[2023-06-28 23:39:53,344] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:39:53,346] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:39:53,346] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cb3138e-6369-4abe-ba6c-0dfa37cab1fb/dqc_reference
[2023-06-28 23:39:54,812] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:39:54,813] [INFO] Task started: Prodigal
[2023-06-28 23:39:54,813] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9b9afa9-4049-4a3e-820e-f2ff26e0634b/GCA_944376255.1_E0_RM_bin231_genomic.fna.gz | prodigal -d GCA_944376255.1_E0_RM_bin231_genomic.fna/cds.fna -a GCA_944376255.1_E0_RM_bin231_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:40:00,959] [INFO] Task succeeded: Prodigal
[2023-06-28 23:40:00,959] [INFO] Task started: HMMsearch
[2023-06-28 23:40:00,959] [INFO] Running command: hmmsearch --tblout GCA_944376255.1_E0_RM_bin231_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cb3138e-6369-4abe-ba6c-0dfa37cab1fb/dqc_reference/reference_markers.hmm GCA_944376255.1_E0_RM_bin231_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:40:01,215] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:40:01,216] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd9b9afa9-4049-4a3e-820e-f2ff26e0634b/GCA_944376255.1_E0_RM_bin231_genomic.fna.gz]
[2023-06-28 23:40:01,245] [INFO] Query marker FASTA was written to GCA_944376255.1_E0_RM_bin231_genomic.fna/markers.fasta
[2023-06-28 23:40:01,245] [INFO] Task started: Blastn
[2023-06-28 23:40:01,245] [INFO] Running command: blastn -query GCA_944376255.1_E0_RM_bin231_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cb3138e-6369-4abe-ba6c-0dfa37cab1fb/dqc_reference/reference_markers.fasta -out GCA_944376255.1_E0_RM_bin231_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:40:01,922] [INFO] Task succeeded: Blastn
[2023-06-28 23:40:01,926] [INFO] Selected 21 target genomes.
[2023-06-28 23:40:01,926] [INFO] Target genome list was writen to GCA_944376255.1_E0_RM_bin231_genomic.fna/target_genomes.txt
[2023-06-28 23:40:01,938] [INFO] Task started: fastANI
[2023-06-28 23:40:01,938] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9b9afa9-4049-4a3e-820e-f2ff26e0634b/GCA_944376255.1_E0_RM_bin231_genomic.fna.gz --refList GCA_944376255.1_E0_RM_bin231_genomic.fna/target_genomes.txt --output GCA_944376255.1_E0_RM_bin231_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:40:10,902] [INFO] Task succeeded: fastANI
[2023-06-28 23:40:10,903] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cb3138e-6369-4abe-ba6c-0dfa37cab1fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:40:10,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cb3138e-6369-4abe-ba6c-0dfa37cab1fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:40:10,910] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:40:10,910] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 23:40:10,910] [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
Neglectibacter timonensis	strain=SN17	GCA_900048895.1	1776382	1776382	type	True	77.6554	131	603	95	below_threshold
Acutalibacter muris	strain=KB18	GCA_016697365.1	1796620	1796620	type	True	77.3174	128	603	95	below_threshold
Acutalibacter muris	strain=KB18	GCA_002201475.1	1796620	1796620	type	True	77.3157	128	603	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.5895	60	603	95	below_threshold
Bittarella massiliensis	strain=GD6	GCA_001486165.1	1720313	1720313	type	True	76.3243	71	603	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 23:40:10,912] [INFO] DFAST Taxonomy check result was written to GCA_944376255.1_E0_RM_bin231_genomic.fna/tc_result.tsv
[2023-06-28 23:40:10,913] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:40:10,913] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:40:10,913] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cb3138e-6369-4abe-ba6c-0dfa37cab1fb/dqc_reference/checkm_data
[2023-06-28 23:40:10,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:40:10,956] [INFO] Task started: CheckM
[2023-06-28 23:40:10,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944376255.1_E0_RM_bin231_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944376255.1_E0_RM_bin231_genomic.fna/checkm_input GCA_944376255.1_E0_RM_bin231_genomic.fna/checkm_result
[2023-06-28 23:40:35,150] [INFO] Task succeeded: CheckM
[2023-06-28 23:40:35,152] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:40:35,174] [INFO] ===== Completeness check finished =====
[2023-06-28 23:40:35,174] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:40:35,175] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944376255.1_E0_RM_bin231_genomic.fna/markers.fasta)
[2023-06-28 23:40:35,175] [INFO] Task started: Blastn
[2023-06-28 23:40:35,175] [INFO] Running command: blastn -query GCA_944376255.1_E0_RM_bin231_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cb3138e-6369-4abe-ba6c-0dfa37cab1fb/dqc_reference/reference_markers_gtdb.fasta -out GCA_944376255.1_E0_RM_bin231_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:40:36,291] [INFO] Task succeeded: Blastn
[2023-06-28 23:40:36,295] [INFO] Selected 8 target genomes.
[2023-06-28 23:40:36,296] [INFO] Target genome list was writen to GCA_944376255.1_E0_RM_bin231_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:40:36,328] [INFO] Task started: fastANI
[2023-06-28 23:40:36,329] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9b9afa9-4049-4a3e-820e-f2ff26e0634b/GCA_944376255.1_E0_RM_bin231_genomic.fna.gz --refList GCA_944376255.1_E0_RM_bin231_genomic.fna/target_genomes_gtdb.txt --output GCA_944376255.1_E0_RM_bin231_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:40:40,760] [INFO] Task succeeded: fastANI
[2023-06-28 23:40:40,768] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 23:40:40,769] [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_904391645.1	s__Acutalibacter sp904391645	98.0148	409	603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900548545.1	s__Acutalibacter sp900548545	94.1839	462	603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	98.53	98.53	0.88	0.88	2	-
GCA_000435395.1	s__Acutalibacter ornithocaccae	82.7659	359	603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	97.90	97.28	0.83	0.80	5	-
GCA_905215055.1	s__Acutalibacter sp905215055	82.3999	405	603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543555.1	s__Acutalibacter stercoravium	82.0233	372	603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	98.18	97.66	0.89	0.84	11	-
GCA_900755895.1	s__Acutalibacter sp900755895	81.3589	327	603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	96.98	96.98	0.93	0.93	2	-
GCA_000432995.1	s__Acutalibacter sp000432995	81.3553	365	603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	97.39	97.36	0.87	0.86	3	-
GCA_900759575.1	s__Acutalibacter sp900759575	80.7599	263	603	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:40:40,771] [INFO] GTDB search result was written to GCA_944376255.1_E0_RM_bin231_genomic.fna/result_gtdb.tsv
[2023-06-28 23:40:40,771] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:40:40,774] [INFO] DFAST_QC result json was written to GCA_944376255.1_E0_RM_bin231_genomic.fna/dqc_result.json
[2023-06-28 23:40:40,774] [INFO] DFAST_QC completed!
[2023-06-28 23:40:40,774] [INFO] Total running time: 0h0m47s