[2024-01-24 13:32:41,108] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,109] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,109] [INFO] DQC Reference Directory: /var/lib/cwl/stg11d70a02-ef56-4c68-acb1-5ec1c62793e0/dqc_reference
[2024-01-24 13:32:42,418] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,419] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,419] [INFO] Running command: gunzip -c /var/lib/cwl/stg8303b5a1-00c4-4dea-a41e-a68dd5606d77/GCF_000438845.1_ASM43884v1_genomic.fna.gz | prodigal -d GCF_000438845.1_ASM43884v1_genomic.fna/cds.fna -a GCF_000438845.1_ASM43884v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:49,390] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:49,390] [INFO] Task started: HMMsearch
[2024-01-24 13:32:49,390] [INFO] Running command: hmmsearch --tblout GCF_000438845.1_ASM43884v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11d70a02-ef56-4c68-acb1-5ec1c62793e0/dqc_reference/reference_markers.hmm GCF_000438845.1_ASM43884v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:49,705] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:49,706] [INFO] Found 6/6 markers.
[2024-01-24 13:32:49,740] [INFO] Query marker FASTA was written to GCF_000438845.1_ASM43884v1_genomic.fna/markers.fasta
[2024-01-24 13:32:49,740] [INFO] Task started: Blastn
[2024-01-24 13:32:49,740] [INFO] Running command: blastn -query GCF_000438845.1_ASM43884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11d70a02-ef56-4c68-acb1-5ec1c62793e0/dqc_reference/reference_markers.fasta -out GCF_000438845.1_ASM43884v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:50,356] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:50,360] [INFO] Selected 9 target genomes.
[2024-01-24 13:32:50,361] [INFO] Target genome list was writen to GCF_000438845.1_ASM43884v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:50,363] [INFO] Task started: fastANI
[2024-01-24 13:32:50,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg8303b5a1-00c4-4dea-a41e-a68dd5606d77/GCF_000438845.1_ASM43884v1_genomic.fna.gz --refList GCF_000438845.1_ASM43884v1_genomic.fna/target_genomes.txt --output GCF_000438845.1_ASM43884v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:57,837] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:57,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11d70a02-ef56-4c68-acb1-5ec1c62793e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:57,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11d70a02-ef56-4c68-acb1-5ec1c62793e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:57,847] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:32:57,847] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:57,847] [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
Clostridioides difficile	strain=DSM 1296	GCA_000438845.1	1496	1496	type	True	100.0	1386	1387	95	conclusive
Clostridioides difficile	strain=FDAARGOS_1525	GCA_020341515.1	1496	1496	type	True	99.9959	1384	1387	95	conclusive
Clostridioides difficile	strain=ATCC 9689	GCA_000376285.1	1496	1496	type	True	99.9819	1348	1387	95	conclusive
Romboutsia lituseburensis	strain=A25K	GCA_900002825.1	1537	1537	type	True	78.5283	365	1387	95	below_threshold
Romboutsia lituseburensis	strain=DSM 797	GCA_900103615.1	1537	1537	type	True	78.4022	363	1387	95	below_threshold
Romboutsia weinsteinii	strain=CCRI-19649	GCA_002250835.2	2020949	2020949	type	True	78.3882	352	1387	95	below_threshold
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	78.1017	315	1387	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_006802875.1	1490	1490	type	True	77.9194	309	1387	95	below_threshold
Paraclostridium dentum	strain=SKVG24	GCA_012922555.1	2662455	2662455	type	True	77.7793	312	1387	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:57,849] [INFO] DFAST Taxonomy check result was written to GCF_000438845.1_ASM43884v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:57,850] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:57,850] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:57,850] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11d70a02-ef56-4c68-acb1-5ec1c62793e0/dqc_reference/checkm_data
[2024-01-24 13:32:57,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:57,895] [INFO] Task started: CheckM
[2024-01-24 13:32:57,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000438845.1_ASM43884v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000438845.1_ASM43884v1_genomic.fna/checkm_input GCF_000438845.1_ASM43884v1_genomic.fna/checkm_result
[2024-01-24 13:33:25,771] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:25,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:25,801] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:25,801] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:25,802] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000438845.1_ASM43884v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:25,802] [INFO] Task started: Blastn
[2024-01-24 13:33:25,802] [INFO] Running command: blastn -query GCF_000438845.1_ASM43884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11d70a02-ef56-4c68-acb1-5ec1c62793e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000438845.1_ASM43884v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:26,623] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:26,627] [INFO] Selected 8 target genomes.
[2024-01-24 13:33:26,627] [INFO] Target genome list was writen to GCF_000438845.1_ASM43884v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:26,632] [INFO] Task started: fastANI
[2024-01-24 13:33:26,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg8303b5a1-00c4-4dea-a41e-a68dd5606d77/GCF_000438845.1_ASM43884v1_genomic.fna.gz --refList GCF_000438845.1_ASM43884v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000438845.1_ASM43884v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:33,722] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:33,734] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:33,734] [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_001077535.1	s__Clostridioides difficile	99.9954	1344	1387	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridioides	95.0	98.86	95.94	0.94	0.86	2225	conclusive
GCF_900243075.1	s__Clostridioides difficile_D	93.8258	1157	1387	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridioides	95.0	99.09	99.09	0.92	0.92	2	-
GCF_000449425.2	s__Clostridioides difficile_E	91.1694	1180	1387	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001299635.1	s__Clostridioides difficile_A	91.0718	1126	1387	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridioides	95.0	98.74	95.22	0.93	0.91	9	-
GCF_002251085.2	s__Romboutsia_B maritimum	79.0549	359	1387	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002250835.2	s__Romboutsia_A weinsteinii	78.4024	354	1387	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904418825.1	s__Romboutsia sp904418825	78.3623	275	1387	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	99.17	99.17	0.88	0.88	2	-
GCA_900604495.1	s__GCA-900066495 sp900066495	78.3185	318	1387	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__GCA-900066495	95.0	99.74	99.60	0.96	0.94	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:33,737] [INFO] GTDB search result was written to GCF_000438845.1_ASM43884v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:33,737] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:33,740] [INFO] DFAST_QC result json was written to GCF_000438845.1_ASM43884v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:33,740] [INFO] DFAST_QC completed!
[2024-01-24 13:33:33,740] [INFO] Total running time: 0h0m53s