[2023-06-07 23:37:29,793] [INFO] DFAST_QC pipeline started.
[2023-06-07 23:37:29,796] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 23:37:29,796] [INFO] DQC Reference Directory: /var/lib/cwl/stg46223643-6087-44cd-9933-b71b9aa38486/dqc_reference
[2023-06-07 23:37:31,193] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 23:37:31,194] [INFO] Task started: Prodigal
[2023-06-07 23:37:31,194] [INFO] Running command: gunzip -c /var/lib/cwl/stg3141a6db-4df6-4af2-bd95-756ca29f2b13/GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna.gz | prodigal -d GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/cds.fna -a GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 23:37:36,478] [INFO] Task succeeded: Prodigal
[2023-06-07 23:37:36,478] [INFO] Task started: HMMsearch
[2023-06-07 23:37:36,478] [INFO] Running command: hmmsearch --tblout GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46223643-6087-44cd-9933-b71b9aa38486/dqc_reference/reference_markers.hmm GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/protein.faa > /dev/null
[2023-06-07 23:37:36,667] [INFO] Task succeeded: HMMsearch
[2023-06-07 23:37:36,669] [INFO] Found 6/6 markers.
[2023-06-07 23:37:36,692] [INFO] Query marker FASTA was written to GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/markers.fasta
[2023-06-07 23:37:36,692] [INFO] Task started: Blastn
[2023-06-07 23:37:36,692] [INFO] Running command: blastn -query GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/markers.fasta -db /var/lib/cwl/stg46223643-6087-44cd-9933-b71b9aa38486/dqc_reference/reference_markers.fasta -out GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:37:37,326] [INFO] Task succeeded: Blastn
[2023-06-07 23:37:37,330] [INFO] Selected 22 target genomes.
[2023-06-07 23:37:37,331] [INFO] Target genome list was writen to GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/target_genomes.txt
[2023-06-07 23:37:37,335] [INFO] Task started: fastANI
[2023-06-07 23:37:37,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg3141a6db-4df6-4af2-bd95-756ca29f2b13/GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna.gz --refList GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/target_genomes.txt --output GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 23:37:48,915] [INFO] Task succeeded: fastANI
[2023-06-07 23:37:48,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46223643-6087-44cd-9933-b71b9aa38486/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 23:37:48,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46223643-6087-44cd-9933-b71b9aa38486/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 23:37:48,920] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 23:37:48,920] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 23:37:48,920] [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
Negativibacillus massiliensis	strain=Marseille-P3213	GCA_900148495.1	1871035	1871035	type	True	80.7438	314	608	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 23:37:48,923] [INFO] DFAST Taxonomy check result was written to GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/tc_result.tsv
[2023-06-07 23:37:48,924] [INFO] ===== Taxonomy check completed =====
[2023-06-07 23:37:48,924] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 23:37:48,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46223643-6087-44cd-9933-b71b9aa38486/dqc_reference/checkm_data
[2023-06-07 23:37:48,925] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 23:37:48,951] [INFO] Task started: CheckM
[2023-06-07 23:37:48,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/checkm_input GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/checkm_result
[2023-06-07 23:38:10,431] [INFO] Task succeeded: CheckM
[2023-06-07 23:38:10,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.72%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 23:38:10,450] [INFO] ===== Completeness check finished =====
[2023-06-07 23:38:10,450] [INFO] ===== Start GTDB Search =====
[2023-06-07 23:38:10,450] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/markers.fasta)
[2023-06-07 23:38:10,451] [INFO] Task started: Blastn
[2023-06-07 23:38:10,451] [INFO] Running command: blastn -query GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/markers.fasta -db /var/lib/cwl/stg46223643-6087-44cd-9933-b71b9aa38486/dqc_reference/reference_markers_gtdb.fasta -out GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:38:11,503] [INFO] Task succeeded: Blastn
[2023-06-07 23:38:11,507] [INFO] Selected 13 target genomes.
[2023-06-07 23:38:11,507] [INFO] Target genome list was writen to GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 23:38:11,513] [INFO] Task started: fastANI
[2023-06-07 23:38:11,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg3141a6db-4df6-4af2-bd95-756ca29f2b13/GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna.gz --refList GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/target_genomes_gtdb.txt --output GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 23:38:17,343] [INFO] Task succeeded: fastANI
[2023-06-07 23:38:17,349] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 23:38:17,349] [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_900148495.1	s__Negativibacillus massiliensis	80.7399	313	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus	95.0	97.84	97.23	0.93	0.91	5	-
GCA_000435195.1	s__Negativibacillus sp000435195	79.4041	243	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus	95.0	98.99	98.94	0.90	0.88	5	-
GCA_900547015.1	s__Negativibacillus sp900547015	79.2796	218	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus	95.0	97.91	97.91	0.85	0.85	2	-
GCA_900547455.1	s__Negativibacillus faecipullorum	79.2291	275	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus	95.0	97.80	97.60	0.92	0.88	7	-
GCA_905197685.1	s__Negativibacillus sp905197685	77.9985	187	608	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 23:38:17,351] [INFO] GTDB search result was written to GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/result_gtdb.tsv
[2023-06-07 23:38:17,352] [INFO] ===== GTDB Search completed =====
[2023-06-07 23:38:17,354] [INFO] DFAST_QC result json was written to GCA_947856445.1_dsm_us_coassembly_bin111_genomic.fna/dqc_result.json
[2023-06-07 23:38:17,354] [INFO] DFAST_QC completed!
[2023-06-07 23:38:17,354] [INFO] Total running time: 0h0m48s