[2024-01-24 14:05:33,430] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:33,432] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:33,432] [INFO] DQC Reference Directory: /var/lib/cwl/stg72c02205-0531-41f6-b8b4-301373e9f3eb/dqc_reference
[2024-01-24 14:05:34,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:34,681] [INFO] Task started: Prodigal
[2024-01-24 14:05:34,681] [INFO] Running command: gunzip -c /var/lib/cwl/stg2092ee04-1a7e-47f9-8c40-293225ab330f/GCF_013003985.1_ASM1300398v1_genomic.fna.gz | prodigal -d GCF_013003985.1_ASM1300398v1_genomic.fna/cds.fna -a GCF_013003985.1_ASM1300398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:47,422] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:47,423] [INFO] Task started: HMMsearch
[2024-01-24 14:05:47,423] [INFO] Running command: hmmsearch --tblout GCF_013003985.1_ASM1300398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72c02205-0531-41f6-b8b4-301373e9f3eb/dqc_reference/reference_markers.hmm GCF_013003985.1_ASM1300398v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:47,716] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:47,718] [INFO] Found 6/6 markers.
[2024-01-24 14:05:47,769] [INFO] Query marker FASTA was written to GCF_013003985.1_ASM1300398v1_genomic.fna/markers.fasta
[2024-01-24 14:05:47,769] [INFO] Task started: Blastn
[2024-01-24 14:05:47,769] [INFO] Running command: blastn -query GCF_013003985.1_ASM1300398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72c02205-0531-41f6-b8b4-301373e9f3eb/dqc_reference/reference_markers.fasta -out GCF_013003985.1_ASM1300398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:48,689] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:48,692] [INFO] Selected 21 target genomes.
[2024-01-24 14:05:48,692] [INFO] Target genome list was writen to GCF_013003985.1_ASM1300398v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:48,700] [INFO] Task started: fastANI
[2024-01-24 14:05:48,701] [INFO] Running command: fastANI --query /var/lib/cwl/stg2092ee04-1a7e-47f9-8c40-293225ab330f/GCF_013003985.1_ASM1300398v1_genomic.fna.gz --refList GCF_013003985.1_ASM1300398v1_genomic.fna/target_genomes.txt --output GCF_013003985.1_ASM1300398v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:06,013] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:06,013] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72c02205-0531-41f6-b8b4-301373e9f3eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:06,014] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72c02205-0531-41f6-b8b4-301373e9f3eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:06,035] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:06,036] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:06,036] [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 palustris	strain=Swamp67	GCA_013003985.1	2732487	2732487	type	True	100.0	1318	1319	95	conclusive
Usitatibacter rugosus	strain=0125_3	GCA_013003965.1	2732067	2732067	type	True	81.6775	799	1319	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	77.3432	196	1319	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	77.28	205	1319	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	77.2362	202	1319	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_017894365.1	76115	76115	type	True	77.2275	180	1319	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	77.1342	223	1319	95	below_threshold
Aromatoleum aromaticum	strain=EbN1	GCA_000025965.1	551760	551760	type	True	77.1335	164	1319	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	77.0721	195	1319	95	below_threshold
Aquabacterium olei	strain=NBRC 110486	GCA_003100395.1	1296669	1296669	type	True	77.051	154	1319	95	below_threshold
Casimicrobium huifangae	strain=SJ-1	GCA_009746125.1	2591109	2591109	type	True	76.8202	131	1319	95	below_threshold
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	76.7199	189	1319	95	below_threshold
Aquabacterium fontiphilum	strain=CS-6	GCA_009909205.1	450365	450365	type	True	76.7013	109	1319	95	below_threshold
Burkholderia glumae	strain=ATCC 33617	GCA_000960995.1	337	337	type	True	76.6977	280	1319	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	76.6348	178	1319	95	below_threshold
Burkholderia glumae	strain=LMG 2196	GCA_902832765.1	337	337	type	True	76.568	281	1319	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	76.4191	194	1319	95	below_threshold
Jeongeupia chitinilytica	strain=KCTC 23701	GCA_014652315.1	1041641	1041641	type	True	76.3377	139	1319	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	76.288	120	1319	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	76.285	100	1319	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.1302	222	1319	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:06,038] [INFO] DFAST Taxonomy check result was written to GCF_013003985.1_ASM1300398v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:06,038] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:06,038] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:06,038] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72c02205-0531-41f6-b8b4-301373e9f3eb/dqc_reference/checkm_data
[2024-01-24 14:06:06,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:06,087] [INFO] Task started: CheckM
[2024-01-24 14:06:06,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013003985.1_ASM1300398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013003985.1_ASM1300398v1_genomic.fna/checkm_input GCF_013003985.1_ASM1300398v1_genomic.fna/checkm_result
[2024-01-24 14:06:54,555] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:54,556] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:54,578] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:54,578] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:54,578] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013003985.1_ASM1300398v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:54,579] [INFO] Task started: Blastn
[2024-01-24 14:06:54,579] [INFO] Running command: blastn -query GCF_013003985.1_ASM1300398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72c02205-0531-41f6-b8b4-301373e9f3eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_013003985.1_ASM1300398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:56,006] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:56,009] [INFO] Selected 14 target genomes.
[2024-01-24 14:06:56,009] [INFO] Target genome list was writen to GCF_013003985.1_ASM1300398v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:56,028] [INFO] Task started: fastANI
[2024-01-24 14:06:56,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg2092ee04-1a7e-47f9-8c40-293225ab330f/GCF_013003985.1_ASM1300398v1_genomic.fna.gz --refList GCF_013003985.1_ASM1300398v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013003985.1_ASM1300398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:07,853] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:07,877] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:07,877] [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_013003985.1	s__Usitatibacter palustris	100.0	1318	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__Usitatibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013003965.1	s__Usitatibacter rugosus	81.6447	803	1319	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	81.3559	819	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__Usitatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003105245.1	s__FEB-7 sp003105245	80.1367	479	1319	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_016709665.1	s__FEB-7 sp016709665	79.9269	624	1319	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	79.8151	617	1319	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_017880705.1	s__Usitatibacter sp017880705	79.7433	449	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__Usitatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012274175.1	s__Usitatibacter sp012274175	79.6733	399	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__Usitatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391275.1	s__FEB-7 sp011391275	79.6596	451	1319	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	79.4113	573	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__FEB-7	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003865015.1	s__Sulfurisoma sediminicola	77.28	205	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfurisoma	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000025965.1	s__Aromatoleum aromaticum	77.1335	164	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	98.48	98.48	0.91	0.91	2	-
GCF_001274695.1	s__Aromatoleum sp001274695	77.0862	199	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489115.1	s__Thauera_A sp014489115	76.9453	210	1319	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:07,879] [INFO] GTDB search result was written to GCF_013003985.1_ASM1300398v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:07,879] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:07,883] [INFO] DFAST_QC result json was written to GCF_013003985.1_ASM1300398v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:07,883] [INFO] DFAST_QC completed!
[2024-01-24 14:07:07,883] [INFO] Total running time: 0h1m34s