:47:28,097] [INFO] Query marker FASTA was written to GCF_021049305.1_ASM2104930v1_genomic.fna/markers.fasta
[2024-01-24 10:47:28,098] [INFO] Task started: Blastn
[2024-01-24 10:47:28,098] [INFO] Running command: blastn -query GCF_021049305.1_ASM2104930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg815b3f1b-ba97-4d93-96be-4d0a8f8580e2/dqc_reference/reference_markers.fasta -out GCF_021049305.1_ASM2104930v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:29,191] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:29,195] [INFO] Selected 12 target genomes.
[2024-01-24 10:47:29,195] [INFO] Target genome list was writen to GCF_021049305.1_ASM2104930v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:30,052] [INFO] Task started: fastANI
[2024-01-24 10:47:30,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f994478-a9dd-410f-b268-7fe2dbb59b80/GCF_021049305.1_ASM2104930v1_genomic.fna.gz --refList GCF_021049305.1_ASM2104930v1_genomic.fna/target_genomes.txt --output GCF_021049305.1_ASM2104930v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:47,060] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:47,060] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg815b3f1b-ba97-4d93-96be-4d0a8f8580e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:47,061] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg815b3f1b-ba97-4d93-96be-4d0a8f8580e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:47,072] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:47,072] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:47,073] [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 dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	100.0	1513	1514	95	conclusive
Ideonella dechloratans	strain=CCUG 30977	GCA_008801845.1	36863	36863	type	True	99.9318	1426	1514	95	conclusive
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	88.5921	1124	1514	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	82.2217	646	1514	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	81.3628	752	1514	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	80.9289	681	1514	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.8783	612	1514	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	80.5047	729	1514	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	80.2605	723	1514	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	79.9099	597	1514	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	79.6452	627	1514	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.4997	563	1514	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:47,074] [INFO] DFAST Taxonomy check result was written to GCF_021049305.1_ASM2104930v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:47,075] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:47,075] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:47,076] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg815b3f1b-ba97-4d93-96be-4d0a8f8580e2/dqc_reference/checkm_data
[2024-01-24 10:47:47,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:47,124] [INFO] Task started: CheckM
[2024-01-24 10:47:47,125] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021049305.1_ASM2104930v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021049305.1_ASM2104930v1_genomic.fna/checkm_input GCF_021049305.1_ASM2104930v1_genomic.fna/checkm_result
[2024-01-24 10:50:01,897] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:01,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:01,929] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:01,929] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:01,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021049305.1_ASM2104930v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:01,930] [INFO] Task started: Blastn
[2024-01-24 10:50:01,930] [INFO] Running command: blastn -query GCF_021049305.1_ASM2104930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg815b3f1b-ba97-4d93-96be-4d0a8f8580e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_021049305.1_ASM2104930v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:04,077] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:04,081] [INFO] Selected 11 target genomes.
[2024-01-24 10:50:04,081] [INFO] Target genome list was writen to GCF_021049305.1_ASM2104930v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:04,091] [INFO] Task started: fastANI
[2024-01-24 10:50:04,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f994478-a9dd-410f-b268-7fe2dbb59b80/GCF_021049305.1_ASM2104930v1_genomic.fna.gz --refList GCF_021049305.1_ASM2104930v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021049305.1_ASM2104930v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:16,947] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:16,961] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:16,962] [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_008801845.1	s__Ideonella dechloratans	99.9318	1426	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000333615.1	s__Ideonella sp000333615	93.0391	1002	1514	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	82.4935	847	1514	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	82.4626	828	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302485.1	s__Ideonella sp017302485	82.3606	548	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780145.1	s__Ideonella sp018780145	81.3941	743	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213265.1	s__Ideonella sp016213265	81.3587	725	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010499455.1	s__Ideonella sp010499455	81.3539	753	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017992055.1	s__Aquabacterium_A sp017992055	80.9407	810	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476235.1	s__Schlegelella thermodepolymerans	80.886	613	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella	95.0	99.89	99.68	0.98	0.95	4	-
GCF_009760915.1	s__Azohydromonas aeria	80.2127	729	1514	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:16,963] [INFO] GTDB search result was written to GCF_021049305.1_ASM2104930v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:16,966] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:16,971] [INFO] DFAST_QC result json was written to GCF_021049305.1_ASM2104930v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:16,971] [INFO] DFAST_QC completed!
[2024-01-24 10:50:16,971] [INFO] Total running time: 0h3m10s