[2024-01-24 14:19:31,465] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:31,473] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:31,473] [INFO] DQC Reference Directory: /var/lib/cwl/stgfba24efb-d6d2-4a15-8391-681a7e1e6bd1/dqc_reference
[2024-01-24 14:19:32,899] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:32,900] [INFO] Task started: Prodigal
[2024-01-24 14:19:32,901] [INFO] Running command: gunzip -c /var/lib/cwl/stgd65c7961-7e97-44bf-96ad-5b51eec161a9/GCF_003024655.1_ASM302465v1_genomic.fna.gz | prodigal -d GCF_003024655.1_ASM302465v1_genomic.fna/cds.fna -a GCF_003024655.1_ASM302465v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:52,107] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:52,108] [INFO] Task started: HMMsearch
[2024-01-24 14:19:52,108] [INFO] Running command: hmmsearch --tblout GCF_003024655.1_ASM302465v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfba24efb-d6d2-4a15-8391-681a7e1e6bd1/dqc_reference/reference_markers.hmm GCF_003024655.1_ASM302465v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:52,485] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:52,487] [INFO] Found 6/6 markers.
[2024-01-24 14:19:52,546] [INFO] Query marker FASTA was written to GCF_003024655.1_ASM302465v1_genomic.fna/markers.fasta
[2024-01-24 14:19:52,546] [INFO] Task started: Blastn
[2024-01-24 14:19:52,546] [INFO] Running command: blastn -query GCF_003024655.1_ASM302465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfba24efb-d6d2-4a15-8391-681a7e1e6bd1/dqc_reference/reference_markers.fasta -out GCF_003024655.1_ASM302465v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:53,249] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:53,252] [INFO] Selected 17 target genomes.
[2024-01-24 14:19:53,252] [INFO] Target genome list was writen to GCF_003024655.1_ASM302465v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:53,284] [INFO] Task started: fastANI
[2024-01-24 14:19:53,285] [INFO] Running command: fastANI --query /var/lib/cwl/stgd65c7961-7e97-44bf-96ad-5b51eec161a9/GCF_003024655.1_ASM302465v1_genomic.fna.gz --refList GCF_003024655.1_ASM302465v1_genomic.fna/target_genomes.txt --output GCF_003024655.1_ASM302465v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:08,124] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:08,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfba24efb-d6d2-4a15-8391-681a7e1e6bd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:08,125] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfba24efb-d6d2-4a15-8391-681a7e1e6bd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:08,141] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:20:08,141] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:20:08,141] [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
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	94.5208	1677	2123	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	94.3038	1682	2123	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	78.6884	436	2123	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	78.6383	444	2123	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	78.6243	436	2123	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	78.3021	444	2123	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	78.2581	444	2123	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	78.2493	452	2123	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	77.9744	113	2123	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	77.2731	219	2123	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	77.2315	104	2123	95	below_threshold
Qiania dongpingensis	strain=NSJ-38	GCA_014337195.1	2763669	2763669	type	True	77.2313	72	2123	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.6906	96	2123	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	76.6472	95	2123	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:08,145] [INFO] DFAST Taxonomy check result was written to GCF_003024655.1_ASM302465v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:08,147] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:08,147] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:08,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfba24efb-d6d2-4a15-8391-681a7e1e6bd1/dqc_reference/checkm_data
[2024-01-24 14:20:08,150] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:08,222] [INFO] Task started: CheckM
[2024-01-24 14:20:08,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003024655.1_ASM302465v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003024655.1_ASM302465v1_genomic.fna/checkm_input GCF_003024655.1_ASM302465v1_genomic.fna/checkm_result
[2024-01-24 14:21:02,192] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:02,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.57%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:02,218] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:02,218] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:02,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003024655.1_ASM302465v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:02,219] [INFO] Task started: Blastn
[2024-01-24 14:21:02,219] [INFO] Running command: blastn -query GCF_003024655.1_ASM302465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfba24efb-d6d2-4a15-8391-681a7e1e6bd1/dqc_reference/reference_markers_gtdb.fasta -out GCF_003024655.1_ASM302465v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:03,407] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:03,411] [INFO] Selected 9 target genomes.
[2024-01-24 14:21:03,411] [INFO] Target genome list was writen to GCF_003024655.1_ASM302465v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:03,432] [INFO] Task started: fastANI
[2024-01-24 14:21:03,433] [INFO] Running command: fastANI --query /var/lib/cwl/stgd65c7961-7e97-44bf-96ad-5b51eec161a9/GCF_003024655.1_ASM302465v1_genomic.fna.gz --refList GCF_003024655.1_ASM302465v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003024655.1_ASM302465v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:13,813] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:13,826] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:13,826] [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_902364025.1	s__Enterocloster lavalensis	98.0242	1754	2123	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.58	98.12	0.90	0.83	6	conclusive
GCF_000158075.1	s__Enterocloster asparagiformis	94.3038	1682	2123	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_018380885.1	s__Enterocloster sp900555905	86.4765	1304	2123	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.89	98.89	0.95	0.95	2	-
GCA_900555045.1	s__Enterocloster sp900555045	83.1733	883	2123	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_900551225.1	s__Enterocloster sp900551225	80.1432	689	2123	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005845215.1	s__Enterocloster sp005845215	79.22	437	2123	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.62	99.13	0.95	0.86	6	-
GCF_002234575.2	s__Enterocloster bolteae	78.3057	443	2123	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.46	96.97	0.88	0.78	35	-
GCA_900547035.1	s__Enterocloster excrementigallinarum	78.2064	285	2123	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.35	98.28	0.80	0.77	6	-
GCA_019116745.1	s__Lachnoclostridium_A stercorigallinarum	77.2751	187	2123	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	99.47	99.47	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:13,828] [INFO] GTDB search result was written to GCF_003024655.1_ASM302465v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:13,829] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:13,832] [INFO] DFAST_QC result json was written to GCF_003024655.1_ASM302465v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:13,832] [INFO] DFAST_QC completed!
[2024-01-24 14:21:13,833] [INFO] Total running time: 0h1m42s