[2024-01-24 14:12:46,269] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:46,271] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:46,271] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b31b334-18ad-4335-aea1-ac3a712c69ba/dqc_reference
[2024-01-24 14:12:47,549] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:47,550] [INFO] Task started: Prodigal
[2024-01-24 14:12:47,550] [INFO] Running command: gunzip -c /var/lib/cwl/stg118b9ef9-2e39-4ecc-b405-89fa739f758a/GCF_003050905.1_ASM305090v1_genomic.fna.gz | prodigal -d GCF_003050905.1_ASM305090v1_genomic.fna/cds.fna -a GCF_003050905.1_ASM305090v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:59,747] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:59,748] [INFO] Task started: HMMsearch
[2024-01-24 14:12:59,748] [INFO] Running command: hmmsearch --tblout GCF_003050905.1_ASM305090v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b31b334-18ad-4335-aea1-ac3a712c69ba/dqc_reference/reference_markers.hmm GCF_003050905.1_ASM305090v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:00,019] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:00,021] [INFO] Found 6/6 markers.
[2024-01-24 14:13:00,062] [INFO] Query marker FASTA was written to GCF_003050905.1_ASM305090v1_genomic.fna/markers.fasta
[2024-01-24 14:13:00,063] [INFO] Task started: Blastn
[2024-01-24 14:13:00,063] [INFO] Running command: blastn -query GCF_003050905.1_ASM305090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b31b334-18ad-4335-aea1-ac3a712c69ba/dqc_reference/reference_markers.fasta -out GCF_003050905.1_ASM305090v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:01,036] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:01,040] [INFO] Selected 10 target genomes.
[2024-01-24 14:13:01,040] [INFO] Target genome list was writen to GCF_003050905.1_ASM305090v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:01,044] [INFO] Task started: fastANI
[2024-01-24 14:13:01,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg118b9ef9-2e39-4ecc-b405-89fa739f758a/GCF_003050905.1_ASM305090v1_genomic.fna.gz --refList GCF_003050905.1_ASM305090v1_genomic.fna/target_genomes.txt --output GCF_003050905.1_ASM305090v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:10,608] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:10,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b31b334-18ad-4335-aea1-ac3a712c69ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:10,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b31b334-18ad-4335-aea1-ac3a712c69ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:10,623] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:13:10,623] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:13:10,623] [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
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	100.0	1432	1434	95	inconclusive
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	95.5707	1181	1434	95	inconclusive
Cereibacter johrii	strain=JA192	GCA_001720585.1	445629	445629	type	True	87.2503	964	1434	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_003046325.1	445629	445629	type	True	87.212	1062	1434	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_003324715.1	1063	1063	type	True	87.1207	1068	1434	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	87.1121	1070	1434	95	below_threshold
Cereibacter sphaeroides	strain=NBRC 12203	GCA_007991035.1	1063	1063	type	True	87.0359	1059	1434	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	83.6806	827	1434	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	79.528	532	1434	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	79.5108	533	1434	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:10,625] [INFO] DFAST Taxonomy check result was written to GCF_003050905.1_ASM305090v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:10,625] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:10,625] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:10,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b31b334-18ad-4335-aea1-ac3a712c69ba/dqc_reference/checkm_data
[2024-01-24 14:13:10,627] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:10,668] [INFO] Task started: CheckM
[2024-01-24 14:13:10,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003050905.1_ASM305090v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003050905.1_ASM305090v1_genomic.fna/checkm_input GCF_003050905.1_ASM305090v1_genomic.fna/checkm_result
[2024-01-24 14:13:57,362] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:57,363] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:57,383] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:57,384] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:57,384] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003050905.1_ASM305090v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:57,384] [INFO] Task started: Blastn
[2024-01-24 14:13:57,384] [INFO] Running command: blastn -query GCF_003050905.1_ASM305090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b31b334-18ad-4335-aea1-ac3a712c69ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_003050905.1_ASM305090v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:59,419] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:59,423] [INFO] Selected 6 target genomes.
[2024-01-24 14:13:59,423] [INFO] Target genome list was writen to GCF_003050905.1_ASM305090v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:59,430] [INFO] Task started: fastANI
[2024-01-24 14:13:59,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg118b9ef9-2e39-4ecc-b405-89fa739f758a/GCF_003050905.1_ASM305090v1_genomic.fna.gz --refList GCF_003050905.1_ASM305090v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003050905.1_ASM305090v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:06,287] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:06,293] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:06,293] [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_017599285.1	s__Cereibacter_A azotoformans	99.6665	1030	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	98.54	95.54	0.92	0.86	6	conclusive
GCF_001720585.1	s__Cereibacter_A johrii	87.2429	965	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.42	97.86	0.94	0.91	6	-
GCF_000012905.2	s__Cereibacter_A sphaeroides	87.0917	1071	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.82	96.57	0.94	0.87	24	-
GCF_002407205.1	s__Cereibacter_A sp002407205	85.5082	996	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900207575.1	s__Cereibacter_A ovatus	83.6882	826	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034985.1	s__Cereibacter changlensis	82.2983	777	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:06,295] [INFO] GTDB search result was written to GCF_003050905.1_ASM305090v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:06,295] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:06,298] [INFO] DFAST_QC result json was written to GCF_003050905.1_ASM305090v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:06,298] [INFO] DFAST_QC completed!
[2024-01-24 14:14:06,298] [INFO] Total running time: 0h1m20s