[2023-06-05 18:09:14,604] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:09:14,622] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:09:14,622] [INFO] DQC Reference Directory: /var/lib/cwl/stga0b62e34-bea4-4e66-aacb-fa481984e5aa/dqc_reference
[2023-06-05 18:09:16,582] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:09:16,589] [INFO] Task started: Prodigal
[2023-06-05 18:09:16,589] [INFO] Running command: gunzip -c /var/lib/cwl/stg022fe6fc-c0e8-4353-839c-3e69d8f1b676/GCA_001830495.1_ASM183049v1_genomic.fna.gz | prodigal -d GCA_001830495.1_ASM183049v1_genomic.fna/cds.fna -a GCA_001830495.1_ASM183049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:09:20,878] [INFO] Task succeeded: Prodigal
[2023-06-05 18:09:20,878] [INFO] Task started: HMMsearch
[2023-06-05 18:09:20,878] [INFO] Running command: hmmsearch --tblout GCA_001830495.1_ASM183049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0b62e34-bea4-4e66-aacb-fa481984e5aa/dqc_reference/reference_markers.hmm GCA_001830495.1_ASM183049v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:09:21,175] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:09:21,176] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg022fe6fc-c0e8-4353-839c-3e69d8f1b676/GCA_001830495.1_ASM183049v1_genomic.fna.gz]
[2023-06-05 18:09:21,200] [INFO] Query marker FASTA was written to GCA_001830495.1_ASM183049v1_genomic.fna/markers.fasta
[2023-06-05 18:09:21,200] [INFO] Task started: Blastn
[2023-06-05 18:09:21,200] [INFO] Running command: blastn -query GCA_001830495.1_ASM183049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0b62e34-bea4-4e66-aacb-fa481984e5aa/dqc_reference/reference_markers.fasta -out GCA_001830495.1_ASM183049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:09:21,979] [INFO] Task succeeded: Blastn
[2023-06-05 18:09:21,982] [INFO] Selected 21 target genomes.
[2023-06-05 18:09:21,982] [INFO] Target genome list was writen to GCA_001830495.1_ASM183049v1_genomic.fna/target_genomes.txt
[2023-06-05 18:09:21,987] [INFO] Task started: fastANI
[2023-06-05 18:09:21,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg022fe6fc-c0e8-4353-839c-3e69d8f1b676/GCA_001830495.1_ASM183049v1_genomic.fna.gz --refList GCA_001830495.1_ASM183049v1_genomic.fna/target_genomes.txt --output GCA_001830495.1_ASM183049v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:09:35,562] [INFO] Task succeeded: fastANI
[2023-06-05 18:09:35,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0b62e34-bea4-4e66-aacb-fa481984e5aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:09:35,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0b62e34-bea4-4e66-aacb-fa481984e5aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:09:35,565] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:09:35,565] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:09:35,565] [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
--------------------------------------------------------------------------------
[2023-06-05 18:09:35,567] [INFO] DFAST Taxonomy check result was written to GCA_001830495.1_ASM183049v1_genomic.fna/tc_result.tsv
[2023-06-05 18:09:35,567] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:09:35,567] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:09:35,567] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0b62e34-bea4-4e66-aacb-fa481984e5aa/dqc_reference/checkm_data
[2023-06-05 18:09:35,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:09:35,583] [INFO] Task started: CheckM
[2023-06-05 18:09:35,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001830495.1_ASM183049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001830495.1_ASM183049v1_genomic.fna/checkm_input GCA_001830495.1_ASM183049v1_genomic.fna/checkm_result
[2023-06-05 18:09:49,184] [INFO] Task succeeded: CheckM
[2023-06-05 18:09:49,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:09:49,199] [INFO] ===== Completeness check finished =====
[2023-06-05 18:09:49,200] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:09:49,201] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001830495.1_ASM183049v1_genomic.fna/markers.fasta)
[2023-06-05 18:09:49,201] [INFO] Task started: Blastn
[2023-06-05 18:09:49,201] [INFO] Running command: blastn -query GCA_001830495.1_ASM183049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0b62e34-bea4-4e66-aacb-fa481984e5aa/dqc_reference/reference_markers_gtdb.fasta -out GCA_001830495.1_ASM183049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:09:49,816] [INFO] Task succeeded: Blastn
[2023-06-05 18:09:49,820] [INFO] Selected 11 target genomes.
[2023-06-05 18:09:49,820] [INFO] Target genome list was writen to GCA_001830495.1_ASM183049v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:09:49,837] [INFO] Task started: fastANI
[2023-06-05 18:09:49,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg022fe6fc-c0e8-4353-839c-3e69d8f1b676/GCA_001830495.1_ASM183049v1_genomic.fna.gz --refList GCA_001830495.1_ASM183049v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001830495.1_ASM183049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:09:55,071] [INFO] Task succeeded: fastANI
[2023-06-05 18:09:55,078] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:09:55,078] [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_011620315.1	s__Sideroxydans sp011620315	87.5483	61	67	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013791855.1	s__Sideroxydans sp013791855	86.2373	61	67	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	99.90	99.88	0.98	0.96	4	-
GCA_018819205.1	s__Sideroxydans sp018819205	84.9124	54	67	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	99.83	99.83	0.84	0.84	2	-
GCA_018814405.1	s__Sideroxydans sp018814405	84.3778	63	67	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	100.00	100.00	0.99	0.99	3	-
GCA_016214695.1	s__Sideroxydans sp016214695	81.2678	53	67	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208015.1	s__Sideroxydans sp016208015	80.9664	56	67	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003445795.1	s__Sideroxydans sp003445795	80.7977	52	67	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018813765.1	s__Sideroxydans sp018813765	80.482	54	67	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	99.93	99.86	0.97	0.93	3	-
GCA_016235045.1	s__Sideroxydans sp016235045	80.1589	52	67	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Gallionellaceae;g__Sideroxydans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:09:55,080] [INFO] GTDB search result was written to GCA_001830495.1_ASM183049v1_genomic.fna/result_gtdb.tsv
[2023-06-05 18:09:55,081] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:09:55,083] [INFO] DFAST_QC result json was written to GCA_001830495.1_ASM183049v1_genomic.fna/dqc_result.json
[2023-06-05 18:09:55,083] [INFO] DFAST_QC completed!
[2023-06-05 18:09:55,083] [INFO] Total running time: 0h0m40s