[2024-01-25 18:20:05,488] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:20:05,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:20:05,491] [INFO] DQC Reference Directory: /var/lib/cwl/stgd92ae3d8-26ee-4278-8c6b-0b719a76a482/dqc_reference
[2024-01-25 18:20:06,601] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:20:06,601] [INFO] Task started: Prodigal
[2024-01-25 18:20:06,602] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf2f5d5e-37bd-4e28-979d-8c552bb4a40b/GCF_014323405.1_ASM1432340v1_genomic.fna.gz | prodigal -d GCF_014323405.1_ASM1432340v1_genomic.fna/cds.fna -a GCF_014323405.1_ASM1432340v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:20:11,107] [INFO] Task succeeded: Prodigal
[2024-01-25 18:20:11,108] [INFO] Task started: HMMsearch
[2024-01-25 18:20:11,108] [INFO] Running command: hmmsearch --tblout GCF_014323405.1_ASM1432340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd92ae3d8-26ee-4278-8c6b-0b719a76a482/dqc_reference/reference_markers.hmm GCF_014323405.1_ASM1432340v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:20:11,361] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:20:11,362] [INFO] Found 6/6 markers.
[2024-01-25 18:20:11,391] [INFO] Query marker FASTA was written to GCF_014323405.1_ASM1432340v1_genomic.fna/markers.fasta
[2024-01-25 18:20:11,391] [INFO] Task started: Blastn
[2024-01-25 18:20:11,391] [INFO] Running command: blastn -query GCF_014323405.1_ASM1432340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd92ae3d8-26ee-4278-8c6b-0b719a76a482/dqc_reference/reference_markers.fasta -out GCF_014323405.1_ASM1432340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:20:11,923] [INFO] Task succeeded: Blastn
[2024-01-25 18:20:11,925] [INFO] Selected 11 target genomes.
[2024-01-25 18:20:11,925] [INFO] Target genome list was writen to GCF_014323405.1_ASM1432340v1_genomic.fna/target_genomes.txt
[2024-01-25 18:20:11,942] [INFO] Task started: fastANI
[2024-01-25 18:20:11,943] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf2f5d5e-37bd-4e28-979d-8c552bb4a40b/GCF_014323405.1_ASM1432340v1_genomic.fna.gz --refList GCF_014323405.1_ASM1432340v1_genomic.fna/target_genomes.txt --output GCF_014323405.1_ASM1432340v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:20:19,621] [INFO] Task succeeded: fastANI
[2024-01-25 18:20:19,621] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd92ae3d8-26ee-4278-8c6b-0b719a76a482/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:20:19,622] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd92ae3d8-26ee-4278-8c6b-0b719a76a482/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:20:19,629] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:20:19,629] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:20:19,630] [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 ilealis	strain=CRIB	GCA_900015215.1	1115758	1115758	type	True	80.0325	405	1142	95	below_threshold
Romboutsia weinsteinii	strain=CCRI-19649	GCA_002250835.2	2020949	2020949	type	True	79.8077	445	1142	95	below_threshold
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	79.8004	435	1142	95	below_threshold
[Clostridium] dakarense	strain=FF1	GCA_000499525.1	1301100	1301100	type	True	79.7508	455	1142	95	below_threshold
Romboutsia hominis	strain=FRIFI	GCA_900002575.1	1507512	1507512	type	True	79.6624	414	1142	95	below_threshold
Romboutsia lituseburensis	strain=A25K	GCA_900002825.1	1537	1537	type	True	79.3332	440	1142	95	below_threshold
Terrisporobacter othiniensis	strain=08-306576	GCA_000808015.1	1577792	1577792	type	True	78.7919	381	1142	95	below_threshold
Paeniclostridium sordellii	strain=ATCC9714	GCA_000953675.1	1505	1505	type	True	78.7449	360	1142	95	below_threshold
Intestinibacter bartlettii	strain=DSM 16795	GCA_025148965.1	261299	261299	type	True	78.3656	270	1142	95	below_threshold
Intestinibacter bartlettii	strain=DSM 16795	GCA_000154445.1	261299	261299	type	True	78.3274	269	1142	95	below_threshold
