[2023-06-08 15:04:31,304] [INFO] DFAST_QC pipeline started.
[2023-06-08 15:04:31,308] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 15:04:31,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg997eb8c1-d78e-4585-90d7-da15cdca0320/dqc_reference
[2023-06-08 15:04:32,620] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 15:04:32,621] [INFO] Task started: Prodigal
[2023-06-08 15:04:32,622] [INFO] Running command: gunzip -c /var/lib/cwl/stg35c3b10a-97f3-4aae-b8a4-2320f3a6c3e0/GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 15:04:39,520] [INFO] Task succeeded: Prodigal
[2023-06-08 15:04:39,520] [INFO] Task started: HMMsearch
[2023-06-08 15:04:39,520] [INFO] Running command: hmmsearch --tblout GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg997eb8c1-d78e-4585-90d7-da15cdca0320/dqc_reference/reference_markers.hmm GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 15:04:39,811] [INFO] Task succeeded: HMMsearch
[2023-06-08 15:04:39,812] [INFO] Found 6/6 markers.
[2023-06-08 15:04:39,845] [INFO] Query marker FASTA was written to GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 15:04:39,845] [INFO] Task started: Blastn
[2023-06-08 15:04:39,845] [INFO] Running command: blastn -query GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg997eb8c1-d78e-4585-90d7-da15cdca0320/dqc_reference/reference_markers.fasta -out GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:04:40,464] [INFO] Task succeeded: Blastn
[2023-06-08 15:04:40,468] [INFO] Selected 26 target genomes.
[2023-06-08 15:04:40,468] [INFO] Target genome list was writen to GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 15:04:40,469] [INFO] Task started: fastANI
[2023-06-08 15:04:40,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg35c3b10a-97f3-4aae-b8a4-2320f3a6c3e0/GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 15:04:57,534] [INFO] Task succeeded: fastANI
[2023-06-08 15:04:57,534] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg997eb8c1-d78e-4585-90d7-da15cdca0320/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 15:04:57,535] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg997eb8c1-d78e-4585-90d7-da15cdca0320/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 15:04:57,546] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 15:04:57,546] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 15:04:57,546] [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
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.6948	84	997	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.6477	82	997	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	76.6373	80	997	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.6372	81	997	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	76.4259	93	997	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	76.3445	92	997	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	76.3084	94	997	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	76.2269	92	997	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	76.0434	99	997	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	76.0426	98	997	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	76.0369	98	997	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 15:04:57,548] [INFO] DFAST Taxonomy check result was written to GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 15:04:57,549] [INFO] ===== Taxonomy check completed =====
[2023-06-08 15:04:57,549] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 15:04:57,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg997eb8c1-d78e-4585-90d7-da15cdca0320/dqc_reference/checkm_data
[2023-06-08 15:04:57,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 15:04:57,588] [INFO] Task started: CheckM
[2023-06-08 15:04:57,588] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 15:05:23,298] [INFO] Task succeeded: CheckM
[2023-06-08 15:05:23,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 15:05:23,320] [INFO] ===== Completeness check finished =====
[2023-06-08 15:05:23,320] [INFO] ===== Start GTDB Search =====
[2023-06-08 15:05:23,321] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 15:05:23,321] [INFO] Task started: Blastn
[2023-06-08 15:05:23,321] [INFO] Running command: blastn -query GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg997eb8c1-d78e-4585-90d7-da15cdca0320/dqc_reference/reference_markers_gtdb.fasta -out GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:05:24,393] [INFO] Task succeeded: Blastn
[2023-06-08 15:05:24,397] [INFO] Selected 16 target genomes.
[2023-06-08 15:05:24,397] [INFO] Target genome list was writen to GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 15:05:24,402] [INFO] Task started: fastANI
[2023-06-08 15:05:24,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg35c3b10a-97f3-4aae-b8a4-2320f3a6c3e0/GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 15:05:35,094] [INFO] Task succeeded: fastANI
[2023-06-08 15:05:35,106] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 15:05:35,107] [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_009774615.1	s__Caccovicinus sp009774615	99.086	898	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	99.13	99.13	0.87	0.87	2	conclusive
GCA_910584785.1	s__Caccovicinus sp910584785	85.017	636	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575565.1	s__Caccovicinus sp910575565	77.9334	254	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	99.12	99.12	0.93	0.93	2	-
GCA_018715905.1	s__Caccovicinus merdipullorum	77.36	157	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	98.94	98.69	0.87	0.79	3	-
GCA_910589195.1	s__Caccovicinus sp910589195	77.3407	189	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713255.1	s__Caccovicinus excrementipullorum	77.2987	139	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	99.99	99.99	0.96	0.96	2	-
GCA_017889125.1	s__Caccovicinus sp017889125	77.0685	173	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588325.1	s__UBA3402 sp910588325	76.6256	83	997	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_900540335.1	s__Ventrimonas sp900540335	76.5878	83	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.37	99.36	0.86	0.81	3	-
GCA_018713185.1	s__Copromonas avistercoris	76.4593	50	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	98.24	98.19	0.97	0.95	4	-
GCF_002160755.1	s__Lachnoclostridium_A sp002160755	76.4366	84	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.32	98.32	0.92	0.92	2	-
GCA_019118585.1	s__Enterocloster faecavium	76.4018	70	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.87	99.87	0.86	0.86	2	-
GCF_002899675.1	s__CHH4-2 sp002899675	76.1469	85	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CHH4-2	95.0	100.00	100.00	0.98	0.98	2	-
GCA_910577655.1	s__Ventrimonas sp910577655	76.1365	74	997	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_018380885.1	s__Enterocloster sp900555905	76.082	91	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.89	98.89	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-08 15:05:35,109] [INFO] GTDB search result was written to GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 15:05:35,109] [INFO] ===== GTDB Search completed =====
[2023-06-08 15:05:35,113] [INFO] DFAST_QC result json was written to GCA_947088355.1_SRR14038238_bin.63_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 15:05:35,113] [INFO] DFAST_QC completed!
[2023-06-08 15:05:35,113] [INFO] Total running time: 0h1m4s