[2024-01-25 18:56:35,509] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:56:35,510] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:56:35,510] [INFO] DQC Reference Directory: /var/lib/cwl/stg21629543-0ed5-46cf-98aa-96696495128d/dqc_reference
[2024-01-25 18:56:36,619] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:56:36,620] [INFO] Task started: Prodigal
[2024-01-25 18:56:36,620] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6244e53-b6f2-49ed-b98a-6327d7427a30/GCF_000613845.1_ASM61384v1_genomic.fna.gz | prodigal -d GCF_000613845.1_ASM61384v1_genomic.fna/cds.fna -a GCF_000613845.1_ASM61384v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:56:44,392] [INFO] Task succeeded: Prodigal
[2024-01-25 18:56:44,392] [INFO] Task started: HMMsearch
[2024-01-25 18:56:44,392] [INFO] Running command: hmmsearch --tblout GCF_000613845.1_ASM61384v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21629543-0ed5-46cf-98aa-96696495128d/dqc_reference/reference_markers.hmm GCF_000613845.1_ASM61384v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:56:44,585] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:56:44,586] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd6244e53-b6f2-49ed-b98a-6327d7427a30/GCF_000613845.1_ASM61384v1_genomic.fna.gz]
[2024-01-25 18:56:44,616] [INFO] Query marker FASTA was written to GCF_000613845.1_ASM61384v1_genomic.fna/markers.fasta
[2024-01-25 18:56:44,616] [INFO] Task started: Blastn
[2024-01-25 18:56:44,616] [INFO] Running command: blastn -query GCF_000613845.1_ASM61384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21629543-0ed5-46cf-98aa-96696495128d/dqc_reference/reference_markers.fasta -out GCF_000613845.1_ASM61384v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:45,259] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:45,261] [INFO] Selected 13 target genomes.
[2024-01-25 18:56:45,262] [INFO] Target genome list was writen to GCF_000613845.1_ASM61384v1_genomic.fna/target_genomes.txt
[2024-01-25 18:56:45,273] [INFO] Task started: fastANI
[2024-01-25 18:56:45,274] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6244e53-b6f2-49ed-b98a-6327d7427a30/GCF_000613845.1_ASM61384v1_genomic.fna.gz --refList GCF_000613845.1_ASM61384v1_genomic.fna/target_genomes.txt --output GCF_000613845.1_ASM61384v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:53,303] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:53,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21629543-0ed5-46cf-98aa-96696495128d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:53,304] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21629543-0ed5-46cf-98aa-96696495128d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:53,311] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:56:53,311] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:56:53,312] [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
Asaia astilbis	strain=JCM 15831	GCA_000613845.1	610244	610244	type	True	100.0	1019	1023	95	conclusive
Asaia platycodi	strain=JCM 25414	GCA_000614545.1	610243	610243	type	True	81.3197	591	1023	95	below_threshold
Asaia siamensis	strain=CCM 7132	GCA_014635085.1	110479	110479	type	True	81.261	600	1023	95	below_threshold
Asaia bogorensis	strain=NBRC 16594	GCA_007989265.1	91915	91915	suspected-type	True	80.593	496	1023	95	below_threshold
Asaia bogorensis	strain=NBRC 16594	GCA_001547995.1	91915	91915	suspected-type	True	80.5491	499	1023	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	80.4916	505	1023	95	below_threshold
Asaia prunellae	strain=JCM 25354	GCA_000613885.1	610245	610245	type	True	80.385	486	1023	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	77.5596	143	1023	95	below_threshold
Acidibrevibacterium fodinaquatile	strain=G45-3	GCA_003352165.1	1969806	1969806	type	True	76.1324	58	1023	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:53,313] [INFO] DFAST Taxonomy check result was written to GCF_000613845.1_ASM61384v1_genomic.fna/tc_result.tsv
[2024-01-25 18:56:53,314] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:53,314] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:53,314] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21629543-0ed5-46cf-98aa-96696495128d/dqc_reference/checkm_data
[2024-01-25 18:56:53,315] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:53,347] [INFO] Task started: CheckM
[2024-01-25 18:56:53,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000613845.1_ASM61384v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000613845.1_ASM61384v1_genomic.fna/checkm_input GCF_000613845.1_ASM61384v1_genomic.fna/checkm_result
[2024-01-25 18:57:19,925] [INFO] Task succeeded: CheckM
[2024-01-25 18:57:19,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:57:19,948] [INFO] ===== Completeness check finished =====
[2024-01-25 18:57:19,948] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:57:19,948] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000613845.1_ASM61384v1_genomic.fna/markers.fasta)
[2024-01-25 18:57:19,949] [INFO] Task started: Blastn
[2024-01-25 18:57:19,949] [INFO] Running command: blastn -query GCF_000613845.1_ASM61384v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21629543-0ed5-46cf-98aa-96696495128d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000613845.1_ASM61384v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:20,989] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:20,992] [INFO] Selected 9 target genomes.
[2024-01-25 18:57:20,992] [INFO] Target genome list was writen to GCF_000613845.1_ASM61384v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:57:21,013] [INFO] Task started: fastANI
[2024-01-25 18:57:21,014] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6244e53-b6f2-49ed-b98a-6327d7427a30/GCF_000613845.1_ASM61384v1_genomic.fna.gz --refList GCF_000613845.1_ASM61384v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000613845.1_ASM61384v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:26,829] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:26,835] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:57:26,835] [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_000613845.1	s__Asaia astilbis	100.0	1019	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000614545.1	s__Asaia platycodi	81.3197	591	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635085.1	s__Asaia siamensis	81.2496	601	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900465345.1	s__Asaia bogorensis_A	80.5826	492	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994335.1	s__Asaia sp003994335	80.5688	520	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001547995.1	s__Asaia bogorensis	80.5491	499	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	96.55	95.04	0.93	0.88	6	-
GCF_000613885.1	s__Asaia prunellae	80.385	486	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007988945.1	s__Swaminathania salitolerans	79.6066	385	1023	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Swaminathania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:57:26,837] [INFO] GTDB search result was written to GCF_000613845.1_ASM61384v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:26,838] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:26,841] [INFO] DFAST_QC result json was written to GCF_000613845.1_ASM61384v1_genomic.fna/dqc_result.json
[2024-01-25 18:57:26,841] [INFO] DFAST_QC completed!
[2024-01-25 18:57:26,842] [INFO] Total running time: 0h0m51s