[2024-01-24 13:58:25,237] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:25,239] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:25,239] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f11c00f-adc2-4a23-af29-f75d573c8dd4/dqc_reference
[2024-01-24 13:58:26,513] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:26,514] [INFO] Task started: Prodigal
[2024-01-24 13:58:26,515] [INFO] Running command: gunzip -c /var/lib/cwl/stg66431845-16cf-41c3-afa1-6421bc394086/GCF_013282095.1_ASM1328209v1_genomic.fna.gz | prodigal -d GCF_013282095.1_ASM1328209v1_genomic.fna/cds.fna -a GCF_013282095.1_ASM1328209v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:36,058] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:36,058] [INFO] Task started: HMMsearch
[2024-01-24 13:58:36,058] [INFO] Running command: hmmsearch --tblout GCF_013282095.1_ASM1328209v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f11c00f-adc2-4a23-af29-f75d573c8dd4/dqc_reference/reference_markers.hmm GCF_013282095.1_ASM1328209v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:36,383] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:36,384] [INFO] Found 6/6 markers.
[2024-01-24 13:58:36,419] [INFO] Query marker FASTA was written to GCF_013282095.1_ASM1328209v1_genomic.fna/markers.fasta
[2024-01-24 13:58:36,420] [INFO] Task started: Blastn
[2024-01-24 13:58:36,420] [INFO] Running command: blastn -query GCF_013282095.1_ASM1328209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f11c00f-adc2-4a23-af29-f75d573c8dd4/dqc_reference/reference_markers.fasta -out GCF_013282095.1_ASM1328209v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:37,088] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:37,092] [INFO] Selected 22 target genomes.
[2024-01-24 13:58:37,092] [INFO] Target genome list was writen to GCF_013282095.1_ASM1328209v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:37,105] [INFO] Task started: fastANI
[2024-01-24 13:58:37,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg66431845-16cf-41c3-afa1-6421bc394086/GCF_013282095.1_ASM1328209v1_genomic.fna.gz --refList GCF_013282095.1_ASM1328209v1_genomic.fna/target_genomes.txt --output GCF_013282095.1_ASM1328209v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:53,747] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:53,747] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f11c00f-adc2-4a23-af29-f75d573c8dd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:53,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f11c00f-adc2-4a23-af29-f75d573c8dd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:53,763] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:53,763] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:53,763] [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
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	80.1927	86	1249	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	79.9868	314	1249	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	79.9785	318	1249	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	79.9778	317	1249	95	below_threshold
Lachnoclostridium edouardi	strain=Marseille-P3397	GCA_900240245.1	1926283	1926283	type	True	79.6214	119	1249	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	79.5952	191	1249	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	79.2636	174	1249	95	below_threshold
Clostridium porci	strain=WCA-389-WT-23D1	GCA_009696375.1	2605778	2605778	type	True	78.7714	216	1249	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	78.6907	294	1249	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	78.5402	289	1249	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	78.433	290	1249	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	78.0965	267	1249	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	78.095	264	1249	95	below_threshold
Lachnoclostridium pacaense	strain=Marseille-P3100	GCA_900566185.1	1917870	1917870	type	True	77.4927	102	1249	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	77.0117	66	1249	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	76.7497	138	1249	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.6556	57	1249	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	76.3306	54	1249	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:53,765] [INFO] DFAST Taxonomy check result was written to GCF_013282095.1_ASM1328209v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:53,765] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:53,765] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:53,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f11c00f-adc2-4a23-af29-f75d573c8dd4/dqc_reference/checkm_data
[2024-01-24 13:58:53,767] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:53,808] [INFO] Task started: CheckM
[2024-01-24 13:58:53,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013282095.1_ASM1328209v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013282095.1_ASM1328209v1_genomic.fna/checkm_input GCF_013282095.1_ASM1328209v1_genomic.fna/checkm_result
[2024-01-24 13:59:28,862] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:28,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:28,887] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:28,888] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:28,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013282095.1_ASM1328209v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:28,888] [INFO] Task started: Blastn
[2024-01-24 13:59:28,889] [INFO] Running command: blastn -query GCF_013282095.1_ASM1328209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f11c00f-adc2-4a23-af29-f75d573c8dd4/dqc_reference/reference_markers_gtdb.fasta -out GCF_013282095.1_ASM1328209v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:29,923] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:29,927] [INFO] Selected 14 target genomes.
[2024-01-24 13:59:29,927] [INFO] Target genome list was writen to GCF_013282095.1_ASM1328209v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:29,951] [INFO] Task started: fastANI
[2024-01-24 13:59:29,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg66431845-16cf-41c3-afa1-6421bc394086/GCF_013282095.1_ASM1328209v1_genomic.fna.gz --refList GCF_013282095.1_ASM1328209v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013282095.1_ASM1328209v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:40,606] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:40,624] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:40,625] [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_013282095.1	s__Enterocloster sp900538485	100.0	1249	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.11	98.91	0.91	0.88	5	conclusive
GCF_001517625.2	s__Enterocloster sp001517625	81.5455	634	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.90	98.46	0.89	0.80	9	-
GCF_003473545.1	s__Enterocloster sp000431375	80.307	331	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.19	98.66	0.91	0.81	15	-
GCF_000233455.1	s__Enterocloster citroniae	79.8681	322	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.23	99.13	0.87	0.84	10	-
GCA_900549235.1	s__Enterocloster sp900549235	79.1307	374	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.03	99.00	0.79	0.77	3	-
GCA_900543885.1	s__Enterocloster sp900543885	78.7302	270	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.55	98.55	0.85	0.85	2	-
GCA_900753815.1	s__Enterocloster sp900753815	78.6404	210	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900759225.1	s__Enterocloster sp900759225	78.2475	195	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.23	98.23	0.78	0.78	2	-
GCF_902364025.1	s__Enterocloster lavalensis	78.1991	242	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.58	98.12	0.90	0.83	6	-
GCF_000158075.1	s__Enterocloster asparagiformis	78.0747	268	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.72	98.33	0.90	0.88	5	-
GCA_900551225.1	s__Enterocloster sp900551225	77.261	187	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715905.1	s__Caccovicinus merdipullorum	77.1232	170	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	98.94	98.69	0.87	0.79	3	-
GCF_003432035.1	s__Lacrimispora indica	76.6595	105	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577765.1	s__Ventrimonas sp910577765	76.5105	106	1249	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:40,627] [INFO] GTDB search result was written to GCF_013282095.1_ASM1328209v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:40,627] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:40,634] [INFO] DFAST_QC result json was written to GCF_013282095.1_ASM1328209v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:40,634] [INFO] DFAST_QC completed!
[2024-01-24 13:59:40,634] [INFO] Total running time: 0h1m15s