[2023-06-29 15:03:58,175] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:03:58,181] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:03:58,181] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e60cc6b-77ab-4217-9814-b416ef2b83cc/dqc_reference
[2023-06-29 15:03:59,945] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:03:59,946] [INFO] Task started: Prodigal
[2023-06-29 15:03:59,947] [INFO] Running command: gunzip -c /var/lib/cwl/stg03a05368-b718-4c7d-aedc-833faf12c608/GCA_021204945.1_ASM2120494v1_genomic.fna.gz | prodigal -d GCA_021204945.1_ASM2120494v1_genomic.fna/cds.fna -a GCA_021204945.1_ASM2120494v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:04:02,895] [INFO] Task succeeded: Prodigal
[2023-06-29 15:04:02,895] [INFO] Task started: HMMsearch
[2023-06-29 15:04:02,895] [INFO] Running command: hmmsearch --tblout GCA_021204945.1_ASM2120494v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e60cc6b-77ab-4217-9814-b416ef2b83cc/dqc_reference/reference_markers.hmm GCA_021204945.1_ASM2120494v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:04:03,137] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:04:03,139] [INFO] Found 6/6 markers.
[2023-06-29 15:04:03,190] [INFO] Query marker FASTA was written to GCA_021204945.1_ASM2120494v1_genomic.fna/markers.fasta
[2023-06-29 15:04:03,191] [INFO] Task started: Blastn
[2023-06-29 15:04:03,191] [INFO] Running command: blastn -query GCA_021204945.1_ASM2120494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e60cc6b-77ab-4217-9814-b416ef2b83cc/dqc_reference/reference_markers.fasta -out GCA_021204945.1_ASM2120494v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:04:04,166] [INFO] Task succeeded: Blastn
[2023-06-29 15:04:04,171] [INFO] Selected 20 target genomes.
[2023-06-29 15:04:04,172] [INFO] Target genome list was writen to GCA_021204945.1_ASM2120494v1_genomic.fna/target_genomes.txt
[2023-06-29 15:04:04,238] [INFO] Task started: fastANI
[2023-06-29 15:04:04,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg03a05368-b718-4c7d-aedc-833faf12c608/GCA_021204945.1_ASM2120494v1_genomic.fna.gz --refList GCA_021204945.1_ASM2120494v1_genomic.fna/target_genomes.txt --output GCA_021204945.1_ASM2120494v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:04:15,925] [INFO] Task succeeded: fastANI
[2023-06-29 15:04:15,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e60cc6b-77ab-4217-9814-b416ef2b83cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:04:15,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e60cc6b-77ab-4217-9814-b416ef2b83cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:04:15,928] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:04:15,929] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 15:04:15,929] [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
--------------------------------------------------------------------------------
[2023-06-29 15:04:15,931] [INFO] DFAST Taxonomy check result was written to GCA_021204945.1_ASM2120494v1_genomic.fna/tc_result.tsv
[2023-06-29 15:04:15,932] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:04:15,932] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:04:15,933] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e60cc6b-77ab-4217-9814-b416ef2b83cc/dqc_reference/checkm_data
[2023-06-29 15:04:15,937] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:04:15,958] [INFO] Task started: CheckM
[2023-06-29 15:04:15,958] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021204945.1_ASM2120494v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021204945.1_ASM2120494v1_genomic.fna/checkm_input GCA_021204945.1_ASM2120494v1_genomic.fna/checkm_result
[2023-06-29 15:04:32,229] [INFO] Task succeeded: CheckM
[2023-06-29 15:04:32,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:04:32,250] [INFO] ===== Completeness check finished =====
[2023-06-29 15:04:32,250] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:04:32,250] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021204945.1_ASM2120494v1_genomic.fna/markers.fasta)
[2023-06-29 15:04:32,251] [INFO] Task started: Blastn
[2023-06-29 15:04:32,251] [INFO] Running command: blastn -query GCA_021204945.1_ASM2120494v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e60cc6b-77ab-4217-9814-b416ef2b83cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_021204945.1_ASM2120494v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:04:33,031] [INFO] Task succeeded: Blastn
[2023-06-29 15:04:33,037] [INFO] Selected 23 target genomes.
[2023-06-29 15:04:33,037] [INFO] Target genome list was writen to GCA_021204945.1_ASM2120494v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:04:33,046] [INFO] Task started: fastANI
[2023-06-29 15:04:33,047] [INFO] Running command: fastANI --query /var/lib/cwl/stg03a05368-b718-4c7d-aedc-833faf12c608/GCA_021204945.1_ASM2120494v1_genomic.fna.gz --refList GCA_021204945.1_ASM2120494v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021204945.1_ASM2120494v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:04:39,924] [INFO] Task succeeded: fastANI
[2023-06-29 15:04:39,938] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 15:04:39,938] [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_905207385.1	s__Coproplasma sp905207385	77.8443	83	419	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018714625.1	s__Coproplasma excrementigallinarum	77.5949	74	419	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	99.92	99.92	0.92	0.92	2	-
GCA_018715195.1	s__Coproplasma excrementavium	77.4667	78	419	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	99.98	99.98	0.97	0.97	2	-
GCA_018713165.1	s__Coproplasma stercoravium	77.4166	87	419	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	98.55	98.33	0.89	0.85	3	-
GCA_900549005.1	s__Coproplasma stercorigallinarum	77.3314	87	419	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	97.42	97.40	0.87	0.83	4	-
GCA_905207235.1	s__Coproplasma sp905207235	76.7325	54	419	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712405.1	s__Coproplasma stercoripullorum	76.7019	60	419	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586035.1	s__Coproplasma sp910586035	76.3982	66	419	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Borkfalkiaceae;g__Coproplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:04:39,940] [INFO] GTDB search result was written to GCA_021204945.1_ASM2120494v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:04:39,941] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:04:39,944] [INFO] DFAST_QC result json was written to GCA_021204945.1_ASM2120494v1_genomic.fna/dqc_result.json
[2023-06-29 15:04:39,944] [INFO] DFAST_QC completed!
[2023-06-29 15:04:39,944] [INFO] Total running time: 0h0m42s