[2024-01-24 11:51:49,780] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:49,784] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:49,784] [INFO] DQC Reference Directory: /var/lib/cwl/stge167d5aa-a9fb-400e-9a4e-af056bbf951b/dqc_reference
[2024-01-24 11:51:51,041] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:51,043] [INFO] Task started: Prodigal
[2024-01-24 11:51:51,043] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c8f5d60-442d-40bd-bf39-738788707c72/GCF_028864255.1_ASM2886425v1_genomic.fna.gz | prodigal -d GCF_028864255.1_ASM2886425v1_genomic.fna/cds.fna -a GCF_028864255.1_ASM2886425v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:03,134] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:03,135] [INFO] Task started: HMMsearch
[2024-01-24 11:52:03,135] [INFO] Running command: hmmsearch --tblout GCF_028864255.1_ASM2886425v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge167d5aa-a9fb-400e-9a4e-af056bbf951b/dqc_reference/reference_markers.hmm GCF_028864255.1_ASM2886425v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:03,424] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:03,426] [INFO] Found 6/6 markers.
[2024-01-24 11:52:03,465] [INFO] Query marker FASTA was written to GCF_028864255.1_ASM2886425v1_genomic.fna/markers.fasta
[2024-01-24 11:52:03,466] [INFO] Task started: Blastn
[2024-01-24 11:52:03,466] [INFO] Running command: blastn -query GCF_028864255.1_ASM2886425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge167d5aa-a9fb-400e-9a4e-af056bbf951b/dqc_reference/reference_markers.fasta -out GCF_028864255.1_ASM2886425v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:04,311] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:04,316] [INFO] Selected 27 target genomes.
[2024-01-24 11:52:04,316] [INFO] Target genome list was writen to GCF_028864255.1_ASM2886425v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:04,358] [INFO] Task started: fastANI
[2024-01-24 11:52:04,359] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c8f5d60-442d-40bd-bf39-738788707c72/GCF_028864255.1_ASM2886425v1_genomic.fna.gz --refList GCF_028864255.1_ASM2886425v1_genomic.fna/target_genomes.txt --output GCF_028864255.1_ASM2886425v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:23,949] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:23,949] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge167d5aa-a9fb-400e-9a4e-af056bbf951b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:23,950] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge167d5aa-a9fb-400e-9a4e-af056bbf951b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:23,967] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:23,967] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:23,967] [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
Dechloromonas hortensis	strain=MA-1	GCA_009469765.1	337779	337779	type	True	82.6611	759	1301	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	82.5385	649	1301	95	below_threshold
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	82.506	762	1301	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	82.4717	615	1301	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	78.8657	438	1301	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	78.8539	372	1301	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.7884	350	1301	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_009469755.1	1066	1066	type	True	78.7536	397	1301	95	below_threshold
Rhodocyclus tenuis	strain=2761	GCA_014197755.1	1066	1066	type	True	78.7243	399	1301	95	below_threshold
Zoogloea oleivorans	strain=Buc	GCA_008107625.1	1552750	1552750	type	True	78.6966	373	1301	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	78.5045	330	1301	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	78.4335	334	1301	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	78.2478	302	1301	95	below_threshold
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	78.1424	315	1301	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	77.9499	302	1301	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	77.203	238	1301	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.1675	236	1301	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.0598	241	1301	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.9986	155	1301	95	below_threshold
Pseudomonas argentinensis	strain=CCUG 50743	GCA_008801645.1	289370	289370	type	True	76.3169	133	1301	95	below_threshold
Pseudomonas argentinensis	strain=LMG 22563	GCA_900113905.1	289370	289370	type	True	76.2602	130	1301	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	76.1708	56	1301	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	76.0517	143	1301	95	below_threshold
Oceanisphaera litoralis	strain=DSM 15406	GCA_016907015.1	225144	225144	type	True	75.6193	51	1301	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:23,971] [INFO] DFAST Taxonomy check result was written to GCF_028864255.1_ASM2886425v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:23,971] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:23,971] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:23,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge167d5aa-a9fb-400e-9a4e-af056bbf951b/dqc_reference/checkm_data
[2024-01-24 11:52:23,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:24,017] [INFO] Task started: CheckM
[2024-01-24 11:52:24,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028864255.1_ASM2886425v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028864255.1_ASM2886425v1_genomic.fna/checkm_input GCF_028864255.1_ASM2886425v1_genomic.fna/checkm_result
[2024-01-24 11:53:02,121] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:02,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:02,147] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:02,148] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:02,148] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028864255.1_ASM2886425v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:02,149] [INFO] Task started: Blastn
[2024-01-24 11:53:02,149] [INFO] Running command: blastn -query GCF_028864255.1_ASM2886425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge167d5aa-a9fb-400e-9a4e-af056bbf951b/dqc_reference/reference_markers_gtdb.fasta -out GCF_028864255.1_ASM2886425v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:03,623] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:03,628] [INFO] Selected 26 target genomes.
