[2024-01-24 11:13:04,350] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:04,352] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:04,352] [INFO] DQC Reference Directory: /var/lib/cwl/stg37e609aa-7509-4e01-a40b-374f8101cc6c/dqc_reference
[2024-01-24 11:13:05,616] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:05,617] [INFO] Task started: Prodigal
[2024-01-24 11:13:05,617] [INFO] Running command: gunzip -c /var/lib/cwl/stg972af306-fc6d-4764-a4b8-9596349b1b8b/GCF_002251085.2_ASM225108v2_genomic.fna.gz | prodigal -d GCF_002251085.2_ASM225108v2_genomic.fna/cds.fna -a GCF_002251085.2_ASM225108v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:09,681] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:09,681] [INFO] Task started: HMMsearch
[2024-01-24 11:13:09,681] [INFO] Running command: hmmsearch --tblout GCF_002251085.2_ASM225108v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37e609aa-7509-4e01-a40b-374f8101cc6c/dqc_reference/reference_markers.hmm GCF_002251085.2_ASM225108v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:09,954] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:09,956] [INFO] Found 6/6 markers.
[2024-01-24 11:13:09,983] [INFO] Query marker FASTA was written to GCF_002251085.2_ASM225108v2_genomic.fna/markers.fasta
[2024-01-24 11:13:09,984] [INFO] Task started: Blastn
[2024-01-24 11:13:09,984] [INFO] Running command: blastn -query GCF_002251085.2_ASM225108v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg37e609aa-7509-4e01-a40b-374f8101cc6c/dqc_reference/reference_markers.fasta -out GCF_002251085.2_ASM225108v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:10,592] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:10,597] [INFO] Selected 12 target genomes.
[2024-01-24 11:13:10,597] [INFO] Target genome list was writen to GCF_002251085.2_ASM225108v2_genomic.fna/target_genomes.txt
[2024-01-24 11:13:10,733] [INFO] Task started: fastANI
[2024-01-24 11:13:10,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg972af306-fc6d-4764-a4b8-9596349b1b8b/GCF_002251085.2_ASM225108v2_genomic.fna.gz --refList GCF_002251085.2_ASM225108v2_genomic.fna/target_genomes.txt --output GCF_002251085.2_ASM225108v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:18,657] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:18,658] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37e609aa-7509-4e01-a40b-374f8101cc6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:18,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37e609aa-7509-4e01-a40b-374f8101cc6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:18,679] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:18,680] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:18,680] [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
[Clostridium] dakarense	strain=FF1	GCA_000499525.1	1301100	1301100	type	True	80.258	434	891	95	below_threshold
Romboutsia lituseburensis	strain=A25K	GCA_900002825.1	1537	1537	type	True	80.0387	480	891	95	below_threshold
Romboutsia weinsteinii	strain=CCRI-19649	GCA_002250835.2	2020949	2020949	type	True	80.036	409	891	95	below_threshold
Romboutsia ilealis	strain=CRIB	GCA_900015215.1	1115758	1115758	type	True	80.0024	363	891	95	below_threshold
Romboutsia hominis	strain=FRIFI	GCA_900002575.1	1507512	1507512	type	True	79.965	409	891	95	below_threshold
Romboutsia lituseburensis	strain=DSM 797	GCA_900103615.1	1537	1537	type	True	79.9554	470	891	95	below_threshold
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	79.864	385	891	95	below_threshold
Clostridioides difficile	strain=FDAARGOS_1525	GCA_020341515.1	1496	1496	type	True	79.1947	364	891	95	below_threshold
Clostridioides difficile	strain=DSM 1296	GCA_000438845.1	1496	1496	type	True	79.0685	357	891	95	below_threshold
Paeniclostridium sordellii	strain=ATCC9714	GCA_000953675.1	1505	1505	type	True	78.9859	363	891	95	below_threshold
Clostridioides difficile	strain=ATCC 9689	GCA_000376285.1	1496	1496	type	True	78.9767	355	891	95	below_threshold
Clostridioides mangenotii	strain=DSM 1289	GCA_017873185.1	1540	1540	suspected-type	True	77.5468	175	891	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:18,682] [INFO] DFAST Taxonomy check result was written to GCF_002251085.2_ASM225108v2_genomic.fna/tc_result.tsv
[2024-01-24 11:13:18,682] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:18,682] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:18,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37e609aa-7509-4e01-a40b-374f8101cc6c/dqc_reference/checkm_data
