[2023-06-28 19:48:10,493] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:48:10,496] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:48:10,496] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbc77ad9-3e0e-4025-9ffa-e5aa6f8004b1/dqc_reference
[2023-06-28 19:48:12,178] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:48:12,179] [INFO] Task started: Prodigal
[2023-06-28 19:48:12,180] [INFO] Running command: gunzip -c /var/lib/cwl/stg80645491-cd51-4a6a-8eeb-20b991c55c0a/GCA_944382045.1_BRZ_LM_bin53_genomic.fna.gz | prodigal -d GCA_944382045.1_BRZ_LM_bin53_genomic.fna/cds.fna -a GCA_944382045.1_BRZ_LM_bin53_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:48:18,304] [INFO] Task succeeded: Prodigal
[2023-06-28 19:48:18,304] [INFO] Task started: HMMsearch
[2023-06-28 19:48:18,304] [INFO] Running command: hmmsearch --tblout GCA_944382045.1_BRZ_LM_bin53_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbc77ad9-3e0e-4025-9ffa-e5aa6f8004b1/dqc_reference/reference_markers.hmm GCA_944382045.1_BRZ_LM_bin53_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:48:18,558] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:48:18,560] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg80645491-cd51-4a6a-8eeb-20b991c55c0a/GCA_944382045.1_BRZ_LM_bin53_genomic.fna.gz]
[2023-06-28 19:48:18,592] [INFO] Query marker FASTA was written to GCA_944382045.1_BRZ_LM_bin53_genomic.fna/markers.fasta
[2023-06-28 19:48:18,593] [INFO] Task started: Blastn
[2023-06-28 19:48:18,593] [INFO] Running command: blastn -query GCA_944382045.1_BRZ_LM_bin53_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbc77ad9-3e0e-4025-9ffa-e5aa6f8004b1/dqc_reference/reference_markers.fasta -out GCA_944382045.1_BRZ_LM_bin53_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:48:19,203] [INFO] Task succeeded: Blastn
[2023-06-28 19:48:19,208] [INFO] Selected 18 target genomes.
[2023-06-28 19:48:19,208] [INFO] Target genome list was writen to GCA_944382045.1_BRZ_LM_bin53_genomic.fna/target_genomes.txt
[2023-06-28 19:48:19,211] [INFO] Task started: fastANI
[2023-06-28 19:48:19,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg80645491-cd51-4a6a-8eeb-20b991c55c0a/GCA_944382045.1_BRZ_LM_bin53_genomic.fna.gz --refList GCA_944382045.1_BRZ_LM_bin53_genomic.fna/target_genomes.txt --output GCA_944382045.1_BRZ_LM_bin53_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:48:36,083] [INFO] Task succeeded: fastANI
[2023-06-28 19:48:36,084] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbc77ad9-3e0e-4025-9ffa-e5aa6f8004b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:48:36,084] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbc77ad9-3e0e-4025-9ffa-e5aa6f8004b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:48:36,094] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:48:36,094] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 19:48:36,095] [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_000158075.1	333367	333367	type	True	78.2908	224	707	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	78.2254	232	707	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	77.7098	208	707	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	77.6877	233	707	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	77.684	227	707	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	77.6621	210	707	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	77.6613	211	707	95	below_threshold
Lachnoclostridium pacaense	strain=Marseille-P3100	GCA_900566185.1	1917870	1917870	type	True	77.2951	75	707	95	below_threshold
Clostridium porci	strain=WCA-389-WT-23D1	GCA_009696375.1	2605778	2605778	type	True	77.0412	106	707	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.5859	72	707	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:48:36,097] [INFO] DFAST Taxonomy check result was written to GCA_944382045.1_BRZ_LM_bin53_genomic.fna/tc_result.tsv
[2023-06-28 19:48:36,097] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:48:36,098] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:48:36,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbc77ad9-3e0e-4025-9ffa-e5aa6f8004b1/dqc_reference/checkm_data
[2023-06-28 19:48:36,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:48:36,134] [INFO] Task started: CheckM
[2023-06-28 19:48:36,134] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944382045.1_BRZ_LM_bin53_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944382045.1_BRZ_LM_bin53_genomic.fna/checkm_input GCA_944382045.1_BRZ_LM_bin53_genomic.fna/checkm_result
[2023-06-28 19:49:01,053] [INFO] Task succeeded: CheckM
[2023-06-28 19:49:01,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.18%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:49:01,077] [INFO] ===== Completeness check finished =====
[2023-06-28 19:49:01,078] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:49:01,078] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944382045.1_BRZ_LM_bin53_genomic.fna/markers.fasta)
[2023-06-28 19:49:01,078] [INFO] Task started: Blastn
[2023-06-28 19:49:01,078] [INFO] Running command: blastn -query GCA_944382045.1_BRZ_LM_bin53_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbc77ad9-3e0e-4025-9ffa-e5aa6f8004b1/dqc_reference/reference_markers_gtdb.fasta -out GCA_944382045.1_BRZ_LM_bin53_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:49:01,890] [INFO] Task succeeded: Blastn
[2023-06-28 19:49:01,894] [INFO] Selected 23 target genomes.
