[2024-01-24 11:44:05,460] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,461] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,461] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bac117f-4df4-461c-816f-1dd5f0cce0aa/dqc_reference
[2024-01-24 11:44:08,836] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,837] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,837] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1339eec-5d72-424a-afcd-20ff4844ce87/GCF_016680995.1_ASM1668099v1_genomic.fna.gz | prodigal -d GCF_016680995.1_ASM1668099v1_genomic.fna/cds.fna -a GCF_016680995.1_ASM1668099v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:17,466] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:17,466] [INFO] Task started: HMMsearch
[2024-01-24 11:44:17,466] [INFO] Running command: hmmsearch --tblout GCF_016680995.1_ASM1668099v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bac117f-4df4-461c-816f-1dd5f0cce0aa/dqc_reference/reference_markers.hmm GCF_016680995.1_ASM1668099v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:17,726] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:17,728] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf1339eec-5d72-424a-afcd-20ff4844ce87/GCF_016680995.1_ASM1668099v1_genomic.fna.gz]
[2024-01-24 11:44:17,760] [INFO] Query marker FASTA was written to GCF_016680995.1_ASM1668099v1_genomic.fna/markers.fasta
[2024-01-24 11:44:17,761] [INFO] Task started: Blastn
[2024-01-24 11:44:17,761] [INFO] Running command: blastn -query GCF_016680995.1_ASM1668099v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bac117f-4df4-461c-816f-1dd5f0cce0aa/dqc_reference/reference_markers.fasta -out GCF_016680995.1_ASM1668099v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:18,486] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:18,490] [INFO] Selected 22 target genomes.
[2024-01-24 11:44:18,491] [INFO] Target genome list was writen to GCF_016680995.1_ASM1668099v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:18,537] [INFO] Task started: fastANI
[2024-01-24 11:44:18,537] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1339eec-5d72-424a-afcd-20ff4844ce87/GCF_016680995.1_ASM1668099v1_genomic.fna.gz --refList GCF_016680995.1_ASM1668099v1_genomic.fna/target_genomes.txt --output GCF_016680995.1_ASM1668099v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:34,924] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:34,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bac117f-4df4-461c-816f-1dd5f0cce0aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:34,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bac117f-4df4-461c-816f-1dd5f0cce0aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:34,929] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:34,929] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:34,929] [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
Ruminococcus bromii	strain=ATCC 27255	GCA_002834225.1	40518	40518	suspected-type	True	76.8572	70	1137	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:34,930] [INFO] DFAST Taxonomy check result was written to GCF_016680995.1_ASM1668099v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:34,931] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:34,931] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:34,931] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bac117f-4df4-461c-816f-1dd5f0cce0aa/dqc_reference/checkm_data
[2024-01-24 11:44:34,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:34,968] [INFO] Task started: CheckM
[2024-01-24 11:44:34,968] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016680995.1_ASM1668099v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016680995.1_ASM1668099v1_genomic.fna/checkm_input GCF_016680995.1_ASM1668099v1_genomic.fna/checkm_result
[2024-01-24 11:45:05,496] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:05,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:05,517] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:05,517] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:05,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016680995.1_ASM1668099v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:05,518] [INFO] Task started: Blastn
[2024-01-24 11:45:05,518] [INFO] Running command: blastn -query GCF_016680995.1_ASM1668099v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bac117f-4df4-461c-816f-1dd5f0cce0aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_016680995.1_ASM1668099v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:06,664] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:06,667] [INFO] Selected 13 target genomes.
[2024-01-24 11:45:06,667] [INFO] Target genome list was writen to GCF_016680995.1_ASM1668099v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:06,703] [INFO] Task started: fastANI
[2024-01-24 11:45:06,703] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1339eec-5d72-424a-afcd-20ff4844ce87/GCF_016680995.1_ASM1668099v1_genomic.fna.gz --refList GCF_016680995.1_ASM1668099v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016680995.1_ASM1668099v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:14,025] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:14,042] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:14,043] [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_016680995.1	s__Ruminococcus_E sp016680995	100.0	1128	1137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902764715.1	s__Ruminococcus_E sp902764715	93.3516	386	1137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320995.1	s__Ruminococcus_E sp900320995	92.8547	398	1137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	100.00	100.00	0.98	0.98	2	-
GCA_900316555.1	s__Ruminococcus_E sp900316555	91.1672	241	1137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.80	96.62	0.88	0.77	62	-
GCA_900314795.1	s__Ruminococcus_E sp900314795	87.2332	502	1137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.68	96.71	0.89	0.84	7	-
GCA_003499325.1	s__Ruminococcus_E sp003499325	86.9283	296	1137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002394725.1	s__Ruminococcus_E sp002394725	86.0316	369	1137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	96.60	96.60	0.78	0.78	2	-
GCA_900100595.1	s__Ruminococcus_E sp900100595	85.2618	316	1137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.87	97.87	0.91	0.78	34	-
GCA_902765625.1	s__Ruminococcus_E sp902765625	84.8923	242	1137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.31	99.27	0.90	0.89	5	-
GCA_017405065.1	s__Ruminococcus_E sp017405065	81.9526	361	1137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017457955.1	s__Ruminococcus_E sp017457955	81.6279	317	1137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320415.1	s__Ruminococcus_E sp900320415	79.5755	129	1137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.69	99.69	0.84	0.84	2	-
GCA_017433905.1	s__Ruminococcus_E sp017433905	78.3426	109	1137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:14,045] [INFO] GTDB search result was written to GCF_016680995.1_ASM1668099v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:14,045] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:14,049] [INFO] DFAST_QC result json was written to GCF_016680995.1_ASM1668099v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:14,049] [INFO] DFAST_QC completed!
[2024-01-24 11:45:14,049] [INFO] Total running time: 0h1m9s