[2024-01-24 11:13:18,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:18,718] [INFO] Task started: CheckM
[2024-01-24 11:13:18,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002251085.2_ASM225108v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002251085.2_ASM225108v2_genomic.fna/checkm_input GCF_002251085.2_ASM225108v2_genomic.fna/checkm_result
[2024-01-24 11:13:38,965] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:38,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:38,993] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:38,993] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:38,994] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002251085.2_ASM225108v2_genomic.fna/markers.fasta)
[2024-01-24 11:13:38,994] [INFO] Task started: Blastn
[2024-01-24 11:13:38,994] [INFO] Running command: blastn -query GCF_002251085.2_ASM225108v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg37e609aa-7509-4e01-a40b-374f8101cc6c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002251085.2_ASM225108v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:39,825] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:39,829] [INFO] Selected 15 target genomes.
[2024-01-24 11:13:39,829] [INFO] Target genome list was writen to GCF_002251085.2_ASM225108v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:39,840] [INFO] Task started: fastANI
[2024-01-24 11:13:39,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg972af306-fc6d-4764-a4b8-9596349b1b8b/GCF_002251085.2_ASM225108v2_genomic.fna.gz --refList GCF_002251085.2_ASM225108v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002251085.2_ASM225108v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:49,263] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:49,279] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:49,279] [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_002251085.2	s__Romboutsia_B maritimum	100.0	890	891	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	conclusive
GCA_000686145.1	s__Romboutsia_D sp000686145	80.6007	471	891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904418825.1	s__Romboutsia sp904418825	80.1297	321	891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	99.17	99.17	0.88	0.88	2	-
GCF_900015215.1	s__Romboutsia ilealis	80.0583	360	891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	98.59	98.59	0.90	0.90	2	-
GCA_900604495.1	s__GCA-900066495 sp900066495	80.0413	385	891	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	-
GCF_002250835.2	s__Romboutsia_A weinsteinii	80.024	408	891	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	-
GCF_017590215.1	s__CCUG-7971 sp017590215	80.0126	470	891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__CCUG-7971	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902362365.1	s__GCA-900066495 sp902362365	80.008	399	891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__GCA-900066495	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900002575.1	s__Romboutsia_C hominis	79.9679	407	891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_C	95.0	98.29	95.25	0.93	0.90	6	-
GCF_014323405.1	s__GCA-900066495 sp014323405	79.9676	400	891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__GCA-900066495	95.0	100.00	100.00	0.98	0.98	2	-
GCF_012317385.1	s__GCA-900066495 sp900545985	79.9466	377	891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__GCA-900066495	95.0	98.78	98.75	0.89	0.89	3	-
GCA_017425305.1	s__Paraclostridium sp017425305	79.8083	142	891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	97.54	97.54	0.79	0.79	2	-
GCF_900106845.1	s__Romboutsia timonensis	79.8065	389	891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	98.20	98.12	0.88	0.86	5	-
GCF_001077535.1	s__Clostridioides difficile	79.1467	357	891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridioides	95.0	98.86	95.94	0.94	0.86	2225	-
GCF_017873185.1	s__Clostridioides_A mangenotii	77.5373	177	891	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridioides_A	95.0	96.86	96.86	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:49,281] [INFO] GTDB search result was written to GCF_002251085.2_ASM225108v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:49,281] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:49,284] [INFO] DFAST_QC result json was written to GCF_002251085.2_ASM225108v2_genomic.fna/dqc_result.json
[2024-01-24 11:13:49,285] [INFO] DFAST_QC completed!
[2024-01-24 11:13:49,285] [INFO] Total running time: 0h0m45s