[2024-01-24 12:21:57,412] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:57,414] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:57,414] [INFO] DQC Reference Directory: /var/lib/cwl/stgec8d256f-77ea-4d51-b968-ed46c012b364/dqc_reference
[2024-01-24 12:21:58,675] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:58,676] [INFO] Task started: Prodigal
[2024-01-24 12:21:58,676] [INFO] Running command: gunzip -c /var/lib/cwl/stgefe29596-cf28-4310-bf02-f042c6302442/GCF_900002575.1_FRIFI_genomic.fna.gz | prodigal -d GCF_900002575.1_FRIFI_genomic.fna/cds.fna -a GCF_900002575.1_FRIFI_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:03,213] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:03,213] [INFO] Task started: HMMsearch
[2024-01-24 12:22:03,213] [INFO] Running command: hmmsearch --tblout GCF_900002575.1_FRIFI_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec8d256f-77ea-4d51-b968-ed46c012b364/dqc_reference/reference_markers.hmm GCF_900002575.1_FRIFI_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:03,495] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:03,502] [INFO] Found 6/6 markers.
[2024-01-24 12:22:03,532] [INFO] Query marker FASTA was written to GCF_900002575.1_FRIFI_genomic.fna/markers.fasta
[2024-01-24 12:22:03,533] [INFO] Task started: Blastn
[2024-01-24 12:22:03,533] [INFO] Running command: blastn -query GCF_900002575.1_FRIFI_genomic.fna/markers.fasta -db /var/lib/cwl/stgec8d256f-77ea-4d51-b968-ed46c012b364/dqc_reference/reference_markers.fasta -out GCF_900002575.1_FRIFI_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:04,181] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:04,184] [INFO] Selected 9 target genomes.
[2024-01-24 12:22:04,185] [INFO] Target genome list was writen to GCF_900002575.1_FRIFI_genomic.fna/target_genomes.txt
[2024-01-24 12:22:04,196] [INFO] Task started: fastANI
[2024-01-24 12:22:04,196] [INFO] Running command: fastANI --query /var/lib/cwl/stgefe29596-cf28-4310-bf02-f042c6302442/GCF_900002575.1_FRIFI_genomic.fna.gz --refList GCF_900002575.1_FRIFI_genomic.fna/target_genomes.txt --output GCF_900002575.1_FRIFI_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:12,235] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:12,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec8d256f-77ea-4d51-b968-ed46c012b364/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:12,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec8d256f-77ea-4d51-b968-ed46c012b364/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:12,246] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:12,246] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:12,246] [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 hominis	strain=FRIFI	GCA_900002575.1	1507512	1507512	type	True	100.0	1013	1013	95	conclusive
Romboutsia lituseburensis	strain=A25K	GCA_900002825.1	1537	1537	type	True	81.7316	567	1013	95	below_threshold
Romboutsia ilealis	strain=CRIB	GCA_900015215.1	1115758	1115758	type	True	81.2829	422	1013	95	below_threshold
Romboutsia lituseburensis	strain=DSM 797	GCA_900103615.1	1537	1537	type	True	81.2304	555	1013	95	below_threshold
[Clostridium] dakarense	strain=FF1	GCA_000499525.1	1301100	1301100	type	True	81.0027	528	1013	95	below_threshold
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	80.9778	455	1013	95	below_threshold
Paeniclostridium sordellii	strain=ATCC9714	GCA_000953675.1	1505	1505	type	True	80.0582	430	1013	95	below_threshold
Romboutsia weinsteinii	strain=CCRI-19649	GCA_002250835.2	2020949	2020949	type	True	79.5864	403	1013	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_006802875.1	1490	1490	type	True	79.0101	409	1013	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:12,249] [INFO] DFAST Taxonomy check result was written to GCF_900002575.1_FRIFI_genomic.fna/tc_result.tsv
[2024-01-24 12:22:12,250] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:12,250] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:12,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec8d256f-77ea-4d51-b968-ed46c012b364/dqc_reference/checkm_data
[2024-01-24 12:22:12,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:12,299] [INFO] Task started: CheckM
[2024-01-24 12:22:12,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900002575.1_FRIFI_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900002575.1_FRIFI_genomic.fna/checkm_input GCF_900002575.1_FRIFI_genomic.fna/checkm_result
[2024-01-24 12:22:32,737] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:32,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:32,763] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:32,763] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:32,764] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900002575.1_FRIFI_genomic.fna/markers.fasta)
[2024-01-24 12:22:32,764] [INFO] Task started: Blastn
[2024-01-24 12:22:32,764] [INFO] Running command: blastn -query GCF_900002575.1_FRIFI_genomic.fna/markers.fasta -db /var/lib/cwl/stgec8d256f-77ea-4d51-b968-ed46c012b364/dqc_reference/reference_markers_gtdb.fasta -out GCF_900002575.1_FRIFI_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:33,569] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:33,576] [INFO] Selected 12 target genomes.
[2024-01-24 12:22:33,576] [INFO] Target genome list was writen to GCF_900002575.1_FRIFI_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:33,585] [INFO] Task started: fastANI
[2024-01-24 12:22:33,585] [INFO] Running command: fastANI --query /var/lib/cwl/stgefe29596-cf28-4310-bf02-f042c6302442/GCF_900002575.1_FRIFI_genomic.fna.gz --refList GCF_900002575.1_FRIFI_genomic.fna/target_genomes_gtdb.txt --output GCF_900002575.1_FRIFI_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:42,670] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:42,681] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:42,681] [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_900002575.1	s__Romboutsia_C hominis	100.0	1013	1013	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	conclusive
GCA_018336475.1	s__Romboutsia sp018336475	81.4461	424	1013	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	81.3567	547	1013	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_900015215.1	s__Romboutsia ilealis	81.3144	421	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	98.59	98.59	0.90	0.90	2	-
GCF_900103615.1	s__Romboutsia_D lituseburensis	81.2758	551	1013	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	-
GCF_000499525.1	s__CCUG-7971 spG000499525	81.0358	525	1013	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	80.9451	513	1013	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_900106845.1	s__Romboutsia timonensis	80.8953	463	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	98.20	98.12	0.88	0.86	5	-
GCA_904418825.1	s__Romboutsia sp904418825	80.7501	365	1013	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_017425305.1	s__Paraclostridium sp017425305	80.3122	172	1013	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_000953675.1	s__Paraclostridium sordellii	80.0844	428	1013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	98.12	96.78	0.93	0.89	59	-
GCF_002250835.2	s__Romboutsia_A weinsteinii	79.6287	402	1013	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	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:42,683] [INFO] GTDB search result was written to GCF_900002575.1_FRIFI_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:42,684] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:42,687] [INFO] DFAST_QC result json was written to GCF_900002575.1_FRIFI_genomic.fna/dqc_result.json
[2024-01-24 12:22:42,688] [INFO] DFAST_QC completed!
[2024-01-24 12:22:42,688] [INFO] Total running time: 0h0m45s