[2023-06-13 21:51:08,558] [INFO] DFAST_QC pipeline started.
[2023-06-13 21:51:08,563] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 21:51:08,563] [INFO] DQC Reference Directory: /var/lib/cwl/stg57bab4aa-de3c-4714-ab87-bdd83beed741/dqc_reference
[2023-06-13 21:51:09,863] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 21:51:09,864] [INFO] Task started: Prodigal
[2023-06-13 21:51:09,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg75b142bc-3497-4bde-8ddf-cff0421e9ef4/GCA_022796695.1_ASM2279669v1_genomic.fna.gz | prodigal -d GCA_022796695.1_ASM2279669v1_genomic.fna/cds.fna -a GCA_022796695.1_ASM2279669v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 21:51:19,634] [INFO] Task succeeded: Prodigal
[2023-06-13 21:51:19,634] [INFO] Task started: HMMsearch
[2023-06-13 21:51:19,634] [INFO] Running command: hmmsearch --tblout GCA_022796695.1_ASM2279669v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57bab4aa-de3c-4714-ab87-bdd83beed741/dqc_reference/reference_markers.hmm GCA_022796695.1_ASM2279669v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 21:51:19,931] [INFO] Task succeeded: HMMsearch
[2023-06-13 21:51:19,933] [INFO] Found 6/6 markers.
[2023-06-13 21:51:19,969] [INFO] Query marker FASTA was written to GCA_022796695.1_ASM2279669v1_genomic.fna/markers.fasta
[2023-06-13 21:51:19,970] [INFO] Task started: Blastn
[2023-06-13 21:51:19,970] [INFO] Running command: blastn -query GCA_022796695.1_ASM2279669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57bab4aa-de3c-4714-ab87-bdd83beed741/dqc_reference/reference_markers.fasta -out GCA_022796695.1_ASM2279669v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:51:20,606] [INFO] Task succeeded: Blastn
[2023-06-13 21:51:20,611] [INFO] Selected 25 target genomes.
[2023-06-13 21:51:20,611] [INFO] Target genome list was writen to GCA_022796695.1_ASM2279669v1_genomic.fna/target_genomes.txt
[2023-06-13 21:51:20,612] [INFO] Task started: fastANI
[2023-06-13 21:51:20,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg75b142bc-3497-4bde-8ddf-cff0421e9ef4/GCA_022796695.1_ASM2279669v1_genomic.fna.gz --refList GCA_022796695.1_ASM2279669v1_genomic.fna/target_genomes.txt --output GCA_022796695.1_ASM2279669v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 21:51:37,232] [INFO] Task succeeded: fastANI
[2023-06-13 21:51:37,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57bab4aa-de3c-4714-ab87-bdd83beed741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 21:51:37,232] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57bab4aa-de3c-4714-ab87-bdd83beed741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 21:51:37,247] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 21:51:37,248] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 21:51:37,248] [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 bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	76.9115	124	1277	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	76.8589	123	1277	95	below_threshold
Clostridium fessum	strain=SNUG30386	GCA_003024715.1	2126740	2126740	type	True	76.8452	54	1277	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	76.8244	119	1277	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	76.8169	138	1277	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	76.7807	138	1277	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.7449	180	1277	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.7115	178	1277	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	76.6893	129	1277	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	76.5446	98	1277	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.4773	104	1277	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	76.4658	63	1277	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	76.4633	110	1277	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	76.2357	92	1277	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	76.1573	93	1277	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 21:51:37,250] [INFO] DFAST Taxonomy check result was written to GCA_022796695.1_ASM2279669v1_genomic.fna/tc_result.tsv
[2023-06-13 21:51:37,251] [INFO] ===== Taxonomy check completed =====
[2023-06-13 21:51:37,251] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 21:51:37,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57bab4aa-de3c-4714-ab87-bdd83beed741/dqc_reference/checkm_data
[2023-06-13 21:51:37,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 21:51:37,293] [INFO] Task started: CheckM
[2023-06-13 21:51:37,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022796695.1_ASM2279669v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022796695.1_ASM2279669v1_genomic.fna/checkm_input GCA_022796695.1_ASM2279669v1_genomic.fna/checkm_result
[2023-06-13 21:52:10,070] [INFO] Task succeeded: CheckM
[2023-06-13 21:52:10,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 21:52:10,094] [INFO] ===== Completeness check finished =====
[2023-06-13 21:52:10,094] [INFO] ===== Start GTDB Search =====
[2023-06-13 21:52:10,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022796695.1_ASM2279669v1_genomic.fna/markers.fasta)
[2023-06-13 21:52:10,095] [INFO] Task started: Blastn
[2023-06-13 21:52:10,095] [INFO] Running command: blastn -query GCA_022796695.1_ASM2279669v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57bab4aa-de3c-4714-ab87-bdd83beed741/dqc_reference/reference_markers_gtdb.fasta -out GCA_022796695.1_ASM2279669v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:52:11,171] [INFO] Task succeeded: Blastn
[2023-06-13 21:52:11,175] [INFO] Selected 12 target genomes.
[2023-06-13 21:52:11,175] [INFO] Target genome list was writen to GCA_022796695.1_ASM2279669v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 21:52:11,176] [INFO] Task started: fastANI
[2023-06-13 21:52:11,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg75b142bc-3497-4bde-8ddf-cff0421e9ef4/GCA_022796695.1_ASM2279669v1_genomic.fna.gz --refList GCA_022796695.1_ASM2279669v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022796695.1_ASM2279669v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 21:52:21,722] [INFO] Task succeeded: fastANI
[2023-06-13 21:52:21,734] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 21:52:21,734] [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_910588865.1	s__UBA3402 sp910588865	99.206	1093	1277	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910577935.1	s__UBA3402 sp910577935	80.617	589	1277	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_910586845.1	s__UBA3402 sp910586845	79.9634	514	1277	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_910585645.1	s__UBA3402 sp910585645	79.283	447	1277	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_910575585.1	s__UBA3402 sp910575585	78.854	468	1277	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	99.89	99.85	0.96	0.96	3	-
GCA_910574345.1	s__UBA3402 sp910574345	78.7335	458	1277	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_910588505.1	s__UBA3402 sp910588505	78.5932	415	1277	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_019114845.1	s__Lachnoclostridium_A stercoripullorum	77.2166	176	1277	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_910577765.1	s__Ventrimonas sp910577765	77.0124	194	1277	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002234575.2	s__Enterocloster bolteae	76.9115	124	1277	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_910575795.1	s__Clostridium_Q sp910575795	76.8127	131	1277	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	99.66	99.05	0.95	0.91	4	-
GCA_000155435.1	s__Enterocloster sp000155435	76.566	128	1277	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.08	98.70	0.90	0.83	5	-
--------------------------------------------------------------------------------
[2023-06-13 21:52:21,736] [INFO] GTDB search result was written to GCA_022796695.1_ASM2279669v1_genomic.fna/result_gtdb.tsv
[2023-06-13 21:52:21,737] [INFO] ===== GTDB Search completed =====
[2023-06-13 21:52:21,741] [INFO] DFAST_QC result json was written to GCA_022796695.1_ASM2279669v1_genomic.fna/dqc_result.json
[2023-06-13 21:52:21,741] [INFO] DFAST_QC completed!
[2023-06-13 21:52:21,741] [INFO] Total running time: 0h1m13s