[2024-01-24 11:53:03,628] [INFO] Target genome list was writen to GCF_028864255.1_ASM2886425v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:03,656] [INFO] Task started: fastANI
[2024-01-24 11:53:03,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c8f5d60-442d-40bd-bf39-738788707c72/GCF_028864255.1_ASM2886425v1_genomic.fna.gz --refList GCF_028864255.1_ASM2886425v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028864255.1_ASM2886425v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:24,270] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:24,294] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:24,294] [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_000519045.1	s__Azonexus agitatus	98.8787	1054	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.62	98.62	0.86	0.86	2	conclusive
GCA_016790885.1	s__Azonexus sp016790885	86.6896	546	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008711155.1	s__Azonexus sp008711155	84.242	817	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	97.59	97.59	0.92	0.92	2	-
GCF_009469585.1	s__Azonexus sp009469585	83.6243	729	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903922075.1	s__Azonexus sp903922075	82.9354	539	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469615.1	s__Azonexus sp009469615	82.9103	710	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469765.1	s__Azonexus hortensis	82.6616	759	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933675.1	s__Azonexus sp008933675	82.6137	644	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001551835.1	s__Azonexus denitrificans	82.5166	760	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429605.1	s__Azonexus hydrophilus	82.4352	618	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	97.24	97.24	0.86	0.86	2	-
GCA_018261895.1	s__Azonexus sp018261895	82.3528	620	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842345.1	s__Azonexus sp002842345	82.3209	636	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848965.1	s__Azonexus aromaticus_B	81.9873	632	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004379165.1	s__Azonexus sp004379165	81.9639	597	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	99.94	99.94	0.95	0.95	2	-
GCF_001956855.1	s__Azonexus hydrophilus_A	81.8519	646	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840765.1	s__Azonexus sp002840765	81.8376	738	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018261905.1	s__Azonexus sp018261905	81.3305	628	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391255.1	s__Azonexus sp011391255	79.0649	389	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112695.1	s__Azospira sp003112695	78.5336	362	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011881425.1	s__Rhodocyclus tenuis_A	78.3103	298	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Rhodocyclus	95.0	98.99	98.97	0.94	0.93	3	-
GCA_002840845.1	s__Desulfobacillus sp002840845	77.6773	249	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214175.1	s__JACRPB01 sp016214175	77.3198	267	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACRPB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900996235.1	s__Paraburkholderia sp900996235	76.6504	163	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836675.1	s__Comamonas sp014836675	76.1708	56	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.72	98.72	0.93	0.93	2	-
GCF_016907015.1	s__Oceanisphaera litoralis	75.6193	51	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:24,296] [INFO] GTDB search result was written to GCF_028864255.1_ASM2886425v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:24,296] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:24,301] [INFO] DFAST_QC result json was written to GCF_028864255.1_ASM2886425v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:24,301] [INFO] DFAST_QC completed!
[2024-01-24 11:53:24,302] [INFO] Total running time: 0h1m35s