[2023-06-13 08:51:53,711] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:51:53,714] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:51:53,715] [INFO] DQC Reference Directory: /var/lib/cwl/stgcffa9c8e-a724-442a-b9c7-2b9801c1dde1/dqc_reference
[2023-06-13 08:51:55,037] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:51:55,038] [INFO] Task started: Prodigal
[2023-06-13 08:51:55,038] [INFO] Running command: gunzip -c /var/lib/cwl/stgcdb5eed4-9fb4-421f-a517-6b4ab0134e5d/GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:52:02,157] [INFO] Task succeeded: Prodigal
[2023-06-13 08:52:02,158] [INFO] Task started: HMMsearch
[2023-06-13 08:52:02,158] [INFO] Running command: hmmsearch --tblout GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcffa9c8e-a724-442a-b9c7-2b9801c1dde1/dqc_reference/reference_markers.hmm GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:52:02,383] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:52:02,384] [INFO] Found 6/6 markers.
[2023-06-13 08:52:02,409] [INFO] Query marker FASTA was written to GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 08:52:02,410] [INFO] Task started: Blastn
[2023-06-13 08:52:02,410] [INFO] Running command: blastn -query GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgcffa9c8e-a724-442a-b9c7-2b9801c1dde1/dqc_reference/reference_markers.fasta -out GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:52:03,141] [INFO] Task succeeded: Blastn
[2023-06-13 08:52:03,151] [INFO] Selected 14 target genomes.
[2023-06-13 08:52:03,151] [INFO] Target genome list was writen to GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 08:52:03,154] [INFO] Task started: fastANI
[2023-06-13 08:52:03,154] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdb5eed4-9fb4-421f-a517-6b4ab0134e5d/GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:52:09,297] [INFO] Task succeeded: fastANI
[2023-06-13 08:52:09,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcffa9c8e-a724-442a-b9c7-2b9801c1dde1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:52:09,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcffa9c8e-a724-442a-b9c7-2b9801c1dde1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:52:09,309] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 08:52:09,309] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 08:52:09,309] [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
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	93.3253	625	761	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	93.3067	633	761	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	93.2416	632	761	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.313	236	761	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	80.028	260	761	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.6956	285	761	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.6586	262	761	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.6126	244	761	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.3491	253	761	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	79.0107	225	761	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 08:52:09,312] [INFO] DFAST Taxonomy check result was written to GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 08:52:09,313] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:52:09,313] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:52:09,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcffa9c8e-a724-442a-b9c7-2b9801c1dde1/dqc_reference/checkm_data
[2023-06-13 08:52:09,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:52:09,346] [INFO] Task started: CheckM
[2023-06-13 08:52:09,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 08:52:35,529] [INFO] Task succeeded: CheckM
[2023-06-13 08:52:35,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:52:35,552] [INFO] ===== Completeness check finished =====
[2023-06-13 08:52:35,553] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:52:35,553] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 08:52:35,553] [INFO] Task started: Blastn
[2023-06-13 08:52:35,554] [INFO] Running command: blastn -query GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgcffa9c8e-a724-442a-b9c7-2b9801c1dde1/dqc_reference/reference_markers_gtdb.fasta -out GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:52:36,860] [INFO] Task succeeded: Blastn
[2023-06-13 08:52:36,865] [INFO] Selected 30 target genomes.
[2023-06-13 08:52:36,865] [INFO] Target genome list was writen to GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:52:36,877] [INFO] Task started: fastANI
[2023-06-13 08:52:36,877] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdb5eed4-9fb4-421f-a517-6b4ab0134e5d/GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:52:51,037] [INFO] Task succeeded: fastANI
[2023-06-13 08:52:51,060] [INFO] Found 30 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-13 08:52:51,060] [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_905215385.1	s__Collinsella sp905215385	95.2603	640	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2035	95.42	95.23	0.87	0.82	17	inconclusive
GCA_900546085.1	s__Collinsella sp900546085	95.0228	501	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0166	N/A	N/A	N/A	N/A	1	inconclusive
GCA_905214435.1	s__Collinsella sp905214435	94.9252	564	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.174	95.31	95.19	0.87	0.85	5	-
GCF_003439125.1	s__Collinsella sp003439125	94.9018	613	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.74	95.07	0.88	0.85	15	-
GCA_900540875.1	s__Collinsella sp900540875	94.8746	613	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.98	99.98	0.98	0.98	2	-
GCA_902399975.1	s__Collinsella sp902399975	94.826	619	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.188	100.00	100.00	1.00	1.00	3	-
GCA_900542325.1	s__Collinsella sp900542325	94.7491	587	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900543945.1	s__Collinsella sp900543945	94.7195	516	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.4468	97.82	95.67	0.91	0.87	3	-
GCA_900552395.1	s__Collinsella sp900552395	94.7184	437	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.15	N/A	N/A	N/A	N/A	1	-
GCA_900550835.1	s__Collinsella sp900550835	94.5888	451	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	98.40	95.47	0.90	0.85	4	-
GCA_905214905.1	s__Collinsella sp905214905	94.5492	540	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757285.1	s__Collinsella sp900757285	94.5325	428	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902388345.1	s__Collinsella sp902388345	94.4707	572	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.98	99.97	0.98	0.97	3	-
GCF_015554145.1	s__Collinsella aerofaciens_AA	94.4172	620	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757615.1	s__Collinsella sp900757615	94.0683	573	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757505.1	s__Collinsella sp900757505	94.0561	542	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900762325.1	s__Collinsella sp900762325	93.8298	582	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541875.1	s__Collinsella sp900541875	93.5609	583	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.60	95.21	0.93	0.87	3	-
GCF_005845035.1	s__Collinsella aerofaciens_I	93.5112	625	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.53	95.20	0.90	0.88	4	-
GCA_900541135.1	s__Collinsella sp900541135	93.4867	566	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003466125.1	s__Collinsella sp003466125	93.3047	590	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.79	97.08	0.91	0.86	19	-
GCA_900550355.1	s__Collinsella sp900550355	93.2678	448	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.039	N/A	N/A	N/A	N/A	1	-
GCA_900542125.1	s__Collinsella sp900542125	93.2431	580	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550785.1	s__Collinsella sp900550785	93.0785	473	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015557435.1	s__Collinsella aerofaciens_Z	92.9086	613	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900751665.1	s__Collinsella sp900751665	92.8557	425	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.75	99.75	0.87	0.87	2	-
GCA_900541785.1	s__Collinsella sp900541785	92.4182	554	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900557505.1	s__Collinsella sp900557505	92.0888	311	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900754745.1	s__Collinsella sp900754745	91.9243	532	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.56	95.20	0.85	0.80	3	-
GCA_900549085.1	s__Collinsella sp900549085	91.852	531	761	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.95	99.95	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-13 08:52:51,062] [INFO] GTDB search result was written to GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 08:52:51,063] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:52:51,067] [INFO] DFAST_QC result json was written to GCA_938009965.1_SRR5091473_bin.6_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 08:52:51,068] [INFO] DFAST_QC completed!
[2023-06-13 08:52:51,068] [INFO] Total running time: 0h0m57s