[2023-06-28 10:00:47,020] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:00:47,022] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:00:47,022] [INFO] DQC Reference Directory: /var/lib/cwl/stgb70ec12c-4c28-44a7-9ec6-13e02313ab49/dqc_reference
[2023-06-28 10:00:48,219] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:00:48,220] [INFO] Task started: Prodigal
[2023-06-28 10:00:48,220] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a9f3fb2-23d0-4eb8-bef5-35621f0f1be4/GCA_017435965.1_ASM1743596v1_genomic.fna.gz | prodigal -d GCA_017435965.1_ASM1743596v1_genomic.fna/cds.fna -a GCA_017435965.1_ASM1743596v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:00:54,403] [INFO] Task succeeded: Prodigal
[2023-06-28 10:00:54,404] [INFO] Task started: HMMsearch
[2023-06-28 10:00:54,404] [INFO] Running command: hmmsearch --tblout GCA_017435965.1_ASM1743596v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb70ec12c-4c28-44a7-9ec6-13e02313ab49/dqc_reference/reference_markers.hmm GCA_017435965.1_ASM1743596v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:00:54,702] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:00:54,703] [INFO] Found 6/6 markers.
[2023-06-28 10:00:54,761] [INFO] Query marker FASTA was written to GCA_017435965.1_ASM1743596v1_genomic.fna/markers.fasta
[2023-06-28 10:00:54,762] [INFO] Task started: Blastn
[2023-06-28 10:00:54,762] [INFO] Running command: blastn -query GCA_017435965.1_ASM1743596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb70ec12c-4c28-44a7-9ec6-13e02313ab49/dqc_reference/reference_markers.fasta -out GCA_017435965.1_ASM1743596v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:00:55,454] [INFO] Task succeeded: Blastn
[2023-06-28 10:00:55,458] [INFO] Selected 21 target genomes.
[2023-06-28 10:00:55,458] [INFO] Target genome list was writen to GCA_017435965.1_ASM1743596v1_genomic.fna/target_genomes.txt
[2023-06-28 10:00:55,459] [INFO] Task started: fastANI
[2023-06-28 10:00:55,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a9f3fb2-23d0-4eb8-bef5-35621f0f1be4/GCA_017435965.1_ASM1743596v1_genomic.fna.gz --refList GCA_017435965.1_ASM1743596v1_genomic.fna/target_genomes.txt --output GCA_017435965.1_ASM1743596v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:01:07,212] [INFO] Task succeeded: fastANI
[2023-06-28 10:01:07,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb70ec12c-4c28-44a7-9ec6-13e02313ab49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:01:07,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb70ec12c-4c28-44a7-9ec6-13e02313ab49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:01:07,215] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:01:07,215] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 10:01:07,215] [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 10:01:07,217] [INFO] DFAST Taxonomy check result was written to GCA_017435965.1_ASM1743596v1_genomic.fna/tc_result.tsv
[2023-06-28 10:01:07,218] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:01:07,218] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:01:07,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb70ec12c-4c28-44a7-9ec6-13e02313ab49/dqc_reference/checkm_data
[2023-06-28 10:01:07,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:01:07,254] [INFO] Task started: CheckM
[2023-06-28 10:01:07,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017435965.1_ASM1743596v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017435965.1_ASM1743596v1_genomic.fna/checkm_input GCA_017435965.1_ASM1743596v1_genomic.fna/checkm_result
[2023-06-28 10:01:33,939] [INFO] Task succeeded: CheckM
[2023-06-28 10:01:33,941] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:01:33,966] [INFO] ===== Completeness check finished =====
[2023-06-28 10:01:33,967] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:01:33,967] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017435965.1_ASM1743596v1_genomic.fna/markers.fasta)
[2023-06-28 10:01:33,967] [INFO] Task started: Blastn
[2023-06-28 10:01:33,968] [INFO] Running command: blastn -query GCA_017435965.1_ASM1743596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb70ec12c-4c28-44a7-9ec6-13e02313ab49/dqc_reference/reference_markers_gtdb.fasta -out GCA_017435965.1_ASM1743596v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:01:34,974] [INFO] Task succeeded: Blastn
[2023-06-28 10:01:34,979] [INFO] Selected 19 target genomes.
[2023-06-28 10:01:34,979] [INFO] Target genome list was writen to GCA_017435965.1_ASM1743596v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:01:34,985] [INFO] Task started: fastANI
[2023-06-28 10:01:34,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a9f3fb2-23d0-4eb8-bef5-35621f0f1be4/GCA_017435965.1_ASM1743596v1_genomic.fna.gz --refList GCA_017435965.1_ASM1743596v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017435965.1_ASM1743596v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:01:43,139] [INFO] Task succeeded: fastANI
[2023-06-28 10:01:43,151] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:01:43,151] [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_017435965.1	s__SIG480 sp017435965	100.0	814	822	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__JAAYXM01;g__SIG480	95.0	96.60	96.60	0.81	0.81	2	conclusive
GCA_017408185.1	s__SIG480 sp017408185	86.5451	251	822	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__JAAYXM01;g__SIG480	95.0	97.20	97.20	0.77	0.77	2	-
GCA_017439555.1	s__SIG480 sp017439555	79.52	218	822	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__JAAYXM01;g__SIG480	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015068085.1	s__SIG480 sp015068085	79.1765	190	822	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__JAAYXM01;g__SIG480	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017409405.1	s__SIG480 sp017409405	78.1196	167	822	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__JAAYXM01;g__SIG480	95.0	98.22	98.17	0.85	0.84	3	-
GCA_017532355.1	s__SIG480 sp017532355	77.9877	94	822	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__JAAYXM01;g__SIG480	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017559985.1	s__SIG480 sp017559985	77.818	114	822	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__JAAYXM01;g__SIG480	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:01:43,154] [INFO] GTDB search result was written to GCA_017435965.1_ASM1743596v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:01:43,155] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:01:43,157] [INFO] DFAST_QC result json was written to GCA_017435965.1_ASM1743596v1_genomic.fna/dqc_result.json
[2023-06-28 10:01:43,157] [INFO] DFAST_QC completed!
[2023-06-28 10:01:43,158] [INFO] Total running time: 0h0m56s