[2024-01-24 13:57:42,178] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,181] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,181] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ffc2c76-bf04-4fe3-851e-10fcdbeb2022/dqc_reference
[2024-01-24 13:57:43,593] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:43,594] [INFO] Task started: Prodigal
[2024-01-24 13:57:43,594] [INFO] Running command: gunzip -c /var/lib/cwl/stgc04b61a1-9e4f-4157-bd33-49b9700e2d2e/GCF_002866925.1_ASM286692v1_genomic.fna.gz | prodigal -d GCF_002866925.1_ASM286692v1_genomic.fna/cds.fna -a GCF_002866925.1_ASM286692v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:59,486] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:59,486] [INFO] Task started: HMMsearch
[2024-01-24 13:57:59,486] [INFO] Running command: hmmsearch --tblout GCF_002866925.1_ASM286692v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ffc2c76-bf04-4fe3-851e-10fcdbeb2022/dqc_reference/reference_markers.hmm GCF_002866925.1_ASM286692v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:59,806] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:59,807] [INFO] Found 6/6 markers.
[2024-01-24 13:57:59,852] [INFO] Query marker FASTA was written to GCF_002866925.1_ASM286692v1_genomic.fna/markers.fasta
[2024-01-24 13:57:59,852] [INFO] Task started: Blastn
[2024-01-24 13:57:59,852] [INFO] Running command: blastn -query GCF_002866925.1_ASM286692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ffc2c76-bf04-4fe3-851e-10fcdbeb2022/dqc_reference/reference_markers.fasta -out GCF_002866925.1_ASM286692v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:00,590] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:00,594] [INFO] Selected 20 target genomes.
[2024-01-24 13:58:00,594] [INFO] Target genome list was writen to GCF_002866925.1_ASM286692v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:00,610] [INFO] Task started: fastANI
[2024-01-24 13:58:00,610] [INFO] Running command: fastANI --query /var/lib/cwl/stgc04b61a1-9e4f-4157-bd33-49b9700e2d2e/GCF_002866925.1_ASM286692v1_genomic.fna.gz --refList GCF_002866925.1_ASM286692v1_genomic.fna/target_genomes.txt --output GCF_002866925.1_ASM286692v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:17,159] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:17,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ffc2c76-bf04-4fe3-851e-10fcdbeb2022/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:17,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ffc2c76-bf04-4fe3-851e-10fcdbeb2022/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:17,171] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:17,171] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:17,171] [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
Cohaesibacter celericrescens	strain=H1304	GCA_002866925.1	2067669	2067669	type	True	100.0	1615	1644	95	conclusive
Cohaesibacter intestini	strain=YE-B6	GCA_003324485.1	2211145	2211145	type	True	77.5656	369	1644	95	below_threshold
Cohaesibacter marisflavi	strain=CGMCC 1.9157	GCA_900115225.1	655353	655353	type	True	77.4909	291	1644	95	below_threshold
Cohaesibacter haloalkalitolerans	strain=JC131	GCA_003574655.1	1162980	1162980	type	True	77.3559	259	1644	95	below_threshold
Cohaesibacter gelatinilyticus	strain=DSM 18289	GCA_900215605.1	372072	372072	type	True	77.0827	183	1644	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:17,174] [INFO] DFAST Taxonomy check result was written to GCF_002866925.1_ASM286692v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:17,174] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:17,174] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:17,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ffc2c76-bf04-4fe3-851e-10fcdbeb2022/dqc_reference/checkm_data
[2024-01-24 13:58:17,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:17,227] [INFO] Task started: CheckM
[2024-01-24 13:58:17,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002866925.1_ASM286692v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002866925.1_ASM286692v1_genomic.fna/checkm_input GCF_002866925.1_ASM286692v1_genomic.fna/checkm_result
[2024-01-24 13:59:06,428] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:06,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:06,461] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:06,461] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:06,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002866925.1_ASM286692v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:06,462] [INFO] Task started: Blastn
[2024-01-24 13:59:06,463] [INFO] Running command: blastn -query GCF_002866925.1_ASM286692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ffc2c76-bf04-4fe3-851e-10fcdbeb2022/dqc_reference/reference_markers_gtdb.fasta -out GCF_002866925.1_ASM286692v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:07,606] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:07,610] [INFO] Selected 16 target genomes.
[2024-01-24 13:59:07,611] [INFO] Target genome list was writen to GCF_002866925.1_ASM286692v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:07,659] [INFO] Task started: fastANI
[2024-01-24 13:59:07,660] [INFO] Running command: fastANI --query /var/lib/cwl/stgc04b61a1-9e4f-4157-bd33-49b9700e2d2e/GCF_002866925.1_ASM286692v1_genomic.fna.gz --refList GCF_002866925.1_ASM286692v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002866925.1_ASM286692v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:20,938] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:20,945] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:20,945] [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_002866925.1	s__Cohaesibacter celericrescens	100.0	1612	1644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Cohaesibacteraceae;g__Cohaesibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003324485.1	s__Cohaesibacter intestini	77.5656	369	1644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Cohaesibacteraceae;g__Cohaesibacter	95.0	98.38	98.38	0.96	0.96	2	-
GCF_900215505.1	s__Cohaesibacter sp900215505	77.5398	301	1644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Cohaesibacteraceae;g__Cohaesibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115225.1	s__Cohaesibacter marisflavi	77.4941	292	1644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Cohaesibacteraceae;g__Cohaesibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574655.1	s__Cohaesibacter haloalkalitolerans	77.3453	260	1644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Cohaesibacteraceae;g__Cohaesibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215605.1	s__Cohaesibacter gelatinilyticus	77.0679	184	1644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Cohaesibacteraceae;g__Cohaesibacter	95.0	98.86	98.83	0.96	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:20,947] [INFO] GTDB search result was written to GCF_002866925.1_ASM286692v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:20,947] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:20,950] [INFO] DFAST_QC result json was written to GCF_002866925.1_ASM286692v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:20,950] [INFO] DFAST_QC completed!
[2024-01-24 13:59:20,950] [INFO] Total running time: 0h1m39s