[2024-01-24 14:19:19,247] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:19,248] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:19,249] [INFO] DQC Reference Directory: /var/lib/cwl/stg59a832b6-9943-4b77-a14f-02ec98de0cad/dqc_reference
[2024-01-24 14:19:20,530] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:20,531] [INFO] Task started: Prodigal
[2024-01-24 14:19:20,531] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfecb536-03bb-411c-b736-a5e83439953c/GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/cds.fna -a GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:34,850] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:34,851] [INFO] Task started: HMMsearch
[2024-01-24 14:19:34,851] [INFO] Running command: hmmsearch --tblout GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59a832b6-9943-4b77-a14f-02ec98de0cad/dqc_reference/reference_markers.hmm GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:35,245] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:35,246] [INFO] Found 6/6 markers.
[2024-01-24 14:19:35,309] [INFO] Query marker FASTA was written to GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:19:35,309] [INFO] Task started: Blastn
[2024-01-24 14:19:35,309] [INFO] Running command: blastn -query GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg59a832b6-9943-4b77-a14f-02ec98de0cad/dqc_reference/reference_markers.fasta -out GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:35,946] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:35,949] [INFO] Selected 13 target genomes.
[2024-01-24 14:19:35,949] [INFO] Target genome list was writen to GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:19:35,954] [INFO] Task started: fastANI
[2024-01-24 14:19:35,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfecb536-03bb-411c-b736-a5e83439953c/GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna.gz --refList GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:47,990] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:47,990] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59a832b6-9943-4b77-a14f-02ec98de0cad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:47,991] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59a832b6-9943-4b77-a14f-02ec98de0cad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:47,998] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:19:47,998] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:47,998] [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
Paenibacillus macquariensis	strain=ATCC 23464	GCA_900156375.1	948756	948756	type	True	100.0	2049	2053	95	conclusive
Paenibacillus macquariensis subsp. macquariensis	strain=DSM 2	GCA_001637165.1	1468	948756	type	True	99.9849	2027	2053	95	conclusive
Paenibacillus antarcticus	strain=CECT 5836	GCA_001637225.1	253703	253703	type	True	91.0597	1354	2053	95	below_threshold
Paenibacillus glacialis	strain=DSM 22343	GCA_001637205.1	494026	494026	type	True	87.6086	1284	2053	95	below_threshold
Paenibacillus crassostreae	strain=LPB0068	GCA_001637335.1	1763538	1763538	type	True	79.4579	546	2053	95	below_threshold
Paenibacillus crassostreae	strain=LPB0068	GCA_001857945.1	1763538	1763538	type	True	79.417	572	2053	95	below_threshold
Paenibacillus albidus	strain=CGMCC 1.16134	GCA_014644435.1	2041023	2041023	type	True	79.0768	137	2053	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:47,999] [INFO] DFAST Taxonomy check result was written to GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:19:48,000] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:48,000] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:48,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59a832b6-9943-4b77-a14f-02ec98de0cad/dqc_reference/checkm_data
[2024-01-24 14:19:48,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:48,059] [INFO] Task started: CheckM
[2024-01-24 14:19:48,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/checkm_input GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:20:35,208] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:35,210] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:35,234] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:35,235] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:35,235] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:20:35,236] [INFO] Task started: Blastn
[2024-01-24 14:20:35,236] [INFO] Running command: blastn -query GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg59a832b6-9943-4b77-a14f-02ec98de0cad/dqc_reference/reference_markers_gtdb.fasta -out GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:36,012] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:36,015] [INFO] Selected 8 target genomes.
[2024-01-24 14:20:36,015] [INFO] Target genome list was writen to GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:36,025] [INFO] Task started: fastANI
[2024-01-24 14:20:36,026] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfecb536-03bb-411c-b736-a5e83439953c/GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna.gz --refList GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:46,217] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:46,235] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:46,236] [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_900156375.1	s__Paenibacillus macquariensis	100.0	2050	2053	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.68	95.38	0.90	0.81	3	conclusive
GCF_001637225.1	s__Paenibacillus antarcticus	91.0738	1353	2053	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001637205.1	s__Paenibacillus glacialis	87.6197	1283	2053	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000949425.1	s__Paenibacillus sp000949425	80.6039	645	2053	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001857945.1	s__Paenibacillus crassostreae	79.4205	574	2053	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014644435.1	s__Paenibacillus albidus	79.0935	136	2053	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.34	96.34	0.80	0.80	2	-
GCF_900109515.1	s__Paenibacillus sp900109515	77.8743	133	2053	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.23	95.20	0.85	0.85	7	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:46,239] [INFO] GTDB search result was written to GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:46,240] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:46,244] [INFO] DFAST_QC result json was written to GCF_900156375.1_IMG-taxon_2681812895_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:20:46,245] [INFO] DFAST_QC completed!
[2024-01-24 14:20:46,245] [INFO] Total running time: 0h1m27s