[2024-01-24 13:58:25,446] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:25,448] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:25,448] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3c7adf0-fb05-4a08-8f01-5183e7cb3821/dqc_reference
[2024-01-24 13:58:26,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:26,765] [INFO] Task started: Prodigal
[2024-01-24 13:58:26,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg426f2eca-873d-40ab-ae9c-3089a47f374f/GCF_018069755.1_ASM1806975v1_genomic.fna.gz | prodigal -d GCF_018069755.1_ASM1806975v1_genomic.fna/cds.fna -a GCF_018069755.1_ASM1806975v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:43,466] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:43,467] [INFO] Task started: HMMsearch
[2024-01-24 13:58:43,467] [INFO] Running command: hmmsearch --tblout GCF_018069755.1_ASM1806975v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3c7adf0-fb05-4a08-8f01-5183e7cb3821/dqc_reference/reference_markers.hmm GCF_018069755.1_ASM1806975v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:43,834] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:43,835] [INFO] Found 6/6 markers.
[2024-01-24 13:58:43,884] [INFO] Query marker FASTA was written to GCF_018069755.1_ASM1806975v1_genomic.fna/markers.fasta
[2024-01-24 13:58:43,884] [INFO] Task started: Blastn
[2024-01-24 13:58:43,884] [INFO] Running command: blastn -query GCF_018069755.1_ASM1806975v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3c7adf0-fb05-4a08-8f01-5183e7cb3821/dqc_reference/reference_markers.fasta -out GCF_018069755.1_ASM1806975v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:45,115] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:45,120] [INFO] Selected 13 target genomes.
[2024-01-24 13:58:45,121] [INFO] Target genome list was writen to GCF_018069755.1_ASM1806975v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:45,135] [INFO] Task started: fastANI
[2024-01-24 13:58:45,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg426f2eca-873d-40ab-ae9c-3089a47f374f/GCF_018069755.1_ASM1806975v1_genomic.fna.gz --refList GCF_018069755.1_ASM1806975v1_genomic.fna/target_genomes.txt --output GCF_018069755.1_ASM1806975v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:59,146] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:59,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3c7adf0-fb05-4a08-8f01-5183e7cb3821/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:59,147] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3c7adf0-fb05-4a08-8f01-5183e7cb3821/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:59,164] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:59,164] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:59,165] [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_008801845.1	36863	36863	type	True	82.336	815	1692	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	82.3164	831	1692	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	81.8996	782	1692	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	81.7954	662	1692	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	81.5703	839	1692	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	81.3166	761	1692	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	81.2982	784	1692	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	81.1951	786	1692	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	80.7892	681	1692	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.7589	702	1692	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	80.716	686	1692	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	79.536	615	1692	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	79.3234	656	1692	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:59,166] [INFO] DFAST Taxonomy check result was written to GCF_018069755.1_ASM1806975v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:59,167] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:59,167] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:59,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3c7adf0-fb05-4a08-8f01-5183e7cb3821/dqc_reference/checkm_data
[2024-01-24 13:58:59,168] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:59,216] [INFO] Task started: CheckM
[2024-01-24 13:58:59,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018069755.1_ASM1806975v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018069755.1_ASM1806975v1_genomic.fna/checkm_input GCF_018069755.1_ASM1806975v1_genomic.fna/checkm_result
[2024-01-24 14:01:00,580] [INFO] Task succeeded: CheckM
[2024-01-24 14:01:00,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:01:00,606] [INFO] ===== Completeness check finished =====
[2024-01-24 14:01:00,606] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:01:00,607] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018069755.1_ASM1806975v1_genomic.fna/markers.fasta)
[2024-01-24 14:01:00,607] [INFO] Task started: Blastn
[2024-01-24 14:01:00,607] [INFO] Running command: blastn -query GCF_018069755.1_ASM1806975v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3c7adf0-fb05-4a08-8f01-5183e7cb3821/dqc_reference/reference_markers_gtdb.fasta -out GCF_018069755.1_ASM1806975v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:01:03,108] [INFO] Task succeeded: Blastn
[2024-01-24 14:01:03,113] [INFO] Selected 14 target genomes.
[2024-01-24 14:01:03,113] [INFO] Target genome list was writen to GCF_018069755.1_ASM1806975v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:01:03,124] [INFO] Task started: fastANI
[2024-01-24 14:01:03,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg426f2eca-873d-40ab-ae9c-3089a47f374f/GCF_018069755.1_ASM1806975v1_genomic.fna.gz --refList GCF_018069755.1_ASM1806975v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018069755.1_ASM1806975v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:19,895] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:19,914] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:19,914] [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_018069755.1	s__Ideonella sp018069755	100.0	1687	1692	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_018069875.1	s__Ideonella sp018069875	92.8189	1466	1692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCA_017302485.1	s__Ideonella sp017302485	89.7868	795	1692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710065.1	s__Ideonella sp016710065	82.3777	908	1692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	99.07	99.00	0.95	0.93	3	-
GCF_008801845.1	s__Ideonella dechloratans	82.2716	822	1692	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	82.0785	693	1692	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	81.8498	868	1692	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	81.7384	772	1692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255925.1	s__Ideonella sp002255925	81.6734	805	1692	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	81.6123	837	1692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770815.1	s__Aquabacterium_A sp001770815	81.1705	823	1692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302505.1	s__Rubrivivax sp017302505	80.9242	648	1692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	80.7439	810	1692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017999135.1	s__Aquabacterium_A sp017999135	80.4451	566	1692	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 14:01:19,915] [INFO] GTDB search result was written to GCF_018069755.1_ASM1806975v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:19,916] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:19,919] [INFO] DFAST_QC result json was written to GCF_018069755.1_ASM1806975v1_genomic.fna/dqc_result.json
[2024-01-24 14:01:19,919] [INFO] DFAST_QC completed!
[2024-01-24 14:01:19,920] [INFO] Total running time: 0h2m54s