[2023-06-05 15:05:22,033] [INFO] DFAST_QC pipeline started.
[2023-06-05 15:05:22,036] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 15:05:22,037] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc08c46a-0158-45f6-bac8-36f3cbd43687/dqc_reference
[2023-06-05 15:05:23,263] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 15:05:23,264] [INFO] Task started: Prodigal
[2023-06-05 15:05:23,264] [INFO] Running command: gunzip -c /var/lib/cwl/stgcffaea36-5a0c-48e7-8d2c-31462eb6544e/GCA_934654765.1_ERR7745990_bin.286_genomic.fna.gz | prodigal -d GCA_934654765.1_ERR7745990_bin.286_genomic.fna/cds.fna -a GCA_934654765.1_ERR7745990_bin.286_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 15:05:28,708] [INFO] Task succeeded: Prodigal
[2023-06-05 15:05:28,708] [INFO] Task started: HMMsearch
[2023-06-05 15:05:28,709] [INFO] Running command: hmmsearch --tblout GCA_934654765.1_ERR7745990_bin.286_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc08c46a-0158-45f6-bac8-36f3cbd43687/dqc_reference/reference_markers.hmm GCA_934654765.1_ERR7745990_bin.286_genomic.fna/protein.faa > /dev/null
[2023-06-05 15:05:28,925] [INFO] Task succeeded: HMMsearch
[2023-06-05 15:05:28,926] [INFO] Found 6/6 markers.
[2023-06-05 15:05:28,950] [INFO] Query marker FASTA was written to GCA_934654765.1_ERR7745990_bin.286_genomic.fna/markers.fasta
[2023-06-05 15:05:28,950] [INFO] Task started: Blastn
[2023-06-05 15:05:28,950] [INFO] Running command: blastn -query GCA_934654765.1_ERR7745990_bin.286_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc08c46a-0158-45f6-bac8-36f3cbd43687/dqc_reference/reference_markers.fasta -out GCA_934654765.1_ERR7745990_bin.286_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 15:05:29,697] [INFO] Task succeeded: Blastn
[2023-06-05 15:05:29,705] [INFO] Selected 15 target genomes.
[2023-06-05 15:05:29,705] [INFO] Target genome list was writen to GCA_934654765.1_ERR7745990_bin.286_genomic.fna/target_genomes.txt
[2023-06-05 15:05:29,712] [INFO] Task started: fastANI
[2023-06-05 15:05:29,712] [INFO] Running command: fastANI --query /var/lib/cwl/stgcffaea36-5a0c-48e7-8d2c-31462eb6544e/GCA_934654765.1_ERR7745990_bin.286_genomic.fna.gz --refList GCA_934654765.1_ERR7745990_bin.286_genomic.fna/target_genomes.txt --output GCA_934654765.1_ERR7745990_bin.286_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 15:05:35,938] [INFO] Task succeeded: fastANI
[2023-06-05 15:05:35,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc08c46a-0158-45f6-bac8-36f3cbd43687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 15:05:35,939] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc08c46a-0158-45f6-bac8-36f3cbd43687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 15:05:35,949] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 15:05:35,950] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 15:05:35,950] [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	92.6014	491	561	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	92.5866	490	561	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	92.4548	493	561	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.0786	187	561	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.9377	203	561	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.8387	212	561	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.6363	182	561	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.3669	207	561	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.2978	200	561	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.2194	195	561	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	79.0572	173	561	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 15:05:35,952] [INFO] DFAST Taxonomy check result was written to GCA_934654765.1_ERR7745990_bin.286_genomic.fna/tc_result.tsv
[2023-06-05 15:05:35,952] [INFO] ===== Taxonomy check completed =====
[2023-06-05 15:05:35,953] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 15:05:35,953] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc08c46a-0158-45f6-bac8-36f3cbd43687/dqc_reference/checkm_data
[2023-06-05 15:05:35,954] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 15:05:35,981] [INFO] Task started: CheckM
[2023-06-05 15:05:35,982] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934654765.1_ERR7745990_bin.286_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934654765.1_ERR7745990_bin.286_genomic.fna/checkm_input GCA_934654765.1_ERR7745990_bin.286_genomic.fna/checkm_result
[2023-06-05 15:05:58,456] [INFO] Task succeeded: CheckM
[2023-06-05 15:05:58,458] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 15:05:58,479] [INFO] ===== Completeness check finished =====
[2023-06-05 15:05:58,480] [INFO] ===== Start GTDB Search =====
[2023-06-05 15:05:58,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934654765.1_ERR7745990_bin.286_genomic.fna/markers.fasta)
[2023-06-05 15:05:58,481] [INFO] Task started: Blastn
[2023-06-05 15:05:58,481] [INFO] Running command: blastn -query GCA_934654765.1_ERR7745990_bin.286_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc08c46a-0158-45f6-bac8-36f3cbd43687/dqc_reference/reference_markers_gtdb.fasta -out GCA_934654765.1_ERR7745990_bin.286_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 15:05:59,678] [INFO] Task succeeded: Blastn
[2023-06-05 15:05:59,682] [INFO] Selected 33 target genomes.
