[2023-06-28 02:42:32,151] [INFO] DFAST_QC pipeline started.
[2023-06-28 02:42:32,154] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 02:42:32,154] [INFO] DQC Reference Directory: /var/lib/cwl/stg4308be0f-cb36-445b-b7cd-abd73cd9e714/dqc_reference
[2023-06-28 02:42:33,448] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 02:42:33,449] [INFO] Task started: Prodigal
[2023-06-28 02:42:33,449] [INFO] Running command: gunzip -c /var/lib/cwl/stga8af6992-1dc6-4e08-bc05-27b7bf7f7ef1/GCA_019634985.1_ASM1963498v1_genomic.fna.gz | prodigal -d GCA_019634985.1_ASM1963498v1_genomic.fna/cds.fna -a GCA_019634985.1_ASM1963498v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 02:42:45,459] [INFO] Task succeeded: Prodigal
[2023-06-28 02:42:45,459] [INFO] Task started: HMMsearch
[2023-06-28 02:42:45,460] [INFO] Running command: hmmsearch --tblout GCA_019634985.1_ASM1963498v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4308be0f-cb36-445b-b7cd-abd73cd9e714/dqc_reference/reference_markers.hmm GCA_019634985.1_ASM1963498v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 02:42:45,771] [INFO] Task succeeded: HMMsearch
[2023-06-28 02:42:45,772] [INFO] Found 6/6 markers.
[2023-06-28 02:42:45,810] [INFO] Query marker FASTA was written to GCA_019634985.1_ASM1963498v1_genomic.fna/markers.fasta
[2023-06-28 02:42:45,811] [INFO] Task started: Blastn
[2023-06-28 02:42:45,811] [INFO] Running command: blastn -query GCA_019634985.1_ASM1963498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4308be0f-cb36-445b-b7cd-abd73cd9e714/dqc_reference/reference_markers.fasta -out GCA_019634985.1_ASM1963498v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:42:46,851] [INFO] Task succeeded: Blastn
[2023-06-28 02:42:46,855] [INFO] Selected 27 target genomes.
[2023-06-28 02:42:46,855] [INFO] Target genome list was writen to GCA_019634985.1_ASM1963498v1_genomic.fna/target_genomes.txt
[2023-06-28 02:42:46,859] [INFO] Task started: fastANI
[2023-06-28 02:42:46,860] [INFO] Running command: fastANI --query /var/lib/cwl/stga8af6992-1dc6-4e08-bc05-27b7bf7f7ef1/GCA_019634985.1_ASM1963498v1_genomic.fna.gz --refList GCA_019634985.1_ASM1963498v1_genomic.fna/target_genomes.txt --output GCA_019634985.1_ASM1963498v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 02:43:09,156] [INFO] Task succeeded: fastANI
[2023-06-28 02:43:09,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4308be0f-cb36-445b-b7cd-abd73cd9e714/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 02:43:09,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4308be0f-cb36-445b-b7cd-abd73cd9e714/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 02:43:09,180] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 02:43:09,181] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 02:43:09,181] [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
Usitatibacter rugosus	strain=0125_3	GCA_013003965.1	2732067	2732067	type	True	80.6135	635	1357	95	below_threshold
Usitatibacter palustris	strain=Swamp67	GCA_013003985.1	2732487	2732487	type	True	79.8848	615	1357	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	77.6669	266	1357	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	77.6459	272	1357	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	77.2229	326	1357	95	below_threshold
Aromatoleum evansii	strain=KB740	GCA_012910805.1	59406	59406	type	True	76.8916	289	1357	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	76.7917	260	1357	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	76.6534	366	1357	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	76.6391	349	1357	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	76.5287	398	1357	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	76.4786	228	1357	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	76.4663	406	1357	95	below_threshold
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	76.4639	226	1357	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_017894385.1	76116	76116	type	True	76.443	270	1357	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_012910985.1	76116	76116	type	True	76.3865	266	1357	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.3334	284	1357	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	76.3215	305	1357	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	76.2784	245	1357	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.1145	406	1357	95	below_threshold
Propionivibrio dicarboxylicus	strain=DSM 5885	GCA_900099695.1	83767	83767	type	True	76.0439	121	1357	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	76.0357	182	1357	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	75.9288	247	1357	95	below_threshold
