[2024-01-25 19:55:35,692] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:55:35,694] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:55:35,694] [INFO] DQC Reference Directory: /var/lib/cwl/stga416ff27-3690-490d-aeb1-fe6c0a8f4f84/dqc_reference
[2024-01-25 19:55:36,851] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:55:36,852] [INFO] Task started: Prodigal
[2024-01-25 19:55:36,852] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3472107-434a-4033-bfb8-64ab138295c5/GCF_000378145.1_ASM37814v1_genomic.fna.gz | prodigal -d GCF_000378145.1_ASM37814v1_genomic.fna/cds.fna -a GCF_000378145.1_ASM37814v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:47,672] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:47,672] [INFO] Task started: HMMsearch
[2024-01-25 19:55:47,672] [INFO] Running command: hmmsearch --tblout GCF_000378145.1_ASM37814v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga416ff27-3690-490d-aeb1-fe6c0a8f4f84/dqc_reference/reference_markers.hmm GCF_000378145.1_ASM37814v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:47,928] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:47,929] [INFO] Found 6/6 markers.
[2024-01-25 19:55:47,972] [INFO] Query marker FASTA was written to GCF_000378145.1_ASM37814v1_genomic.fna/markers.fasta
[2024-01-25 19:55:47,973] [INFO] Task started: Blastn
[2024-01-25 19:55:47,973] [INFO] Running command: blastn -query GCF_000378145.1_ASM37814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga416ff27-3690-490d-aeb1-fe6c0a8f4f84/dqc_reference/reference_markers.fasta -out GCF_000378145.1_ASM37814v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:48,573] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:48,575] [INFO] Selected 14 target genomes.
[2024-01-25 19:55:48,576] [INFO] Target genome list was writen to GCF_000378145.1_ASM37814v1_genomic.fna/target_genomes.txt
[2024-01-25 19:55:48,591] [INFO] Task started: fastANI
[2024-01-25 19:55:48,591] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3472107-434a-4033-bfb8-64ab138295c5/GCF_000378145.1_ASM37814v1_genomic.fna.gz --refList GCF_000378145.1_ASM37814v1_genomic.fna/target_genomes.txt --output GCF_000378145.1_ASM37814v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:56:02,495] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:02,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga416ff27-3690-490d-aeb1-fe6c0a8f4f84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:56:02,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga416ff27-3690-490d-aeb1-fe6c0a8f4f84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:56:02,505] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:56:02,505] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:56:02,505] [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
Saccharibacillus kuerlensis	strain=DSM 22868	GCA_000378145.1	459527	459527	type	True	100.0	1529	1533	95	conclusive
Saccharibacillus kuerlensis	strain=CGMCC 1.6964	GCA_014645255.1	459527	459527	type	True	99.9967	1528	1533	95	conclusive
Saccharibacillus alkalitolerans	strain=VR-M41	GCA_011090185.1	2705290	2705290	type	True	80.8587	1014	1533	95	below_threshold
Saccharibacillus deserti	strain=WLJ055	GCA_013618475.1	1634444	1634444	type	True	80.4828	909	1533	95	below_threshold
Saccharibacillus qingshengii	strain=JCM 31172	GCA_013185195.1	1763540	1763540	type	True	80.4725	866	1533	95	below_threshold
Saccharibacillus brassicae	strain=ATSA2	GCA_006542275.1	2583377	2583377	type	True	80.4027	901	1533	95	below_threshold
Saccharibacillus endophyticus	strain=CCM 8702	GCA_014635605.1	2060666	2060666	type	True	79.9036	832	1533	95	below_threshold
Saccharibacillus endophyticus	strain=CCM 8702	GCA_013185185.1	2060666	2060666	type	True	79.8902	837	1533	95	below_threshold
Paenibacillus faecalis	strain=Marseille-P3787	GCA_900289175.1	2079532	2079532	type	True	76.8052	65	1533	95	below_threshold
Paenibacillus farraposensis	strain=UY79	GCA_020736845.1	2807095	2807095	type	True	76.6413	72	1533	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	76.6292	106	1533	95	below_threshold
Paenibacillus hunanensis	strain=CGMCC 1.8907	GCA_014645615.1	539262	539262	type	True	76.6005	108	1533	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	76.5382	79	1533	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	76.416	92	1533	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:56:02,506] [INFO] DFAST Taxonomy check result was written to GCF_000378145.1_ASM37814v1_genomic.fna/tc_result.tsv
[2024-01-25 19:56:02,507] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:56:02,507] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:56:02,507] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga416ff27-3690-490d-aeb1-fe6c0a8f4f84/dqc_reference/checkm_data
[2024-01-25 19:56:02,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:56:02,557] [INFO] Task started: CheckM
[2024-01-25 19:56:02,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000378145.1_ASM37814v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000378145.1_ASM37814v1_genomic.fna/checkm_input GCF_000378145.1_ASM37814v1_genomic.fna/checkm_result
[2024-01-25 19:56:37,133] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:37,134] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:37,151] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:37,151] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:37,151] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000378145.1_ASM37814v1_genomic.fna/markers.fasta)
[2024-01-25 19:56:37,152] [INFO] Task started: Blastn
[2024-01-25 19:56:37,152] [INFO] Running command: blastn -query GCF_000378145.1_ASM37814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga416ff27-3690-490d-aeb1-fe6c0a8f4f84/dqc_reference/reference_markers_gtdb.fasta -out GCF_000378145.1_ASM37814v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:37,989] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:37,992] [INFO] Selected 9 target genomes.
[2024-01-25 19:56:37,993] [INFO] Target genome list was writen to GCF_000378145.1_ASM37814v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:38,005] [INFO] Task started: fastANI
[2024-01-25 19:56:38,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3472107-434a-4033-bfb8-64ab138295c5/GCF_000378145.1_ASM37814v1_genomic.fna.gz --refList GCF_000378145.1_ASM37814v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000378145.1_ASM37814v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:56:48,421] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:48,428] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:56:48,428] [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_000378145.1	s__Saccharibacillus kuerlensis	100.0	1529	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_011090185.1	s__Saccharibacillus alkalitolerans	80.8526	1015	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013618475.1	s__Saccharibacillus deserti	80.4875	909	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013185195.1	s__Saccharibacillus qingshengii	80.4684	867	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542275.1	s__Saccharibacillus brassicae	80.3916	902	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	97.06	97.06	0.95	0.95	2	-
GCF_002205895.1	s__Saccharibacillus sp002205895	80.0241	821	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013185185.1	s__Saccharibacillus endophyticus	79.8947	836	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000585395.1	s__Saccharibacillus sacchari	79.7762	820	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002189105.1	s__Saccharibacillus sp002189105	79.4292	698	1533	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Saccharibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:56:48,429] [INFO] GTDB search result was written to GCF_000378145.1_ASM37814v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:56:48,430] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:56:48,434] [INFO] DFAST_QC result json was written to GCF_000378145.1_ASM37814v1_genomic.fna/dqc_result.json
[2024-01-25 19:56:48,435] [INFO] DFAST_QC completed!
[2024-01-25 19:56:48,435] [INFO] Total running time: 0h1m13s