[2023-06-05 08:49:15,796] [INFO] DFAST_QC pipeline started.
[2023-06-05 08:49:15,798] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 08:49:15,798] [INFO] DQC Reference Directory: /var/lib/cwl/stg3acf008e-9deb-4489-a682-537f0acffa79/dqc_reference
[2023-06-05 08:49:17,159] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 08:49:17,160] [INFO] Task started: Prodigal
[2023-06-05 08:49:17,161] [INFO] Running command: gunzip -c /var/lib/cwl/stg3fe0f658-ebe6-40a5-bebd-7fbbdf96a22d/GCA_004556205.1_ASM455620v1_genomic.fna.gz | prodigal -d GCA_004556205.1_ASM455620v1_genomic.fna/cds.fna -a GCA_004556205.1_ASM455620v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 08:49:21,424] [INFO] Task succeeded: Prodigal
[2023-06-05 08:49:21,425] [INFO] Task started: HMMsearch
[2023-06-05 08:49:21,425] [INFO] Running command: hmmsearch --tblout GCA_004556205.1_ASM455620v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3acf008e-9deb-4489-a682-537f0acffa79/dqc_reference/reference_markers.hmm GCA_004556205.1_ASM455620v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 08:49:21,662] [INFO] Task succeeded: HMMsearch
[2023-06-05 08:49:21,664] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3fe0f658-ebe6-40a5-bebd-7fbbdf96a22d/GCA_004556205.1_ASM455620v1_genomic.fna.gz]
[2023-06-05 08:49:21,686] [INFO] Query marker FASTA was written to GCA_004556205.1_ASM455620v1_genomic.fna/markers.fasta
[2023-06-05 08:49:21,687] [INFO] Task started: Blastn
[2023-06-05 08:49:21,687] [INFO] Running command: blastn -query GCA_004556205.1_ASM455620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3acf008e-9deb-4489-a682-537f0acffa79/dqc_reference/reference_markers.fasta -out GCA_004556205.1_ASM455620v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:49:22,356] [INFO] Task succeeded: Blastn
[2023-06-05 08:49:22,360] [INFO] Selected 21 target genomes.
[2023-06-05 08:49:22,360] [INFO] Target genome list was writen to GCA_004556205.1_ASM455620v1_genomic.fna/target_genomes.txt
[2023-06-05 08:49:22,361] [INFO] Task started: fastANI
[2023-06-05 08:49:22,362] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fe0f658-ebe6-40a5-bebd-7fbbdf96a22d/GCA_004556205.1_ASM455620v1_genomic.fna.gz --refList GCA_004556205.1_ASM455620v1_genomic.fna/target_genomes.txt --output GCA_004556205.1_ASM455620v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 08:49:33,468] [INFO] Task succeeded: fastANI
[2023-06-05 08:49:33,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3acf008e-9deb-4489-a682-537f0acffa79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 08:49:33,469] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3acf008e-9deb-4489-a682-537f0acffa79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 08:49:33,470] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 08:49:33,470] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 08:49:33,470] [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
--------------------------------------------------------------------------------
[2023-06-05 08:49:33,473] [INFO] DFAST Taxonomy check result was written to GCA_004556205.1_ASM455620v1_genomic.fna/tc_result.tsv
[2023-06-05 08:49:33,473] [INFO] ===== Taxonomy check completed =====
[2023-06-05 08:49:33,474] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 08:49:33,474] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3acf008e-9deb-4489-a682-537f0acffa79/dqc_reference/checkm_data
[2023-06-05 08:49:33,477] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 08:49:33,503] [INFO] Task started: CheckM
[2023-06-05 08:49:33,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004556205.1_ASM455620v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004556205.1_ASM455620v1_genomic.fna/checkm_input GCA_004556205.1_ASM455620v1_genomic.fna/checkm_result
[2023-06-05 08:49:52,683] [INFO] Task succeeded: CheckM
[2023-06-05 08:49:52,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 08:49:52,703] [INFO] ===== Completeness check finished =====
[2023-06-05 08:49:52,703] [INFO] ===== Start GTDB Search =====
[2023-06-05 08:49:52,703] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004556205.1_ASM455620v1_genomic.fna/markers.fasta)
[2023-06-05 08:49:52,704] [INFO] Task started: Blastn
[2023-06-05 08:49:52,704] [INFO] Running command: blastn -query GCA_004556205.1_ASM455620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3acf008e-9deb-4489-a682-537f0acffa79/dqc_reference/reference_markers_gtdb.fasta -out GCA_004556205.1_ASM455620v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:49:53,632] [INFO] Task succeeded: Blastn
[2023-06-05 08:49:53,637] [INFO] Selected 13 target genomes.
[2023-06-05 08:49:53,638] [INFO] Target genome list was writen to GCA_004556205.1_ASM455620v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 08:49:53,642] [INFO] Task started: fastANI
[2023-06-05 08:49:53,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fe0f658-ebe6-40a5-bebd-7fbbdf96a22d/GCA_004556205.1_ASM455620v1_genomic.fna.gz --refList GCA_004556205.1_ASM455620v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004556205.1_ASM455620v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 08:49:57,962] [INFO] Task succeeded: fastANI
[2023-06-05 08:49:57,977] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 08:49:57,977] [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_004556205.1	s__Faecousia sp004556205	100.0	470	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016302005.1	s__Faecousia sp016302005	84.7743	260	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233385.1	s__Faecousia sp905233385	79.7393	192	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551495.1	s__Faecousia sp900551495	79.7114	161	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.39	98.78	0.89	0.81	3	-
GCA_017429835.1	s__Faecousia sp017429835	79.5958	198	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017405865.1	s__Faecousia sp017405865	79.3893	180	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769995.1	s__Faecousia sp900769995	79.3807	165	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235655.1	s__Faecousia sp905235655	79.3443	167	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546415.1	s__Faecousia sp900546415	79.2196	170	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	98.49	97.72	0.83	0.81	4	-
GCA_900544705.1	s__Faecousia sp900544705	78.9068	166	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	98.60	98.49	0.88	0.86	3	-
GCA_016296045.1	s__Faecousia sp016296045	78.8515	133	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577345.1	s__Faecousia sp017577345	78.7318	135	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 08:49:57,979] [INFO] GTDB search result was written to GCA_004556205.1_ASM455620v1_genomic.fna/result_gtdb.tsv
[2023-06-05 08:49:57,979] [INFO] ===== GTDB Search completed =====
[2023-06-05 08:49:57,982] [INFO] DFAST_QC result json was written to GCA_004556205.1_ASM455620v1_genomic.fna/dqc_result.json
[2023-06-05 08:49:57,982] [INFO] DFAST_QC completed!
[2023-06-05 08:49:57,982] [INFO] Total running time: 0h0m42s