Burkholderia mallei	strain=ATCC 23344	GCA_000011705.1	13373	13373	type	True	75.8878	337	1357	95	below_threshold
Burkholderia pseudomallei	strain=ATCC 23343	GCA_001182285.1	28450	28450	type	True	75.7496	376	1357	95	below_threshold
Rivicola pingtungensis	strain=DSM 29661	GCA_003201855.1	1054498	1054498	type	True	75.6705	109	1357	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	75.652	167	1357	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	75.1609	133	1357	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 02:43:09,183] [INFO] DFAST Taxonomy check result was written to GCA_019634985.1_ASM1963498v1_genomic.fna/tc_result.tsv
[2023-06-28 02:43:09,184] [INFO] ===== Taxonomy check completed =====
[2023-06-28 02:43:09,184] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 02:43:09,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4308be0f-cb36-445b-b7cd-abd73cd9e714/dqc_reference/checkm_data
[2023-06-28 02:43:09,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 02:43:09,235] [INFO] Task started: CheckM
[2023-06-28 02:43:09,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019634985.1_ASM1963498v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019634985.1_ASM1963498v1_genomic.fna/checkm_input GCA_019634985.1_ASM1963498v1_genomic.fna/checkm_result
[2023-06-28 02:43:50,342] [INFO] Task succeeded: CheckM
[2023-06-28 02:43:50,344] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 02:43:50,366] [INFO] ===== Completeness check finished =====
[2023-06-28 02:43:50,366] [INFO] ===== Start GTDB Search =====
[2023-06-28 02:43:50,367] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019634985.1_ASM1963498v1_genomic.fna/markers.fasta)
[2023-06-28 02:43:50,367] [INFO] Task started: Blastn
[2023-06-28 02:43:50,367] [INFO] Running command: blastn -query GCA_019634985.1_ASM1963498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4308be0f-cb36-445b-b7cd-abd73cd9e714/dqc_reference/reference_markers_gtdb.fasta -out GCA_019634985.1_ASM1963498v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:43:52,191] [INFO] Task succeeded: Blastn
[2023-06-28 02:43:52,196] [INFO] Selected 11 target genomes.
[2023-06-28 02:43:52,196] [INFO] Target genome list was writen to GCA_019634985.1_ASM1963498v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 02:43:52,225] [INFO] Task started: fastANI
[2023-06-28 02:43:52,225] [INFO] Running command: fastANI --query /var/lib/cwl/stga8af6992-1dc6-4e08-bc05-27b7bf7f7ef1/GCA_019634985.1_ASM1963498v1_genomic.fna.gz --refList GCA_019634985.1_ASM1963498v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019634985.1_ASM1963498v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 02:44:01,878] [INFO] Task succeeded: fastANI
[2023-06-28 02:44:01,895] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 02:44:01,895] [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_003105245.1	s__FEB-7 sp003105245	86.3954	737	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	99.57	99.57	0.92	0.92	2	-
GCA_011391275.1	s__FEB-7 sp011391275	85.694	737	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708825.1	s__FEB-7 sp016708825	83.8815	826	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720855.1	s__FEB-7 sp016720855	82.917	848	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709665.1	s__FEB-7 sp016709665	82.5203	836	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016711875.1	s__FEB-7 sp016711875	82.1497	838	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012274175.1	s__Usitatibacter sp012274175	80.3115	427	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__Usitatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001953215.1	s__Usitatibacter sp001953215	80.1718	624	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__Usitatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013003985.1	s__Usitatibacter palustris	79.8988	613	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__Usitatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017880705.1	s__Usitatibacter sp017880705	79.8335	410	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__Usitatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861105.1	s__VBCG01 sp016861105	77.2257	475	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__VBCG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 02:44:01,897] [INFO] GTDB search result was written to GCA_019634985.1_ASM1963498v1_genomic.fna/result_gtdb.tsv
[2023-06-28 02:44:01,898] [INFO] ===== GTDB Search completed =====
[2023-06-28 02:44:01,902] [INFO] DFAST_QC result json was written to GCA_019634985.1_ASM1963498v1_genomic.fna/dqc_result.json
[2023-06-28 02:44:01,902] [INFO] DFAST_QC completed!
[2023-06-28 02:44:01,903] [INFO] Total running time: 0h1m30s