[2023-06-28 12:04:02,408] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:04:02,411] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:04:02,411] [INFO] DQC Reference Directory: /var/lib/cwl/stg6afdf272-45f4-4798-af56-0392c15d6465/dqc_reference
[2023-06-28 12:04:03,785] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:04:03,786] [INFO] Task started: Prodigal
[2023-06-28 12:04:03,786] [INFO] Running command: gunzip -c /var/lib/cwl/stgb017b43f-255a-4802-b804-c3dfda09a98d/GCA_944338265.1_BRZ_EM_bin56_genomic.fna.gz | prodigal -d GCA_944338265.1_BRZ_EM_bin56_genomic.fna/cds.fna -a GCA_944338265.1_BRZ_EM_bin56_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:04:07,444] [INFO] Task succeeded: Prodigal
[2023-06-28 12:04:07,445] [INFO] Task started: HMMsearch
[2023-06-28 12:04:07,445] [INFO] Running command: hmmsearch --tblout GCA_944338265.1_BRZ_EM_bin56_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6afdf272-45f4-4798-af56-0392c15d6465/dqc_reference/reference_markers.hmm GCA_944338265.1_BRZ_EM_bin56_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:04:07,667] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:04:07,669] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb017b43f-255a-4802-b804-c3dfda09a98d/GCA_944338265.1_BRZ_EM_bin56_genomic.fna.gz]
[2023-06-28 12:04:07,695] [INFO] Query marker FASTA was written to GCA_944338265.1_BRZ_EM_bin56_genomic.fna/markers.fasta
[2023-06-28 12:04:07,695] [INFO] Task started: Blastn
[2023-06-28 12:04:07,695] [INFO] Running command: blastn -query GCA_944338265.1_BRZ_EM_bin56_genomic.fna/markers.fasta -db /var/lib/cwl/stg6afdf272-45f4-4798-af56-0392c15d6465/dqc_reference/reference_markers.fasta -out GCA_944338265.1_BRZ_EM_bin56_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:04:08,387] [INFO] Task succeeded: Blastn
[2023-06-28 12:04:08,392] [INFO] Selected 20 target genomes.
[2023-06-28 12:04:08,392] [INFO] Target genome list was writen to GCA_944338265.1_BRZ_EM_bin56_genomic.fna/target_genomes.txt
[2023-06-28 12:04:08,397] [INFO] Task started: fastANI
[2023-06-28 12:04:08,398] [INFO] Running command: fastANI --query /var/lib/cwl/stgb017b43f-255a-4802-b804-c3dfda09a98d/GCA_944338265.1_BRZ_EM_bin56_genomic.fna.gz --refList GCA_944338265.1_BRZ_EM_bin56_genomic.fna/target_genomes.txt --output GCA_944338265.1_BRZ_EM_bin56_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:04:23,288] [INFO] Task succeeded: fastANI
[2023-06-28 12:04:23,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6afdf272-45f4-4798-af56-0392c15d6465/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:04:23,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6afdf272-45f4-4798-af56-0392c15d6465/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:04:23,292] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:04:23,292] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:04:23,292] [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 12:04:23,295] [INFO] DFAST Taxonomy check result was written to GCA_944338265.1_BRZ_EM_bin56_genomic.fna/tc_result.tsv
[2023-06-28 12:04:23,295] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:04:23,295] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:04:23,296] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6afdf272-45f4-4798-af56-0392c15d6465/dqc_reference/checkm_data
[2023-06-28 12:04:23,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:04:23,319] [INFO] Task started: CheckM
[2023-06-28 12:04:23,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944338265.1_BRZ_EM_bin56_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944338265.1_BRZ_EM_bin56_genomic.fna/checkm_input GCA_944338265.1_BRZ_EM_bin56_genomic.fna/checkm_result
[2023-06-28 12:04:41,298] [INFO] Task succeeded: CheckM
[2023-06-28 12:04:41,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.14%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:04:41,322] [INFO] ===== Completeness check finished =====
[2023-06-28 12:04:41,322] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:04:41,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944338265.1_BRZ_EM_bin56_genomic.fna/markers.fasta)
[2023-06-28 12:04:41,323] [INFO] Task started: Blastn
[2023-06-28 12:04:41,323] [INFO] Running command: blastn -query GCA_944338265.1_BRZ_EM_bin56_genomic.fna/markers.fasta -db /var/lib/cwl/stg6afdf272-45f4-4798-af56-0392c15d6465/dqc_reference/reference_markers_gtdb.fasta -out GCA_944338265.1_BRZ_EM_bin56_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:04:42,494] [INFO] Task succeeded: Blastn
[2023-06-28 12:04:42,502] [INFO] Selected 13 target genomes.
[2023-06-28 12:04:42,503] [INFO] Target genome list was writen to GCA_944338265.1_BRZ_EM_bin56_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:04:42,518] [INFO] Task started: fastANI
[2023-06-28 12:04:42,518] [INFO] Running command: fastANI --query /var/lib/cwl/stgb017b43f-255a-4802-b804-c3dfda09a98d/GCA_944338265.1_BRZ_EM_bin56_genomic.fna.gz --refList GCA_944338265.1_BRZ_EM_bin56_genomic.fna/target_genomes_gtdb.txt --output GCA_944338265.1_BRZ_EM_bin56_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:04:46,943] [INFO] Task succeeded: fastANI
[2023-06-28 12:04:46,968] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:04:46,968] [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_904373325.1	s__Gallimonas merdigallinarum	83.3581	275	385	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	98.69	97.92	0.89	0.88	4	-
GCA_900547645.1	s__Gallimonas faecium	79.7549	195	385	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	98.43	98.37	0.87	0.83	4	-
GCA_019116405.1	s__Gallimonas intestinigallinarum	79.7274	199	385	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904394195.1	s__Gallimonas caecicola	79.4309	157	385	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019117085.1	s__Gallimonas gallistercoris	79.2878	165	385	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548845.1	s__Gallimonas sp900548845	79.1463	131	385	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	97.44	97.44	0.90	0.90	2	-
GCF_904419525.1	s__Gallimonas merdae	78.9323	189	385	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	99.30	98.70	0.95	0.93	3	-
GCF_904391375.1	s__Gallimonas faecavium	78.9161	166	385	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017887095.1	s__Gallimonas sp017887095	78.4971	146	385	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761685.1	s__Gallimonas intestinalis	78.2975	166	385	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	97.36	97.33	0.87	0.87	3	-
GCA_910586675.1	s__Gallimonas sp910586675	77.6924	100	385	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712725.1	s__Scatosoma pullicola	76.9953	67	385	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	99.20	98.54	0.90	0.87	3	-
GCA_019114625.1	s__Borkfalkia faecigallinarum	76.7563	74	385	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	98.33	98.33	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2023-06-28 12:04:46,971] [INFO] GTDB search result was written to GCA_944338265.1_BRZ_EM_bin56_genomic.fna/result_gtdb.tsv
[2023-06-28 12:04:46,971] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:04:46,974] [INFO] DFAST_QC result json was written to GCA_944338265.1_BRZ_EM_bin56_genomic.fna/dqc_result.json
[2023-06-28 12:04:46,974] [INFO] DFAST_QC completed!
[2023-06-28 12:04:46,975] [INFO] Total running time: 0h0m45s