[2024-01-24 10:57:50,264] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:50,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:50,266] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c29f672-46e4-43e1-bad9-51c1b8daf0d1/dqc_reference
[2024-01-24 10:57:52,643] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:52,644] [INFO] Task started: Prodigal
[2024-01-24 10:57:52,644] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3f82df4-31bc-48d3-993d-647ec8f8cf40/GCF_001294535.1_ASM129453v1_genomic.fna.gz | prodigal -d GCF_001294535.1_ASM129453v1_genomic.fna/cds.fna -a GCF_001294535.1_ASM129453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:08,803] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:08,804] [INFO] Task started: HMMsearch
[2024-01-24 10:58:08,804] [INFO] Running command: hmmsearch --tblout GCF_001294535.1_ASM129453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c29f672-46e4-43e1-bad9-51c1b8daf0d1/dqc_reference/reference_markers.hmm GCF_001294535.1_ASM129453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:09,097] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:09,098] [INFO] Found 6/6 markers.
[2024-01-24 10:58:09,147] [INFO] Query marker FASTA was written to GCF_001294535.1_ASM129453v1_genomic.fna/markers.fasta
[2024-01-24 10:58:09,147] [INFO] Task started: Blastn
[2024-01-24 10:58:09,147] [INFO] Running command: blastn -query GCF_001294535.1_ASM129453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c29f672-46e4-43e1-bad9-51c1b8daf0d1/dqc_reference/reference_markers.fasta -out GCF_001294535.1_ASM129453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:10,007] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:10,010] [INFO] Selected 19 target genomes.
[2024-01-24 10:58:10,010] [INFO] Target genome list was writen to GCF_001294535.1_ASM129453v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:10,017] [INFO] Task started: fastANI
[2024-01-24 10:58:10,018] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3f82df4-31bc-48d3-993d-647ec8f8cf40/GCF_001294535.1_ASM129453v1_genomic.fna.gz --refList GCF_001294535.1_ASM129453v1_genomic.fna/target_genomes.txt --output GCF_001294535.1_ASM129453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:24,961] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:24,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c29f672-46e4-43e1-bad9-51c1b8daf0d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:24,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c29f672-46e4-43e1-bad9-51c1b8daf0d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:24,980] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:24,980] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:24,981] [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
Cypionkella psychrotolerans	strain=PAMC 27389	GCA_001294535.1	1678131	1678131	type	True	100.0	1634	1640	95	conclusive
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.6719	540	1640	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	78.2347	504	1640	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	78.1038	548	1640	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	78.082	425	1640	95	below_threshold
Gemmobacter aquarius	strain=HYN0069	GCA_003060865.1	2169400	2169400	type	True	78.0334	459	1640	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	77.9327	404	1640	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	77.8524	455	1640	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	77.8094	458	1640	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	77.7265	443	1640	95	below_threshold
Pseudorhodobacter ferrugineus	strain=DSM 5888	GCA_000420745.1	77008	77008	type	True	77.6764	311	1640	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	77.5791	421	1640	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	77.5753	400	1640	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.4853	237	1640	95	below_threshold
Pseudorhodobacter wandonensis	strain=KCTC 23672	GCA_001202035.1	1120568	1120568	type	True	77.4776	294	1640	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	77.4681	325	1640	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	77.4571	354	1640	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	77.4412	352	1640	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.4139	337	1640	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:24,982] [INFO] DFAST Taxonomy check result was written to GCF_001294535.1_ASM129453v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:24,983] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:24,983] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:24,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c29f672-46e4-43e1-bad9-51c1b8daf0d1/dqc_reference/checkm_data
[2024-01-24 10:58:24,984] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:25,034] [INFO] Task started: CheckM
[2024-01-24 10:58:25,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001294535.1_ASM129453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001294535.1_ASM129453v1_genomic.fna/checkm_input GCF_001294535.1_ASM129453v1_genomic.fna/checkm_result
[2024-01-24 10:59:12,895] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:12,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:12,918] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:12,919] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:12,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001294535.1_ASM129453v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:12,919] [INFO] Task started: Blastn
[2024-01-24 10:59:12,919] [INFO] Running command: blastn -query GCF_001294535.1_ASM129453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c29f672-46e4-43e1-bad9-51c1b8daf0d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_001294535.1_ASM129453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:14,421] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:14,425] [INFO] Selected 11 target genomes.
[2024-01-24 10:59:14,426] [INFO] Target genome list was writen to GCF_001294535.1_ASM129453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:14,439] [INFO] Task started: fastANI
[2024-01-24 10:59:14,439] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3f82df4-31bc-48d3-993d-647ec8f8cf40/GCF_001294535.1_ASM129453v1_genomic.fna.gz --refList GCF_001294535.1_ASM129453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001294535.1_ASM129453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:24,076] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:24,097] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:24,098] [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_001294535.1	s__Cypionkella psychrotolerans	100.0	1635	1640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002256245.1	s__Cypionkella sp002256245	85.1938	1124	1640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773375.1	s__Cypionkella sp009773375	81.9972	825	1640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001828855.1	s__Cypionkella sp001828855	79.9511	747	1640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	99.95	99.91	0.99	0.97	3	-
GCA_011008935.1	s__KMS-5 sp011008935	78.616	538	1640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013328815.1	s__UBA1943 sp013328815	78.4892	601	1640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	97.27	97.27	0.97	0.97	2	-
GCA_018063485.1	s__Cypionkella sp018063485	78.3552	348	1640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443995.1	s__ETT8 sp003443995	78.2499	502	1640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900965.1	s__ETT8 sp002900965	78.0405	409	1640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014243445.1	s__Gemmobacter_B straminiformis	77.8597	454	1640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298675.1	s__Cypionkella sp013298675	77.6299	245	1640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:24,105] [INFO] GTDB search result was written to GCF_001294535.1_ASM129453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:24,106] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:24,110] [INFO] DFAST_QC result json was written to GCF_001294535.1_ASM129453v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:24,111] [INFO] DFAST_QC completed!
[2024-01-24 10:59:24,111] [INFO] Total running time: 0h1m34s