[2023-06-28 15:26:17,711] [INFO] DFAST_QC pipeline started.
[2023-06-28 15:26:17,713] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 15:26:17,713] [INFO] DQC Reference Directory: /var/lib/cwl/stgc261ea7f-0962-4dbf-a3b2-338510063a70/dqc_reference
[2023-06-28 15:26:19,013] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 15:26:19,013] [INFO] Task started: Prodigal
[2023-06-28 15:26:19,014] [INFO] Running command: gunzip -c /var/lib/cwl/stg71650266-5841-49f3-95d3-6c07bf2a252d/GCA_944376455.1_BRZ_CS_bin61_genomic.fna.gz | prodigal -d GCA_944376455.1_BRZ_CS_bin61_genomic.fna/cds.fna -a GCA_944376455.1_BRZ_CS_bin61_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 15:26:23,171] [INFO] Task succeeded: Prodigal
[2023-06-28 15:26:23,171] [INFO] Task started: HMMsearch
[2023-06-28 15:26:23,171] [INFO] Running command: hmmsearch --tblout GCA_944376455.1_BRZ_CS_bin61_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc261ea7f-0962-4dbf-a3b2-338510063a70/dqc_reference/reference_markers.hmm GCA_944376455.1_BRZ_CS_bin61_genomic.fna/protein.faa > /dev/null
[2023-06-28 15:26:23,371] [INFO] Task succeeded: HMMsearch
[2023-06-28 15:26:23,372] [INFO] Found 6/6 markers.
[2023-06-28 15:26:23,389] [INFO] Query marker FASTA was written to GCA_944376455.1_BRZ_CS_bin61_genomic.fna/markers.fasta
[2023-06-28 15:26:23,389] [INFO] Task started: Blastn
[2023-06-28 15:26:23,389] [INFO] Running command: blastn -query GCA_944376455.1_BRZ_CS_bin61_genomic.fna/markers.fasta -db /var/lib/cwl/stgc261ea7f-0962-4dbf-a3b2-338510063a70/dqc_reference/reference_markers.fasta -out GCA_944376455.1_BRZ_CS_bin61_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:26:23,924] [INFO] Task succeeded: Blastn
[2023-06-28 15:26:23,927] [INFO] Selected 25 target genomes.
[2023-06-28 15:26:23,927] [INFO] Target genome list was writen to GCA_944376455.1_BRZ_CS_bin61_genomic.fna/target_genomes.txt
[2023-06-28 15:26:23,930] [INFO] Task started: fastANI
[2023-06-28 15:26:23,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg71650266-5841-49f3-95d3-6c07bf2a252d/GCA_944376455.1_BRZ_CS_bin61_genomic.fna.gz --refList GCA_944376455.1_BRZ_CS_bin61_genomic.fna/target_genomes.txt --output GCA_944376455.1_BRZ_CS_bin61_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 15:26:39,136] [INFO] Task succeeded: fastANI
[2023-06-28 15:26:39,137] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc261ea7f-0962-4dbf-a3b2-338510063a70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 15:26:39,137] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc261ea7f-0962-4dbf-a3b2-338510063a70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 15:26:39,139] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 15:26:39,139] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 15:26:39,139] [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 15:26:39,141] [INFO] DFAST Taxonomy check result was written to GCA_944376455.1_BRZ_CS_bin61_genomic.fna/tc_result.tsv
[2023-06-28 15:26:39,141] [INFO] ===== Taxonomy check completed =====
[2023-06-28 15:26:39,141] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 15:26:39,141] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc261ea7f-0962-4dbf-a3b2-338510063a70/dqc_reference/checkm_data
[2023-06-28 15:26:39,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 15:26:39,167] [INFO] Task started: CheckM
[2023-06-28 15:26:39,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944376455.1_BRZ_CS_bin61_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944376455.1_BRZ_CS_bin61_genomic.fna/checkm_input GCA_944376455.1_BRZ_CS_bin61_genomic.fna/checkm_result
[2023-06-28 15:26:56,569] [INFO] Task succeeded: CheckM
[2023-06-28 15:26:56,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 15:26:56,586] [INFO] ===== Completeness check finished =====
[2023-06-28 15:26:56,586] [INFO] ===== Start GTDB Search =====
[2023-06-28 15:26:56,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944376455.1_BRZ_CS_bin61_genomic.fna/markers.fasta)
[2023-06-28 15:26:56,587] [INFO] Task started: Blastn
[2023-06-28 15:26:56,587] [INFO] Running command: blastn -query GCA_944376455.1_BRZ_CS_bin61_genomic.fna/markers.fasta -db /var/lib/cwl/stgc261ea7f-0962-4dbf-a3b2-338510063a70/dqc_reference/reference_markers_gtdb.fasta -out GCA_944376455.1_BRZ_CS_bin61_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:26:57,365] [INFO] Task succeeded: Blastn
[2023-06-28 15:26:57,369] [INFO] Selected 18 target genomes.
[2023-06-28 15:26:57,369] [INFO] Target genome list was writen to GCA_944376455.1_BRZ_CS_bin61_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 15:26:57,374] [INFO] Task started: fastANI
[2023-06-28 15:26:57,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg71650266-5841-49f3-95d3-6c07bf2a252d/GCA_944376455.1_BRZ_CS_bin61_genomic.fna.gz --refList GCA_944376455.1_BRZ_CS_bin61_genomic.fna/target_genomes_gtdb.txt --output GCA_944376455.1_BRZ_CS_bin61_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 15:27:02,988] [INFO] Task succeeded: fastANI
[2023-06-28 15:27:02,997] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 15:27:02,997] [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_017886575.1	s__RGIG4074 sp017886575	81.6979	302	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__RGIG4074	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017462425.1	s__RGIG4074 sp017462425	77.7377	56	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__RGIG4074	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017508105.1	s__RGIG4074 sp017508105	77.3657	131	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__RGIG4074	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712725.1	s__Scatosoma pullicola	77.2437	92	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	99.20	98.54	0.90	0.87	3	-
GCF_904419525.1	s__Gallimonas merdae	77.0072	94	540	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_904373325.1	s__Gallimonas merdigallinarum	76.9614	94	540	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	76.8414	77	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	98.43	98.37	0.87	0.83	4	-
GCF_904391375.1	s__Gallimonas faecavium	76.7202	78	540	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_900540805.1	s__Scatosoma sp003150575	76.6488	60	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	99.20	98.47	0.92	0.85	5	-
GCA_905209085.1	s__Scatosoma sp900552625	76.4871	71	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	99.19	98.78	0.94	0.91	5	-
GCA_904419075.1	s__Scatosoma sp904419075	76.3666	67	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	97.64	97.64	0.92	0.92	2	-
GCA_018714725.1	s__Scatosoma pullistercoris	76.3576	60	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Scatosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004134775.1	s__Borkfalkia ceftriaxoniphila	76.1023	80	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Borkfalkia	95.0	99.18	98.64	0.97	0.95	4	-
GCA_910586675.1	s__Gallimonas sp910586675	76.0257	60	540	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Gallimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 15:27:02,999] [INFO] GTDB search result was written to GCA_944376455.1_BRZ_CS_bin61_genomic.fna/result_gtdb.tsv
[2023-06-28 15:27:03,000] [INFO] ===== GTDB Search completed =====
[2023-06-28 15:27:03,034] [INFO] DFAST_QC result json was written to GCA_944376455.1_BRZ_CS_bin61_genomic.fna/dqc_result.json
[2023-06-28 15:27:03,035] [INFO] DFAST_QC completed!
[2023-06-28 15:27:03,035] [INFO] Total running time: 0h0m45s