[2023-06-08 17:08:59,919] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:08:59,924] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:08:59,925] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f781db3-2b14-41f2-bad0-def6fdfacdcc/dqc_reference
[2023-06-08 17:09:01,219] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:09:01,220] [INFO] Task started: Prodigal
[2023-06-08 17:09:01,220] [INFO] Running command: gunzip -c /var/lib/cwl/stg430fc76f-ddc2-4af8-8e59-8a42fe6159f8/GCA_945878385.1_MsE-30jul19-236_genomic.fna.gz | prodigal -d GCA_945878385.1_MsE-30jul19-236_genomic.fna/cds.fna -a GCA_945878385.1_MsE-30jul19-236_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:09:09,656] [INFO] Task succeeded: Prodigal
[2023-06-08 17:09:09,656] [INFO] Task started: HMMsearch
[2023-06-08 17:09:09,657] [INFO] Running command: hmmsearch --tblout GCA_945878385.1_MsE-30jul19-236_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f781db3-2b14-41f2-bad0-def6fdfacdcc/dqc_reference/reference_markers.hmm GCA_945878385.1_MsE-30jul19-236_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:09:09,980] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:09:09,984] [INFO] Found 6/6 markers.
[2023-06-08 17:09:10,021] [INFO] Query marker FASTA was written to GCA_945878385.1_MsE-30jul19-236_genomic.fna/markers.fasta
[2023-06-08 17:09:10,021] [INFO] Task started: Blastn
[2023-06-08 17:09:10,022] [INFO] Running command: blastn -query GCA_945878385.1_MsE-30jul19-236_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f781db3-2b14-41f2-bad0-def6fdfacdcc/dqc_reference/reference_markers.fasta -out GCA_945878385.1_MsE-30jul19-236_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:09:10,889] [INFO] Task succeeded: Blastn
[2023-06-08 17:09:10,903] [INFO] Selected 19 target genomes.
[2023-06-08 17:09:10,903] [INFO] Target genome list was writen to GCA_945878385.1_MsE-30jul19-236_genomic.fna/target_genomes.txt
[2023-06-08 17:09:10,905] [INFO] Task started: fastANI
[2023-06-08 17:09:10,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg430fc76f-ddc2-4af8-8e59-8a42fe6159f8/GCA_945878385.1_MsE-30jul19-236_genomic.fna.gz --refList GCA_945878385.1_MsE-30jul19-236_genomic.fna/target_genomes.txt --output GCA_945878385.1_MsE-30jul19-236_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:09:27,972] [INFO] Task succeeded: fastANI
[2023-06-08 17:09:27,973] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f781db3-2b14-41f2-bad0-def6fdfacdcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:09:27,973] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f781db3-2b14-41f2-bad0-def6fdfacdcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:09:27,988] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 17:09:27,989] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 17:09:27,989] [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	79.613	311	729	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.5187	319	729	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	79.4889	332	729	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.3339	305	729	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	79.2908	360	729	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	79.1722	360	729	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	79.1589	260	729	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	79.1198	358	729	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	79.0172	313	729	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	78.9948	253	729	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	78.9043	296	729	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	78.8808	295	729	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	78.7234	306	729	95	below_threshold
Inhella proteolytica	strain=1Y17	GCA_016093275.1	2795029	2795029	type	True	78.6991	301	729	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	78.6706	301	729	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	78.6158	306	729	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	78.4054	300	729	95	below_threshold
Roseateles terrae	strain=CECT 7247	GCA_014192155.1	431060	431060	type	True	78.3765	269	729	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.1441	294	729	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 17:09:27,991] [INFO] DFAST Taxonomy check result was written to GCA_945878385.1_MsE-30jul19-236_genomic.fna/tc_result.tsv