[2023-06-05 15:05:59,682] [INFO] Target genome list was writen to GCA_934654765.1_ERR7745990_bin.286_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 15:05:59,776] [INFO] Task started: fastANI
[2023-06-05 15:05:59,776] [INFO] Running command: fastANI --query /var/lib/cwl/stgcffaea36-5a0c-48e7-8d2c-31462eb6544e/GCA_934654765.1_ERR7745990_bin.286_genomic.fna.gz --refList GCA_934654765.1_ERR7745990_bin.286_genomic.fna/target_genomes_gtdb.txt --output GCA_934654765.1_ERR7745990_bin.286_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 15:06:13,476] [INFO] Task succeeded: fastANI
[2023-06-05 15:06:13,502] [INFO] Found 33 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 15:06:13,503] [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_900768435.1	s__Collinsella sp900768435	93.6476	487	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015561195.1	s__Collinsella aerofaciens_AC	93.5951	507	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547805.1	s__Collinsella sp900547805	93.3195	411	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547765.1	s__Collinsella sp900547765	93.2653	456	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900762345.1	s__Collinsella sp900762345	93.2239	440	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905208635.1	s__Collinsella sp905208635	93.1627	465	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1948	95.37	95.30	0.86	0.85	4	-
GCF_003462685.1	s__Collinsella sp003462685	93.0901	488	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.85	99.71	0.99	0.99	3	-
GCF_003469205.1	s__Collinsella sp003469205	93.0359	480	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.74	95.06	0.88	0.84	17	-
GCA_900546085.1	s__Collinsella sp900546085	93.026	418	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0166	N/A	N/A	N/A	N/A	1	-
GCA_900541645.1	s__Collinsella sp900541645	93.0202	454	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.32	95.32	0.85	0.85	2	-
GCF_003471585.1	s__Collinsella sp003471585	93.0118	473	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1851	100.00	100.00	0.99	0.99	2	-
GCA_900546825.1	s__Collinsella sp900546825	92.9974	448	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900547285.1	s__Collinsella sp900547285	92.985	412	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760215.1	s__Collinsella sp900760215	92.977	461	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540875.1	s__Collinsella sp900540875	92.9469	476	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.98	99.98	0.98	0.98	2	-
GCA_900542945.1	s__Collinsella sp900542945	92.9465	458	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1063	100.00	100.00	0.99	0.99	2	-
GCA_900761995.1	s__Collinsella sp900761995	92.9331	445	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546105.1	s__Collinsella sp900546105	92.9133	423	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542315.1	s__Collinsella sp900542315	92.7868	466	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019041915.1	s__Collinsella sp019041915	92.7829	483	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.145	96.63	95.48	0.93	0.87	6	-
GCA_900544065.1	s__Collinsella sp900544065	92.7519	443	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539035.1	s__Collinsella sp900539035	92.7096	458	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.92	99.92	0.95	0.95	2	-
GCA_900757615.1	s__Collinsella sp900757615	92.6554	460	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552395.1	s__Collinsella sp900552395	92.6467	357	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.15	N/A	N/A	N/A	N/A	1	-
GCA_900757235.1	s__Collinsella sp900757235	92.6121	393	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757385.1	s__Collinsella sp900757385	92.4617	386	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900754385.1	s__Collinsella sp900754385	92.4331	295	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.42	99.42	0.88	0.88	2	-
GCA_900765185.1	s__Collinsella sp900765185	92.3339	359	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551605.1	s__Collinsella sp900551605	92.2616	318	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.27	95.27	0.92	0.92	2	-
GCA_900754075.1	s__Collinsella sp900754075	91.7097	417	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.97	99.97	0.96	0.96	2	-
GCA_900541675.1	s__Collinsella sp900541675	91.4513	449	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551815.1	s__Collinsella sp900551815	91.4081	442	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900756725.1	s__Collinsella sp900756725	91.1995	398	561	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.39	95.39	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-05 15:06:13,505] [INFO] GTDB search result was written to GCA_934654765.1_ERR7745990_bin.286_genomic.fna/result_gtdb.tsv
[2023-06-05 15:06:13,506] [INFO] ===== GTDB Search completed =====
[2023-06-05 15:06:13,511] [INFO] DFAST_QC result json was written to GCA_934654765.1_ERR7745990_bin.286_genomic.fna/dqc_result.json
[2023-06-05 15:06:13,511] [INFO] DFAST_QC completed!
[2023-06-05 15:06:13,511] [INFO] Total running time: 0h0m51s