[2023-06-17 18:03:39,144] [INFO] DFAST_QC pipeline started.
[2023-06-17 18:03:39,145] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 18:03:39,145] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a313b93-b342-4a0f-82b5-159cf3d06e76/dqc_reference
[2023-06-17 18:03:40,347] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 18:03:40,348] [INFO] Task started: Prodigal
[2023-06-17 18:03:40,348] [INFO] Running command: gunzip -c /var/lib/cwl/stgebfc9fe0-6532-441e-9c81-ae2056c97797/GCA_028708595.1_ASM2870859v1_genomic.fna.gz | prodigal -d GCA_028708595.1_ASM2870859v1_genomic.fna/cds.fna -a GCA_028708595.1_ASM2870859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 18:03:43,266] [INFO] Task succeeded: Prodigal
[2023-06-17 18:03:43,267] [INFO] Task started: HMMsearch
[2023-06-17 18:03:43,267] [INFO] Running command: hmmsearch --tblout GCA_028708595.1_ASM2870859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a313b93-b342-4a0f-82b5-159cf3d06e76/dqc_reference/reference_markers.hmm GCA_028708595.1_ASM2870859v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 18:03:43,439] [INFO] Task succeeded: HMMsearch
[2023-06-17 18:03:43,441] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgebfc9fe0-6532-441e-9c81-ae2056c97797/GCA_028708595.1_ASM2870859v1_genomic.fna.gz]
[2023-06-17 18:03:43,459] [INFO] Query marker FASTA was written to GCA_028708595.1_ASM2870859v1_genomic.fna/markers.fasta
[2023-06-17 18:03:43,460] [INFO] Task started: Blastn
[2023-06-17 18:03:43,460] [INFO] Running command: blastn -query GCA_028708595.1_ASM2870859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a313b93-b342-4a0f-82b5-159cf3d06e76/dqc_reference/reference_markers.fasta -out GCA_028708595.1_ASM2870859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 18:03:43,999] [INFO] Task succeeded: Blastn
[2023-06-17 18:03:44,003] [INFO] Selected 9 target genomes.
[2023-06-17 18:03:44,004] [INFO] Target genome list was writen to GCA_028708595.1_ASM2870859v1_genomic.fna/target_genomes.txt
[2023-06-17 18:03:44,006] [INFO] Task started: fastANI
[2023-06-17 18:03:44,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgebfc9fe0-6532-441e-9c81-ae2056c97797/GCA_028708595.1_ASM2870859v1_genomic.fna.gz --refList GCA_028708595.1_ASM2870859v1_genomic.fna/target_genomes.txt --output GCA_028708595.1_ASM2870859v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 18:03:48,270] [INFO] Task succeeded: fastANI
[2023-06-17 18:03:48,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a313b93-b342-4a0f-82b5-159cf3d06e76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 18:03:48,271] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a313b93-b342-4a0f-82b5-159cf3d06e76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 18:03:48,275] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 18:03:48,276] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 18:03:48,276] [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
Sedimentibacter saalensis	strain=DSM 13558	GCA_007830175.1	130788	130788	type	True	77.339	142	484	95	below_threshold
Sedimentibacter hydroxybenzoicus	strain=DSM 7310	GCA_013403245.1	29345	29345	type	True	77.135	129	484	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 18:03:48,277] [INFO] DFAST Taxonomy check result was written to GCA_028708595.1_ASM2870859v1_genomic.fna/tc_result.tsv
[2023-06-17 18:03:48,278] [INFO] ===== Taxonomy check completed =====
[2023-06-17 18:03:48,278] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 18:03:48,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a313b93-b342-4a0f-82b5-159cf3d06e76/dqc_reference/checkm_data
[2023-06-17 18:03:48,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 18:03:48,299] [INFO] Task started: CheckM
[2023-06-17 18:03:48,299] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028708595.1_ASM2870859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028708595.1_ASM2870859v1_genomic.fna/checkm_input GCA_028708595.1_ASM2870859v1_genomic.fna/checkm_result
[2023-06-17 18:04:03,828] [INFO] Task succeeded: CheckM
[2023-06-17 18:04:03,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.98%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 18:04:03,848] [INFO] ===== Completeness check finished =====
[2023-06-17 18:04:03,848] [INFO] ===== Start GTDB Search =====
[2023-06-17 18:04:03,848] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028708595.1_ASM2870859v1_genomic.fna/markers.fasta)
[2023-06-17 18:04:03,849] [INFO] Task started: Blastn
[2023-06-17 18:04:03,849] [INFO] Running command: blastn -query GCA_028708595.1_ASM2870859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a313b93-b342-4a0f-82b5-159cf3d06e76/dqc_reference/reference_markers_gtdb.fasta -out GCA_028708595.1_ASM2870859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 18:04:04,588] [INFO] Task succeeded: Blastn
[2023-06-17 18:04:04,592] [INFO] Selected 7 target genomes.
[2023-06-17 18:04:04,592] [INFO] Target genome list was writen to GCA_028708595.1_ASM2870859v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 18:04:04,623] [INFO] Task started: fastANI
[2023-06-17 18:04:04,624] [INFO] Running command: fastANI --query /var/lib/cwl/stgebfc9fe0-6532-441e-9c81-ae2056c97797/GCA_028708595.1_ASM2870859v1_genomic.fna.gz --refList GCA_028708595.1_ASM2870859v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028708595.1_ASM2870859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 18:04:07,773] [INFO] Task succeeded: fastANI
[2023-06-17 18:04:07,780] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 18:04:07,781] [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_003487955.1	s__Sedimentibacter sp003487955	88.0187	317	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003483345.1	s__Sedimentibacter sp003483345	86.0865	277	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	97.32	97.20	0.62	0.58	3	-
GCA_012519555.1	s__Sedimentibacter sp012519555	83.8877	312	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017995755.1	s__Sedimentibacter sp017995755	82.4954	281	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012520455.1	s__Sedimentibacter sp012520455	80.0493	256	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003457065.1	s__Sedimentibacter sp003457065	77.2326	99	484	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter	95.0	98.22	98.22	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2023-06-17 18:04:07,782] [INFO] GTDB search result was written to GCA_028708595.1_ASM2870859v1_genomic.fna/result_gtdb.tsv
[2023-06-17 18:04:07,783] [INFO] ===== GTDB Search completed =====
[2023-06-17 18:04:07,786] [INFO] DFAST_QC result json was written to GCA_028708595.1_ASM2870859v1_genomic.fna/dqc_result.json
[2023-06-17 18:04:07,786] [INFO] DFAST_QC completed!
[2023-06-17 18:04:07,786] [INFO] Total running time: 0h0m29s