[2023-06-19 14:29:39,889] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:29:39,896] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:29:39,897] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c18b06a-016a-431f-9a58-21ca74b04940/dqc_reference
[2023-06-19 14:29:42,414] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:29:42,415] [INFO] Task started: Prodigal
[2023-06-19 14:29:42,416] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c2723c8-8350-4362-81a2-f99ea4470c18/GCA_018004435.1_ASM1800443v1_genomic.fna.gz | prodigal -d GCA_018004435.1_ASM1800443v1_genomic.fna/cds.fna -a GCA_018004435.1_ASM1800443v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:29:44,869] [INFO] Task succeeded: Prodigal
[2023-06-19 14:29:44,870] [INFO] Task started: HMMsearch
[2023-06-19 14:29:44,870] [INFO] Running command: hmmsearch --tblout GCA_018004435.1_ASM1800443v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c18b06a-016a-431f-9a58-21ca74b04940/dqc_reference/reference_markers.hmm GCA_018004435.1_ASM1800443v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:29:45,139] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:29:45,141] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8c2723c8-8350-4362-81a2-f99ea4470c18/GCA_018004435.1_ASM1800443v1_genomic.fna.gz]
[2023-06-19 14:29:45,156] [INFO] Query marker FASTA was written to GCA_018004435.1_ASM1800443v1_genomic.fna/markers.fasta
[2023-06-19 14:29:45,156] [INFO] Task started: Blastn
[2023-06-19 14:29:45,156] [INFO] Running command: blastn -query GCA_018004435.1_ASM1800443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c18b06a-016a-431f-9a58-21ca74b04940/dqc_reference/reference_markers.fasta -out GCA_018004435.1_ASM1800443v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:29:49,348] [INFO] Task succeeded: Blastn
[2023-06-19 14:29:49,352] [INFO] Selected 12 target genomes.
[2023-06-19 14:29:49,352] [INFO] Target genome list was writen to GCA_018004435.1_ASM1800443v1_genomic.fna/target_genomes.txt
[2023-06-19 14:29:49,358] [INFO] Task started: fastANI
[2023-06-19 14:29:49,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c2723c8-8350-4362-81a2-f99ea4470c18/GCA_018004435.1_ASM1800443v1_genomic.fna.gz --refList GCA_018004435.1_ASM1800443v1_genomic.fna/target_genomes.txt --output GCA_018004435.1_ASM1800443v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:29:59,334] [INFO] Task succeeded: fastANI
[2023-06-19 14:29:59,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c18b06a-016a-431f-9a58-21ca74b04940/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:29:59,335] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c18b06a-016a-431f-9a58-21ca74b04940/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:29:59,342] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:29:59,342] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 14:29:59,343] [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
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	77.7097	69	237	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	77.557	57	237	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	77.4738	65	237	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	77.2756	57	237	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	76.7722	59	237	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.6984	55	237	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 14:29:59,347] [INFO] DFAST Taxonomy check result was written to GCA_018004435.1_ASM1800443v1_genomic.fna/tc_result.tsv
[2023-06-19 14:29:59,348] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:29:59,348] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:29:59,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c18b06a-016a-431f-9a58-21ca74b04940/dqc_reference/checkm_data
[2023-06-19 14:29:59,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:29:59,378] [INFO] Task started: CheckM
[2023-06-19 14:29:59,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018004435.1_ASM1800443v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018004435.1_ASM1800443v1_genomic.fna/checkm_input GCA_018004435.1_ASM1800443v1_genomic.fna/checkm_result
[2023-06-19 14:30:16,754] [INFO] Task succeeded: CheckM
[2023-06-19 14:30:16,755] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 14:30:16,779] [INFO] ===== Completeness check finished =====
[2023-06-19 14:30:16,780] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:30:16,780] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018004435.1_ASM1800443v1_genomic.fna/markers.fasta)
[2023-06-19 14:30:16,780] [INFO] Task started: Blastn
[2023-06-19 14:30:16,781] [INFO] Running command: blastn -query GCA_018004435.1_ASM1800443v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c18b06a-016a-431f-9a58-21ca74b04940/dqc_reference/reference_markers_gtdb.fasta -out GCA_018004435.1_ASM1800443v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:30:17,524] [INFO] Task succeeded: Blastn
[2023-06-19 14:30:17,528] [INFO] Selected 7 target genomes.
[2023-06-19 14:30:17,529] [INFO] Target genome list was writen to GCA_018004435.1_ASM1800443v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:30:17,534] [INFO] Task started: fastANI
[2023-06-19 14:30:17,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c2723c8-8350-4362-81a2-f99ea4470c18/GCA_018004435.1_ASM1800443v1_genomic.fna.gz --refList GCA_018004435.1_ASM1800443v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018004435.1_ASM1800443v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:30:23,169] [INFO] Task succeeded: fastANI
[2023-06-19 14:30:23,177] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 14:30:23,177] [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_016714645.1	s__M0108 sp016714645	90.6421	206	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018435665.1	s__M0108 sp018435665	81.2966	165	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	99.16	99.16	0.79	0.79	2	-
GCA_019136395.1	s__M0108 sp019136395	80.7849	140	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009928645.1	s__M0108 sp009928645	80.4102	139	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227775.1	s__M0108 sp006227775	80.3044	120	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025485.1	s__Allochromatium vinosum	77.2756	57	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	97.59	97.59	0.87	0.87	2	-
GCA_011392765.1	s__Thiosymbion ectosymbiont	76.831	61	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiosymbion	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 14:30:23,179] [INFO] GTDB search result was written to GCA_018004435.1_ASM1800443v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:30:23,180] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:30:23,185] [INFO] DFAST_QC result json was written to GCA_018004435.1_ASM1800443v1_genomic.fna/dqc_result.json
[2023-06-19 14:30:23,185] [INFO] DFAST_QC completed!
[2023-06-19 14:30:23,185] [INFO] Total running time: 0h0m43s