[2023-06-28 00:20:37,323] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:20:37,325] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:20:37,325] [INFO] DQC Reference Directory: /var/lib/cwl/stgd92f8fdb-430f-45c9-a60f-faa95dd5c17f/dqc_reference
[2023-06-28 00:20:38,599] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:20:38,600] [INFO] Task started: Prodigal
[2023-06-28 00:20:38,600] [INFO] Running command: gunzip -c /var/lib/cwl/stg14c88fe7-e41e-4af4-9442-1c7e541abc5c/GCA_017542545.1_ASM1754254v1_genomic.fna.gz | prodigal -d GCA_017542545.1_ASM1754254v1_genomic.fna/cds.fna -a GCA_017542545.1_ASM1754254v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:20:45,041] [INFO] Task succeeded: Prodigal
[2023-06-28 00:20:45,042] [INFO] Task started: HMMsearch
[2023-06-28 00:20:45,042] [INFO] Running command: hmmsearch --tblout GCA_017542545.1_ASM1754254v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd92f8fdb-430f-45c9-a60f-faa95dd5c17f/dqc_reference/reference_markers.hmm GCA_017542545.1_ASM1754254v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:20:45,300] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:20:45,301] [INFO] Found 6/6 markers.
[2023-06-28 00:20:45,325] [INFO] Query marker FASTA was written to GCA_017542545.1_ASM1754254v1_genomic.fna/markers.fasta
[2023-06-28 00:20:45,325] [INFO] Task started: Blastn
[2023-06-28 00:20:45,325] [INFO] Running command: blastn -query GCA_017542545.1_ASM1754254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd92f8fdb-430f-45c9-a60f-faa95dd5c17f/dqc_reference/reference_markers.fasta -out GCA_017542545.1_ASM1754254v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:20:45,963] [INFO] Task succeeded: Blastn
[2023-06-28 00:20:45,970] [INFO] Selected 19 target genomes.
[2023-06-28 00:20:45,970] [INFO] Target genome list was writen to GCA_017542545.1_ASM1754254v1_genomic.fna/target_genomes.txt
[2023-06-28 00:20:45,977] [INFO] Task started: fastANI
[2023-06-28 00:20:45,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg14c88fe7-e41e-4af4-9442-1c7e541abc5c/GCA_017542545.1_ASM1754254v1_genomic.fna.gz --refList GCA_017542545.1_ASM1754254v1_genomic.fna/target_genomes.txt --output GCA_017542545.1_ASM1754254v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:20:57,971] [INFO] Task succeeded: fastANI
[2023-06-28 00:20:57,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd92f8fdb-430f-45c9-a60f-faa95dd5c17f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:20:57,973] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd92f8fdb-430f-45c9-a60f-faa95dd5c17f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:20:57,976] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:20:57,976] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 00:20:57,976] [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
--------------------------------------------------------------------------------
[2023-06-28 00:20:57,979] [INFO] DFAST Taxonomy check result was written to GCA_017542545.1_ASM1754254v1_genomic.fna/tc_result.tsv
[2023-06-28 00:20:57,979] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:20:57,980] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:20:57,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd92f8fdb-430f-45c9-a60f-faa95dd5c17f/dqc_reference/checkm_data
[2023-06-28 00:20:57,984] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:20:58,019] [INFO] Task started: CheckM
[2023-06-28 00:20:58,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017542545.1_ASM1754254v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017542545.1_ASM1754254v1_genomic.fna/checkm_input GCA_017542545.1_ASM1754254v1_genomic.fna/checkm_result
[2023-06-28 00:21:23,402] [INFO] Task succeeded: CheckM
[2023-06-28 00:21:23,403] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:21:23,428] [INFO] ===== Completeness check finished =====
[2023-06-28 00:21:23,429] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:21:23,429] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017542545.1_ASM1754254v1_genomic.fna/markers.fasta)
[2023-06-28 00:21:23,430] [INFO] Task started: Blastn
[2023-06-28 00:21:23,430] [INFO] Running command: blastn -query GCA_017542545.1_ASM1754254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd92f8fdb-430f-45c9-a60f-faa95dd5c17f/dqc_reference/reference_markers_gtdb.fasta -out GCA_017542545.1_ASM1754254v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:21:24,454] [INFO] Task succeeded: Blastn
[2023-06-28 00:21:24,459] [INFO] Selected 24 target genomes.
[2023-06-28 00:21:24,459] [INFO] Target genome list was writen to GCA_017542545.1_ASM1754254v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:21:24,531] [INFO] Task started: fastANI
[2023-06-28 00:21:24,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg14c88fe7-e41e-4af4-9442-1c7e541abc5c/GCA_017542545.1_ASM1754254v1_genomic.fna.gz --refList GCA_017542545.1_ASM1754254v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017542545.1_ASM1754254v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:21:33,704] [INFO] Task succeeded: fastANI
[2023-06-28 00:21:33,721] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 00:21:33,721] [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_002395525.1	s__CAG-353 sp002395525	96.3737	619	744	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	96.47	96.29	0.90	0.88	5	conclusive
GCA_018110985.1	s__CAG-353 sp018110985	78.7605	196	744	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018110925.1	s__CAG-353 sp018110925	78.4028	117	744	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017829005.1	s__CAG-353 sp017829005	77.6888	92	744	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900768995.1	s__CAG-353 sp900768995	77.6869	100	744	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	95.84	95.84	0.78	0.78	2	-
GCA_902363145.1	s__CAG-353 sp900066885	77.6027	123	744	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	98.51	98.32	0.91	0.87	6	-
GCA_017394475.1	s__CAG-353 sp017394475	77.4564	100	744	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017410745.1	s__CAG-353 sp017410745	77.4377	121	744	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782875.1	s__CAG-353 sp902782875	77.2841	85	744	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018110855.1	s__CAG-353 sp018110855	76.9345	57	744	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-353	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017847885.1	s__RGIG8773 sp017847885	76.8012	61	744	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__RGIG8773	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584715.1	s__RGIG8773 sp910584715	76.5281	60	744	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__RGIG8773	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 00:21:33,725] [INFO] GTDB search result was written to GCA_017542545.1_ASM1754254v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:21:33,726] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:21:33,730] [INFO] DFAST_QC result json was written to GCA_017542545.1_ASM1754254v1_genomic.fna/dqc_result.json
[2023-06-28 00:21:33,730] [INFO] DFAST_QC completed!
[2023-06-28 00:21:33,730] [INFO] Total running time: 0h0m56s