[2024-01-24 12:06:14,112] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,114] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,115] [INFO] DQC Reference Directory: /var/lib/cwl/stg94cd8cee-ef4b-4328-be01-731039790995/dqc_reference
[2024-01-24 12:06:15,509] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,510] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,510] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3d80d1f-4fbb-4d6b-bc02-1576c7ab3ee1/GCF_028595305.1_ASM2859530v1_genomic.fna.gz | prodigal -d GCF_028595305.1_ASM2859530v1_genomic.fna/cds.fna -a GCF_028595305.1_ASM2859530v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:32,646] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:32,647] [INFO] Task started: HMMsearch
[2024-01-24 12:06:32,647] [INFO] Running command: hmmsearch --tblout GCF_028595305.1_ASM2859530v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94cd8cee-ef4b-4328-be01-731039790995/dqc_reference/reference_markers.hmm GCF_028595305.1_ASM2859530v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:32,992] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:32,993] [INFO] Found 6/6 markers.
[2024-01-24 12:06:33,035] [INFO] Query marker FASTA was written to GCF_028595305.1_ASM2859530v1_genomic.fna/markers.fasta
[2024-01-24 12:06:33,036] [INFO] Task started: Blastn
[2024-01-24 12:06:33,036] [INFO] Running command: blastn -query GCF_028595305.1_ASM2859530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94cd8cee-ef4b-4328-be01-731039790995/dqc_reference/reference_markers.fasta -out GCF_028595305.1_ASM2859530v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:33,860] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:33,864] [INFO] Selected 20 target genomes.
[2024-01-24 12:06:33,864] [INFO] Target genome list was writen to GCF_028595305.1_ASM2859530v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:33,875] [INFO] Task started: fastANI
[2024-01-24 12:06:33,875] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3d80d1f-4fbb-4d6b-bc02-1576c7ab3ee1/GCF_028595305.1_ASM2859530v1_genomic.fna.gz --refList GCF_028595305.1_ASM2859530v1_genomic.fna/target_genomes.txt --output GCF_028595305.1_ASM2859530v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:53,802] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:53,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94cd8cee-ef4b-4328-be01-731039790995/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:53,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94cd8cee-ef4b-4328-be01-731039790995/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:53,820] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:06:53,820] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:06:53,821] [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
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	79.027	505	1439	95	below_threshold
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	78.9886	542	1439	95	below_threshold
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	78.9627	478	1439	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	78.9243	511	1439	95	below_threshold
Roseateles terrae	strain=CECT 7247	GCA_014192155.1	431060	431060	type	True	78.8727	445	1439	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	78.8564	336	1439	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	78.7644	445	1439	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	78.6638	394	1439	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	78.6039	366	1439	95	below_threshold
Ideonella paludis	strain=KCTC 32238	GCA_018069865.1	1233411	1233411	type	True	78.3037	355	1439	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	78.1684	305	1439	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	78.1153	311	1439	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	78.088	309	1439	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	78.0575	314	1439	95	below_threshold
Rhizobacter gummiphilus	strain=NS21	GCA_002116905.1	946333	946333	type	True	78.0575	314	1439	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	78.0569	338	1439	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	77.6106	257	1439	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	77.4372	204	1439	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	77.3809	260	1439	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	77.3288	262	1439	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:53,829] [INFO] DFAST Taxonomy check result was written to GCF_028595305.1_ASM2859530v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:53,830] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:53,830] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:53,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94cd8cee-ef4b-4328-be01-731039790995/dqc_reference/checkm_data
[2024-01-24 12:06:53,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:53,889] [INFO] Task started: CheckM
[2024-01-24 12:06:53,889] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028595305.1_ASM2859530v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028595305.1_ASM2859530v1_genomic.fna/checkm_input GCF_028595305.1_ASM2859530v1_genomic.fna/checkm_result
[2024-01-24 12:07:49,540] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:49,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:49,569] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:49,569] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:49,570] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028595305.1_ASM2859530v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:49,570] [INFO] Task started: Blastn
[2024-01-24 12:07:49,570] [INFO] Running command: blastn -query GCF_028595305.1_ASM2859530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94cd8cee-ef4b-4328-be01-731039790995/dqc_reference/reference_markers_gtdb.fasta -out GCF_028595305.1_ASM2859530v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:50,850] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:50,855] [INFO] Selected 14 target genomes.
[2024-01-24 12:07:50,855] [INFO] Target genome list was writen to GCF_028595305.1_ASM2859530v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:50,869] [INFO] Task started: fastANI
[2024-01-24 12:07:50,869] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3d80d1f-4fbb-4d6b-bc02-1576c7ab3ee1/GCF_028595305.1_ASM2859530v1_genomic.fna.gz --refList GCF_028595305.1_ASM2859530v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028595305.1_ASM2859530v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:06,971] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:06,990] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:08:06,990] [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_001477625.1	s__Paucibacter_A sp001477625	81.5079	835	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204525.1	s__Paucibacter_A oligotrophus	81.2962	797	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852425.1	s__Paucibacter_A sp003852425	81.0993	814	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255955.1	s__Paucibacter_A sp002255955	80.3817	669	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002885975.1	s__Paucibacter_A aquatile	80.2225	670	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503085.1	s__Paucibacter_A sp005503085	79.7005	603	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013824165.1	s__Kinneretia sp013824165	79.2683	521	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kinneretia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984095.1	s__KK5 sp001984095	79.2087	537	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__KK5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002205845.1	s__Pelomonas puraquae	78.9243	511	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002205125.1	s__Mitsuaria noduli	78.9024	426	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780415.1	s__Paucibacter_A sp018780415	78.7811	527	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963005.1	s__Pelomonas sp003963005	78.4292	439	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016505.1	s__Rubrivivax rivuli	78.2413	368	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002116905.1	s__Rhizobacter gummiphilus	78.0462	315	1439	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:06,992] [INFO] GTDB search result was written to GCF_028595305.1_ASM2859530v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:06,993] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:06,997] [INFO] DFAST_QC result json was written to GCF_028595305.1_ASM2859530v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:06,998] [INFO] DFAST_QC completed!
[2024-01-24 12:08:06,998] [INFO] Total running time: 0h1m53s