[2024-01-24 12:14:34,888] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,889] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,889] [INFO] DQC Reference Directory: /var/lib/cwl/stg9dcb6072-fce5-42b6-b909-89d81d298b24/dqc_reference
[2024-01-24 12:14:36,176] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:36,177] [INFO] Task started: Prodigal
[2024-01-24 12:14:36,177] [INFO] Running command: gunzip -c /var/lib/cwl/stgc59d70f1-bc76-4370-b696-274869cd861d/GCF_012911005.2_ASM1291100v2_genomic.fna.gz | prodigal -d GCF_012911005.2_ASM1291100v2_genomic.fna/cds.fna -a GCF_012911005.2_ASM1291100v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:54,307] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:54,308] [INFO] Task started: HMMsearch
[2024-01-24 12:14:54,308] [INFO] Running command: hmmsearch --tblout GCF_012911005.2_ASM1291100v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9dcb6072-fce5-42b6-b909-89d81d298b24/dqc_reference/reference_markers.hmm GCF_012911005.2_ASM1291100v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:54,600] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:54,601] [INFO] Found 6/6 markers.
[2024-01-24 12:14:54,654] [INFO] Query marker FASTA was written to GCF_012911005.2_ASM1291100v2_genomic.fna/markers.fasta
[2024-01-24 12:14:54,654] [INFO] Task started: Blastn
[2024-01-24 12:14:54,654] [INFO] Running command: blastn -query GCF_012911005.2_ASM1291100v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dcb6072-fce5-42b6-b909-89d81d298b24/dqc_reference/reference_markers.fasta -out GCF_012911005.2_ASM1291100v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:55,598] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:55,602] [INFO] Selected 12 target genomes.
[2024-01-24 12:14:55,602] [INFO] Target genome list was writen to GCF_012911005.2_ASM1291100v2_genomic.fna/target_genomes.txt
[2024-01-24 12:14:55,604] [INFO] Task started: fastANI
[2024-01-24 12:14:55,605] [INFO] Running command: fastANI --query /var/lib/cwl/stgc59d70f1-bc76-4370-b696-274869cd861d/GCF_012911005.2_ASM1291100v2_genomic.fna.gz --refList GCF_012911005.2_ASM1291100v2_genomic.fna/target_genomes.txt --output GCF_012911005.2_ASM1291100v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:09,401] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:09,401] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9dcb6072-fce5-42b6-b909-89d81d298b24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:09,401] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9dcb6072-fce5-42b6-b909-89d81d298b24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:09,411] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:09,412] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:09,412] [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
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	100.0	1916	1945	95	conclusive
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	93.2908	1347	1945	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	89.6927	1379	1945	95	below_threshold
Aromatoleum evansii	strain=KB740	GCA_012910805.1	59406	59406	type	True	89.3607	1326	1945	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_012910985.1	76116	76116	type	True	88.9036	1258	1945	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_017894385.1	76116	76116	type	True	88.8587	1313	1945	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	87.5479	1121	1945	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	82.4493	852	1945	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	82.2735	777	1945	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.9235	510	1945	95	below_threshold
Thauera hydrothermalis	strain=GD-2	GCA_003345255.1	2184083	2184083	type	True	78.1807	366	1945	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	77.9553	341	1945	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:09,414] [INFO] DFAST Taxonomy check result was written to GCF_012911005.2_ASM1291100v2_genomic.fna/tc_result.tsv
[2024-01-24 12:15:09,415] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:09,415] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:09,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9dcb6072-fce5-42b6-b909-89d81d298b24/dqc_reference/checkm_data
[2024-01-24 12:15:09,417] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:09,475] [INFO] Task started: CheckM
[2024-01-24 12:15:09,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012911005.2_ASM1291100v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012911005.2_ASM1291100v2_genomic.fna/checkm_input GCF_012911005.2_ASM1291100v2_genomic.fna/checkm_result
[2024-01-24 12:16:02,897] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:02,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.56%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:02,927] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:02,927] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:02,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012911005.2_ASM1291100v2_genomic.fna/markers.fasta)
[2024-01-24 12:16:02,928] [INFO] Task started: Blastn
[2024-01-24 12:16:02,928] [INFO] Running command: blastn -query GCF_012911005.2_ASM1291100v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dcb6072-fce5-42b6-b909-89d81d298b24/dqc_reference/reference_markers_gtdb.fasta -out GCF_012911005.2_ASM1291100v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:04,547] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:04,550] [INFO] Selected 11 target genomes.
[2024-01-24 12:16:04,550] [INFO] Target genome list was writen to GCF_012911005.2_ASM1291100v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:04,554] [INFO] Task started: fastANI
[2024-01-24 12:16:04,554] [INFO] Running command: fastANI --query /var/lib/cwl/stgc59d70f1-bc76-4370-b696-274869cd861d/GCF_012911005.2_ASM1291100v2_genomic.fna.gz --refList GCF_012911005.2_ASM1291100v2_genomic.fna/target_genomes_gtdb.txt --output GCF_012911005.2_ASM1291100v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:18,523] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:18,533] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:18,533] [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_012911005.1	s__Aromatoleum toluolicum	100.0	1902	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001190925.1	s__Aromatoleum sp001190925	93.6036	1436	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156155.1	s__Aromatoleum tolulyticum	93.277	1348	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014822185.1	s__Aromatoleum sp014822185	92.4703	1324	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378245.1	s__Aromatoleum toluclasticum	89.697	1379	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910805.1	s__Aromatoleum evansii	89.3607	1326	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017894385.1	s__Aromatoleum petrolei	88.8415	1314	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012910905.1	s__Aromatoleum toluvorans	87.544	1122	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910705.1	s__Aromatoleum anaerobium	82.5863	812	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034845.1	s__Thauera_A sp003034845	80.5865	564	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361735.1	s__Azoarcus indigens	79.9097	595	1945	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:18,535] [INFO] GTDB search result was written to GCF_012911005.2_ASM1291100v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:18,535] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:18,539] [INFO] DFAST_QC result json was written to GCF_012911005.2_ASM1291100v2_genomic.fna/dqc_result.json
[2024-01-24 12:16:18,539] [INFO] DFAST_QC completed!
[2024-01-24 12:16:18,539] [INFO] Total running time: 0h1m44s