[2024-01-24 11:51:11,222] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:11,226] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:11,227] [INFO] DQC Reference Directory: /var/lib/cwl/stga9286578-53bf-49e7-8337-4ae0ae8679c8/dqc_reference
[2024-01-24 11:51:12,657] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,658] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,658] [INFO] Running command: gunzip -c /var/lib/cwl/stgdae32919-7797-4006-8cb5-66ad84e95dae/GCF_002250835.2_ASM225083v2_genomic.fna.gz | prodigal -d GCF_002250835.2_ASM225083v2_genomic.fna/cds.fna -a GCF_002250835.2_ASM225083v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:18,696] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:18,696] [INFO] Task started: HMMsearch
[2024-01-24 11:51:18,696] [INFO] Running command: hmmsearch --tblout GCF_002250835.2_ASM225083v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9286578-53bf-49e7-8337-4ae0ae8679c8/dqc_reference/reference_markers.hmm GCF_002250835.2_ASM225083v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:19,031] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:19,033] [INFO] Found 6/6 markers.
[2024-01-24 11:51:19,068] [INFO] Query marker FASTA was written to GCF_002250835.2_ASM225083v2_genomic.fna/markers.fasta
[2024-01-24 11:51:19,069] [INFO] Task started: Blastn
[2024-01-24 11:51:19,069] [INFO] Running command: blastn -query GCF_002250835.2_ASM225083v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga9286578-53bf-49e7-8337-4ae0ae8679c8/dqc_reference/reference_markers.fasta -out GCF_002250835.2_ASM225083v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:19,731] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:19,734] [INFO] Selected 12 target genomes.
[2024-01-24 11:51:19,735] [INFO] Target genome list was writen to GCF_002250835.2_ASM225083v2_genomic.fna/target_genomes.txt
[2024-01-24 11:51:19,739] [INFO] Task started: fastANI
[2024-01-24 11:51:19,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgdae32919-7797-4006-8cb5-66ad84e95dae/GCF_002250835.2_ASM225083v2_genomic.fna.gz --refList GCF_002250835.2_ASM225083v2_genomic.fna/target_genomes.txt --output GCF_002250835.2_ASM225083v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:27,819] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:27,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9286578-53bf-49e7-8337-4ae0ae8679c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:27,820] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9286578-53bf-49e7-8337-4ae0ae8679c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:27,831] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:27,831] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:27,831] [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 weinsteinii	strain=CCRI-19649	GCA_002250835.2	2020949	2020949	type	True	100.0	1305	1315	95	conclusive
[Clostridium] dakarense	strain=FF1	GCA_000499525.1	1301100	1301100	type	True	80.5352	536	1315	95	below_threshold
Romboutsia ilealis	strain=CRIB	GCA_900015215.1	1115758	1115758	type	True	79.7738	375	1315	95	below_threshold
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	79.582	416	1315	95	below_threshold
Romboutsia hominis	strain=FRIFI	GCA_900002575.1	1507512	1507512	type	True	79.5756	419	1315	95	below_threshold
Romboutsia lituseburensis	strain=DSM 797	GCA_900103615.1	1537	1537	type	True	79.5731	469	1315	95	below_threshold
Romboutsia lituseburensis	strain=A25K	GCA_900002825.1	1537	1537	type	True	79.5661	476	1315	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_006802875.1	1490	1490	type	True	78.6229	367	1315	95	below_threshold
Paeniclostridium sordellii	strain=ATCC9714	GCA_000953675.1	1505	1505	type	True	78.5701	409	1315	95	below_threshold
Terrisporobacter othiniensis	strain=08-306576	GCA_000808015.1	1577792	1577792	type	True	78.2225	337	1315	95	below_threshold
Peptacetobacter hiranonis	strain=DSM 13275	GCA_008151785.1	89152	89152	type	True	77.3064	156	1315	95	below_threshold
Clostridioides mangenotii	strain=DSM 1289	GCA_017873185.1	1540	1540	suspected-type	True	77.205	202	1315	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:27,833] [INFO] DFAST Taxonomy check result was written to GCF_002250835.2_ASM225083v2_genomic.fna/tc_result.tsv
[2024-01-24 11:51:27,834] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:27,834] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:27,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9286578-53bf-49e7-8337-4ae0ae8679c8/dqc_reference/checkm_data
[2024-01-24 11:51:27,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:27,878] [INFO] Task started: CheckM
[2024-01-24 11:51:27,878] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002250835.2_ASM225083v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002250835.2_ASM225083v2_genomic.fna/checkm_input GCF_002250835.2_ASM225083v2_genomic.fna/checkm_result
[2024-01-24 11:51:52,146] [INFO] Task succeeded: CheckM
[2024-01-24 11:51:52,147] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:51:52,172] [INFO] ===== Completeness check finished =====
[2024-01-24 11:51:52,172] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:51:52,173] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002250835.2_ASM225083v2_genomic.fna/markers.fasta)
[2024-01-24 11:51:52,173] [INFO] Task started: Blastn
[2024-01-24 11:51:52,173] [INFO] Running command: blastn -query GCF_002250835.2_ASM225083v2_genomic.fna/markers.fasta -db /var/lib/cwl/stga9286578-53bf-49e7-8337-4ae0ae8679c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002250835.2_ASM225083v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:53,009] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:53,013] [INFO] Selected 16 target genomes.
[2024-01-24 11:51:53,013] [INFO] Target genome list was writen to GCF_002250835.2_ASM225083v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:51:53,026] [INFO] Task started: fastANI
[2024-01-24 11:51:53,027] [INFO] Running command: fastANI --query /var/lib/cwl/stgdae32919-7797-4006-8cb5-66ad84e95dae/GCF_002250835.2_ASM225083v2_genomic.fna.gz --refList GCF_002250835.2_ASM225083v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002250835.2_ASM225083v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:02,716] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:02,729] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:02,730] [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_002250835.2	s__Romboutsia_A weinsteinii	100.0	1305	1315	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	conclusive
GCF_017590215.1	s__CCUG-7971 sp017590215	80.6421	555	1315	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_000499525.1	s__CCUG-7971 spG000499525	80.5404	536	1315	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_002251085.2	s__Romboutsia_B maritimum	80.1507	415	1315	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	-
GCA_000686145.1	s__Romboutsia_D sp000686145	79.9569	472	1315	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_902362365.1	s__GCA-900066495 sp902362365	79.9531	437	1315	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_014323405.1	s__GCA-900066495 sp014323405	79.9285	448	1315	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	79.6242	408	1315	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_904418825.1	s__Romboutsia sp904418825	79.6215	352	1315	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	79.6195	159	1315	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	79.5822	416	1315	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_900002575.1	s__Romboutsia_C hominis	79.5526	420	1315	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_900129815.1	s__Asaccharospora irregularis	78.9155	281	1315	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Asaccharospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363255.1	s__Terrisporobacter sp902363255	78.0725	364	1315	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018917435.1	s__Intestinibacter bartlettii_A	77.6886	238	1315	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Intestinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900557165.1	s__Terrisporobacter sp900557165	77.5727	218	1315	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.06	99.06	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:02,731] [INFO] GTDB search result was written to GCF_002250835.2_ASM225083v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:02,732] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:02,737] [INFO] DFAST_QC result json was written to GCF_002250835.2_ASM225083v2_genomic.fna/dqc_result.json
[2024-01-24 11:52:02,737] [INFO] DFAST_QC completed!
[2024-01-24 11:52:02,737] [INFO] Total running time: 0h0m52s