[2023-06-28 19:49:01,894] [INFO] Target genome list was writen to GCA_944382045.1_BRZ_LM_bin53_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:49:01,902] [INFO] Task started: fastANI
[2023-06-28 19:49:01,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg80645491-cd51-4a6a-8eeb-20b991c55c0a/GCA_944382045.1_BRZ_LM_bin53_genomic.fna.gz --refList GCA_944382045.1_BRZ_LM_bin53_genomic.fna/target_genomes_gtdb.txt --output GCA_944382045.1_BRZ_LM_bin53_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:49:17,707] [INFO] Task succeeded: fastANI
[2023-06-28 19:49:17,732] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 19:49:17,732] [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
GCA_019119575.1	s__Enterocloster excrementipullorum	82.2473	484	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.43	99.23	0.94	0.92	5	-
GCA_900555045.1	s__Enterocloster sp900555045	78.4682	222	707	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_902364025.1	s__Enterocloster lavalensis	78.4518	232	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.58	98.12	0.90	0.83	6	-
GCA_018380885.1	s__Enterocloster sp900555905	78.4156	239	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.89	98.89	0.95	0.95	2	-
GCF_000158075.1	s__Enterocloster asparagiformis	78.2872	223	707	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_900770345.1	s__Enterocloster sp900770345	78.0117	159	707	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_019114845.1	s__Lachnoclostridium_A stercoripullorum	77.87	176	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.44	98.44	0.80	0.80	2	-
GCA_900753815.1	s__Enterocloster sp900753815	77.7888	173	707	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_900549235.1	s__Enterocloster sp900549235	77.716	209	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.03	99.00	0.79	0.77	3	-
GCF_900113155.1	s__Enterocloster clostridioformis	77.7079	208	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.82	97.34	0.84	0.75	45	-
GCF_000424325.1	s__Enterocloster clostridioformis_A	77.624	201	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.02	99.02	0.92	0.92	2	-
GCA_000155435.1	s__Enterocloster sp000155435	77.5963	194	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.08	98.70	0.90	0.83	5	-
GCF_000233455.1	s__Enterocloster citroniae	77.5508	199	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.23	99.13	0.87	0.84	10	-
GCF_005845215.1	s__Enterocloster sp005845215	77.4807	227	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.62	99.13	0.95	0.86	6	-
GCA_019119775.1	s__Lachnoclostridium_A pullistercoris	77.3495	130	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	99.96	99.96	0.95	0.95	2	-
GCA_019114465.1	s__Lachnoclostridium_A avicola	77.293	161	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	99.23	98.89	0.92	0.90	3	-
GCA_018715565.1	s__Ventrimonas merdavium	77.1072	131	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.46	99.46	0.97	0.97	2	-
GCA_910588865.1	s__UBA3402 sp910588865	76.9617	105	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577765.1	s__Ventrimonas sp910577765	76.865	131	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585615.1	s__Acetatifactor sp910585615	76.8355	56	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014385265.1	s__Copromonas sp000435795	76.7386	88	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	98.24	96.73	0.89	0.84	6	-
GCA_019115665.1	s__Eisenbergiella pullistercoris	76.1024	69	707	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 19:49:17,734] [INFO] GTDB search result was written to GCA_944382045.1_BRZ_LM_bin53_genomic.fna/result_gtdb.tsv
[2023-06-28 19:49:17,735] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:49:17,739] [INFO] DFAST_QC result json was written to GCA_944382045.1_BRZ_LM_bin53_genomic.fna/dqc_result.json
[2023-06-28 19:49:17,739] [INFO] DFAST_QC completed!
[2023-06-28 19:49:17,739] [INFO] Total running time: 0h1m7s