[2024-01-24 10:47:09,597] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:09,604] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:09,605] [INFO] DQC Reference Directory: /var/lib/cwl/stgac588b3d-9350-4d97-8bb3-d618effda16a/dqc_reference
[2024-01-24 10:47:11,833] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,908] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,909] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a38edae-5a12-43d7-a105-4096fde62d70/GCF_016908355.1_ASM1690835v1_genomic.fna.gz | prodigal -d GCF_016908355.1_ASM1690835v1_genomic.fna/cds.fna -a GCF_016908355.1_ASM1690835v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:17,950] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:17,950] [INFO] Task started: HMMsearch
[2024-01-24 10:47:17,950] [INFO] Running command: hmmsearch --tblout GCF_016908355.1_ASM1690835v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac588b3d-9350-4d97-8bb3-d618effda16a/dqc_reference/reference_markers.hmm GCF_016908355.1_ASM1690835v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:18,217] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:18,219] [INFO] Found 6/6 markers.
[2024-01-24 10:47:18,243] [INFO] Query marker FASTA was written to GCF_016908355.1_ASM1690835v1_genomic.fna/markers.fasta
[2024-01-24 10:47:18,244] [INFO] Task started: Blastn
[2024-01-24 10:47:18,244] [INFO] Running command: blastn -query GCF_016908355.1_ASM1690835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac588b3d-9350-4d97-8bb3-d618effda16a/dqc_reference/reference_markers.fasta -out GCF_016908355.1_ASM1690835v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:19,632] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:19,636] [INFO] Selected 14 target genomes.
[2024-01-24 10:47:19,637] [INFO] Target genome list was writen to GCF_016908355.1_ASM1690835v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:19,904] [INFO] Task started: fastANI
[2024-01-24 10:47:19,905] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a38edae-5a12-43d7-a105-4096fde62d70/GCF_016908355.1_ASM1690835v1_genomic.fna.gz --refList GCF_016908355.1_ASM1690835v1_genomic.fna/target_genomes.txt --output GCF_016908355.1_ASM1690835v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:26,746] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:26,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac588b3d-9350-4d97-8bb3-d618effda16a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:26,747] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac588b3d-9350-4d97-8bb3-d618effda16a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:26,752] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:26,752] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:26,752] [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
Fusibacter tunisiensis	strain=DSM 24436	GCA_016908355.1	1008308	1008308	type	True	100.0	853	855	95	conclusive
Fusibacter ferrireducens	strain=Q10-2	GCA_015352425.1	2785058	2785058	type	True	78.1229	89	855	95	below_threshold
Fusibacter paucivorans	strain=DSM 12116	GCA_018390735.1	76009	76009	type	True	77.3352	51	855	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:26,754] [INFO] DFAST Taxonomy check result was written to GCF_016908355.1_ASM1690835v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:26,755] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:26,755] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:26,755] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac588b3d-9350-4d97-8bb3-d618effda16a/dqc_reference/checkm_data
[2024-01-24 10:47:26,756] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:26,794] [INFO] Task started: CheckM
[2024-01-24 10:47:26,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908355.1_ASM1690835v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908355.1_ASM1690835v1_genomic.fna/checkm_input GCF_016908355.1_ASM1690835v1_genomic.fna/checkm_result
[2024-01-24 10:47:51,517] [INFO] Task succeeded: CheckM
[2024-01-24 10:47:51,518] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:47:51,540] [INFO] ===== Completeness check finished =====
[2024-01-24 10:47:51,541] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:47:51,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908355.1_ASM1690835v1_genomic.fna/markers.fasta)
[2024-01-24 10:47:51,541] [INFO] Task started: Blastn
[2024-01-24 10:47:51,542] [INFO] Running command: blastn -query GCF_016908355.1_ASM1690835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac588b3d-9350-4d97-8bb3-d618effda16a/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908355.1_ASM1690835v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:52,666] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:52,671] [INFO] Selected 25 target genomes.
[2024-01-24 10:47:52,671] [INFO] Target genome list was writen to GCF_016908355.1_ASM1690835v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:47:52,860] [INFO] Task started: fastANI
[2024-01-24 10:47:52,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a38edae-5a12-43d7-a105-4096fde62d70/GCF_016908355.1_ASM1690835v1_genomic.fna.gz --refList GCF_016908355.1_ASM1690835v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908355.1_ASM1690835v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:05,069] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:05,076] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:05,077] [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_016908355.1	s__Fusibacter_C tunisiensis	100.0	853	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002412775.1	s__Fusibacter_C sp002412775	78.4805	99	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_C	95.0	99.85	99.85	0.95	0.95	2	-
GCF_015352425.1	s__Fusibacter_A sp015352425	78.1365	88	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859095.1	s__Fusibacter_C sp014859095	78.0295	99	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452745.1	s__Fusibacter_A sp002452745	77.9275	70	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390735.1	s__Fusibacter paucivorans	77.3352	51	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001748365.1	s__Fusibacter_A sp001748365	77.2915	85	855	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Acidaminobacteraceae;g__Fusibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:05,078] [INFO] GTDB search result was written to GCF_016908355.1_ASM1690835v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:05,079] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:05,082] [INFO] DFAST_QC result json was written to GCF_016908355.1_ASM1690835v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:05,082] [INFO] DFAST_QC completed!
[2024-01-24 10:48:05,083] [INFO] Total running time: 0h0m55s