[2023-06-08 17:09:27,992] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:09:27,992] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:09:27,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f781db3-2b14-41f2-bad0-def6fdfacdcc/dqc_reference/checkm_data
[2023-06-08 17:09:27,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:09:28,028] [INFO] Task started: CheckM
[2023-06-08 17:09:28,029] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945878385.1_MsE-30jul19-236_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945878385.1_MsE-30jul19-236_genomic.fna/checkm_input GCA_945878385.1_MsE-30jul19-236_genomic.fna/checkm_result
[2023-06-08 17:10:03,864] [INFO] Task succeeded: CheckM
[2023-06-08 17:10:03,865] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 17:10:03,888] [INFO] ===== Completeness check finished =====
[2023-06-08 17:10:03,888] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:10:03,889] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945878385.1_MsE-30jul19-236_genomic.fna/markers.fasta)
[2023-06-08 17:10:03,889] [INFO] Task started: Blastn
[2023-06-08 17:10:03,889] [INFO] Running command: blastn -query GCA_945878385.1_MsE-30jul19-236_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f781db3-2b14-41f2-bad0-def6fdfacdcc/dqc_reference/reference_markers_gtdb.fasta -out GCA_945878385.1_MsE-30jul19-236_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:10:05,508] [INFO] Task succeeded: Blastn
[2023-06-08 17:10:05,513] [INFO] Selected 14 target genomes.
[2023-06-08 17:10:05,514] [INFO] Target genome list was writen to GCA_945878385.1_MsE-30jul19-236_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:10:05,584] [INFO] Task started: fastANI
[2023-06-08 17:10:05,585] [INFO] Running command: fastANI --query /var/lib/cwl/stg430fc76f-ddc2-4af8-8e59-8a42fe6159f8/GCA_945878385.1_MsE-30jul19-236_genomic.fna.gz --refList GCA_945878385.1_MsE-30jul19-236_genomic.fna/target_genomes_gtdb.txt --output GCA_945878385.1_MsE-30jul19-236_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:10:15,988] [INFO] Task succeeded: fastANI
[2023-06-08 17:10:16,007] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 17:10:16,007] [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
GCA_009923315.1	s__RFTU01 sp009923315	82.4969	475	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RFTU01	95.0	99.55	99.38	0.93	0.92	4	-
GCA_009925955.1	s__RFTU01 sp009925955	82.3782	240	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RFTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009918225.1	s__RFTU01 sp009918225	81.3	335	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RFTU01	95.0	98.76	98.76	0.88	0.88	2	-
GCA_016868355.1	s__RFTU01 sp016868355	80.5903	445	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RFTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969605.1	s__Aquincola tertiaricarbonis	79.6096	369	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008801845.1	s__Ideonella dechloratans	79.587	314	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571085.1	s__Azohydromonas lata	79.489	332	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302505.1	s__Rubrivivax sp017302505	79.4446	292	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000244995.1	s__Aquabacterium_A sp000244995	79.364	392	729	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_012927045.1	s__Azohydromonas caseinilytica	79.1328	357	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213265.1	s__Ideonella sp016213265	78.9942	327	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476235.1	s__Schlegelella thermodepolymerans	78.6163	306	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella	95.0	99.89	99.68	0.98	0.95	4	-
GCF_003574675.1	s__Calidifontimicrobium sediminis	78.565	283	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Calidifontimicrobium	95.0	96.54	96.54	0.86	0.86	2	-
GCF_000768065.1	s__Aquabacterium sp000768065	78.4028	248	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 17:10:16,010] [INFO] GTDB search result was written to GCA_945878385.1_MsE-30jul19-236_genomic.fna/result_gtdb.tsv
[2023-06-08 17:10:16,010] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:10:16,014] [INFO] DFAST_QC result json was written to GCA_945878385.1_MsE-30jul19-236_genomic.fna/dqc_result.json
[2023-06-08 17:10:16,014] [INFO] DFAST_QC completed!
[2023-06-08 17:10:16,014] [INFO] Total running time: 0h1m16s