[2024-01-24 13:40:30,580] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:30,582] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:30,582] [INFO] DQC Reference Directory: /var/lib/cwl/stg9476ab62-4544-4814-8e28-9aca62dc5fcb/dqc_reference
[2024-01-24 13:40:31,913] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,915] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,915] [INFO] Running command: gunzip -c /var/lib/cwl/stge6fb15de-77b1-4244-bfda-e717b55f5e83/GCF_900106845.1_PRJEB14233_genomic.fna.gz | prodigal -d GCF_900106845.1_PRJEB14233_genomic.fna/cds.fna -a GCF_900106845.1_PRJEB14233_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:36,687] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:36,688] [INFO] Task started: HMMsearch
[2024-01-24 13:40:36,688] [INFO] Running command: hmmsearch --tblout GCF_900106845.1_PRJEB14233_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9476ab62-4544-4814-8e28-9aca62dc5fcb/dqc_reference/reference_markers.hmm GCF_900106845.1_PRJEB14233_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:36,979] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:36,980] [INFO] Found 6/6 markers.
[2024-01-24 13:40:37,008] [INFO] Query marker FASTA was written to GCF_900106845.1_PRJEB14233_genomic.fna/markers.fasta
[2024-01-24 13:40:37,009] [INFO] Task started: Blastn
[2024-01-24 13:40:37,009] [INFO] Running command: blastn -query GCF_900106845.1_PRJEB14233_genomic.fna/markers.fasta -db /var/lib/cwl/stg9476ab62-4544-4814-8e28-9aca62dc5fcb/dqc_reference/reference_markers.fasta -out GCF_900106845.1_PRJEB14233_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:37,615] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:37,619] [INFO] Selected 6 target genomes.
[2024-01-24 13:40:37,619] [INFO] Target genome list was writen to GCF_900106845.1_PRJEB14233_genomic.fna/target_genomes.txt
[2024-01-24 13:40:37,628] [INFO] Task started: fastANI
[2024-01-24 13:40:37,628] [INFO] Running command: fastANI --query /var/lib/cwl/stge6fb15de-77b1-4244-bfda-e717b55f5e83/GCF_900106845.1_PRJEB14233_genomic.fna.gz --refList GCF_900106845.1_PRJEB14233_genomic.fna/target_genomes.txt --output GCF_900106845.1_PRJEB14233_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:43,588] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:43,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9476ab62-4544-4814-8e28-9aca62dc5fcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:43,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9476ab62-4544-4814-8e28-9aca62dc5fcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:43,599] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:43,600] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:43,600] [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
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	99.9999	1025	1027	95	conclusive
Romboutsia ilealis	strain=CRIB	GCA_900015215.1	1115758	1115758	type	True	91.913	710	1027	95	below_threshold
Romboutsia hominis	strain=FRIFI	GCA_900002575.1	1507512	1507512	type	True	80.8491	467	1027	95	below_threshold
[Clostridium] dakarense	strain=FF1	GCA_000499525.1	1301100	1301100	type	True	80.7296	474	1027	95	below_threshold
Romboutsia lituseburensis	strain=A25K	GCA_900002825.1	1537	1537	type	True	80.5958	472	1027	95	below_threshold
Romboutsia lituseburensis	strain=DSM 797	GCA_900103615.1	1537	1537	type	True	80.4941	470	1027	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:43,602] [INFO] DFAST Taxonomy check result was written to GCF_900106845.1_PRJEB14233_genomic.fna/tc_result.tsv
[2024-01-24 13:40:43,602] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:43,603] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:43,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9476ab62-4544-4814-8e28-9aca62dc5fcb/dqc_reference/checkm_data
[2024-01-24 13:40:43,604] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:43,636] [INFO] Task started: CheckM
[2024-01-24 13:40:43,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900106845.1_PRJEB14233_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900106845.1_PRJEB14233_genomic.fna/checkm_input GCF_900106845.1_PRJEB14233_genomic.fna/checkm_result
[2024-01-24 13:41:05,858] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:05,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:05,885] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:05,885] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:05,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900106845.1_PRJEB14233_genomic.fna/markers.fasta)
[2024-01-24 13:41:05,886] [INFO] Task started: Blastn
[2024-01-24 13:41:05,886] [INFO] Running command: blastn -query GCF_900106845.1_PRJEB14233_genomic.fna/markers.fasta -db /var/lib/cwl/stg9476ab62-4544-4814-8e28-9aca62dc5fcb/dqc_reference/reference_markers_gtdb.fasta -out GCF_900106845.1_PRJEB14233_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:06,764] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:06,768] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:06,768] [INFO] Target genome list was writen to GCF_900106845.1_PRJEB14233_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:06,784] [INFO] Task started: fastANI
[2024-01-24 13:41:06,785] [INFO] Running command: fastANI --query /var/lib/cwl/stge6fb15de-77b1-4244-bfda-e717b55f5e83/GCF_900106845.1_PRJEB14233_genomic.fna.gz --refList GCF_900106845.1_PRJEB14233_genomic.fna/target_genomes_gtdb.txt --output GCF_900106845.1_PRJEB14233_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:17,408] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:17,419] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:17,420] [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_900106845.1	s__Romboutsia timonensis	99.9999	1025	1027	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	98.20	98.12	0.88	0.86	5	conclusive
GCF_900015215.1	s__Romboutsia ilealis	91.9548	709	1027	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_904418825.1	s__Romboutsia sp904418825	89.7688	544	1027	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_018336475.1	s__Romboutsia sp018336475	86.7735	635	1027	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000686145.1	s__Romboutsia_D sp000686145	80.8012	449	1027	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	-
GCF_900002575.1	s__Romboutsia_C hominis	80.7684	475	1027	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	-
GCA_017425305.1	s__Paraclostridium sp017425305	80.7214	174	1027	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_000499525.1	s__CCUG-7971 spG000499525	80.6909	477	1027	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__CCUG-7971	95.0	100.00	100.00	0.99	0.99	2	-
GCF_017590215.1	s__CCUG-7971 sp017590215	80.5811	473	1027	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	-
GCF_900103615.1	s__Romboutsia_D lituseburensis	80.4324	476	1027	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_D	95.0	99.98	99.98	1.00	1.00	2	-
GCA_900604495.1	s__GCA-900066495 sp900066495	80.1574	437	1027	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_014323405.1	s__GCA-900066495 sp014323405	79.8569	428	1027	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:17,421] [INFO] GTDB search result was written to GCF_900106845.1_PRJEB14233_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:17,422] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:17,426] [INFO] DFAST_QC result json was written to GCF_900106845.1_PRJEB14233_genomic.fna/dqc_result.json
[2024-01-24 13:41:17,426] [INFO] DFAST_QC completed!
[2024-01-24 13:41:17,426] [INFO] Total running time: 0h0m47s