Intestinibacter bartlettii	strain=DSM 16795	GCA_900167285.1	261299	261299	type	True	78.3249	264	1142	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:20:19,632] [INFO] DFAST Taxonomy check result was written to GCF_014323405.1_ASM1432340v1_genomic.fna/tc_result.tsv
[2024-01-25 18:20:19,633] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:20:19,633] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:20:19,633] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd92ae3d8-26ee-4278-8c6b-0b719a76a482/dqc_reference/checkm_data
[2024-01-25 18:20:19,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:20:19,671] [INFO] Task started: CheckM
[2024-01-25 18:20:19,672] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014323405.1_ASM1432340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014323405.1_ASM1432340v1_genomic.fna/checkm_input GCF_014323405.1_ASM1432340v1_genomic.fna/checkm_result
[2024-01-25 18:20:38,783] [INFO] Task succeeded: CheckM
[2024-01-25 18:20:38,784] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:20:38,812] [INFO] ===== Completeness check finished =====
[2024-01-25 18:20:38,812] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:20:38,812] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014323405.1_ASM1432340v1_genomic.fna/markers.fasta)
[2024-01-25 18:20:38,812] [INFO] Task started: Blastn
[2024-01-25 18:20:38,813] [INFO] Running command: blastn -query GCF_014323405.1_ASM1432340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd92ae3d8-26ee-4278-8c6b-0b719a76a482/dqc_reference/reference_markers_gtdb.fasta -out GCF_014323405.1_ASM1432340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:20:39,551] [INFO] Task succeeded: Blastn
[2024-01-25 18:20:39,554] [INFO] Selected 10 target genomes.
[2024-01-25 18:20:39,554] [INFO] Target genome list was writen to GCF_014323405.1_ASM1432340v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:20:39,565] [INFO] Task started: fastANI
[2024-01-25 18:20:39,565] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf2f5d5e-37bd-4e28-979d-8c552bb4a40b/GCF_014323405.1_ASM1432340v1_genomic.fna.gz --refList GCF_014323405.1_ASM1432340v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014323405.1_ASM1432340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:20:46,287] [INFO] Task succeeded: fastANI
[2024-01-25 18:20:46,294] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:20:46,294] [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_014323405.1	s__GCA-900066495 sp014323405	100.0	1142	1142	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	conclusive
GCA_902362365.1	s__GCA-900066495 sp902362365	92.644	862	1142	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_012317385.1	s__GCA-900066495 sp900545985	83.3266	665	1142	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_900604495.1	s__GCA-900066495 sp900066495	83.2848	691	1142	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	-
GCA_017425305.1	s__Paraclostridium sp017425305	80.0914	151	1142	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	97.54	97.54	0.79	0.79	2	-
GCA_904418825.1	s__Romboutsia sp904418825	79.9712	345	1142	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_002250835.2	s__Romboutsia_A weinsteinii	79.8069	445	1142	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_900106845.1	s__Romboutsia timonensis	79.7997	435	1142	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_000499525.1	s__CCUG-7971 spG000499525	79.7334	456	1142	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_900002575.1	s__Romboutsia_C hominis	79.6283	414	1142	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	-
--------------------------------------------------------------------------------
[2024-01-25 18:20:46,295] [INFO] GTDB search result was written to GCF_014323405.1_ASM1432340v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:20:46,296] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:20:46,299] [INFO] DFAST_QC result json was written to GCF_014323405.1_ASM1432340v1_genomic.fna/dqc_result.json
[2024-01-25 18:20:46,300] [INFO] DFAST_QC completed!
[2024-01-25 18:20:46,300] [INFO] Total running time: 0h0m41s