[2023-06-30 14:27:11,436] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:27:11,441] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:27:11,442] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e73914b-3f84-4bab-a0e9-eb4ec8e3080b/dqc_reference
[2023-06-30 14:27:12,713] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:27:12,714] [INFO] Task started: Prodigal
[2023-06-30 14:27:12,715] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc1c9140-f887-4b54-a0fc-58b6189103b8/GCA_900752235.1_ERS235563_53_genomic.fna.gz | prodigal -d GCA_900752235.1_ERS235563_53_genomic.fna/cds.fna -a GCA_900752235.1_ERS235563_53_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:27:18,439] [INFO] Task succeeded: Prodigal
[2023-06-30 14:27:18,439] [INFO] Task started: HMMsearch
[2023-06-30 14:27:18,439] [INFO] Running command: hmmsearch --tblout GCA_900752235.1_ERS235563_53_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e73914b-3f84-4bab-a0e9-eb4ec8e3080b/dqc_reference/reference_markers.hmm GCA_900752235.1_ERS235563_53_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:27:18,614] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:27:18,615] [INFO] Found 6/6 markers.
[2023-06-30 14:27:18,636] [INFO] Query marker FASTA was written to GCA_900752235.1_ERS235563_53_genomic.fna/markers.fasta
[2023-06-30 14:27:18,637] [INFO] Task started: Blastn
[2023-06-30 14:27:18,637] [INFO] Running command: blastn -query GCA_900752235.1_ERS235563_53_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e73914b-3f84-4bab-a0e9-eb4ec8e3080b/dqc_reference/reference_markers.fasta -out GCA_900752235.1_ERS235563_53_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:27:19,361] [INFO] Task succeeded: Blastn
[2023-06-30 14:27:19,365] [INFO] Selected 15 target genomes.
[2023-06-30 14:27:19,366] [INFO] Target genome list was writen to GCA_900752235.1_ERS235563_53_genomic.fna/target_genomes.txt
[2023-06-30 14:27:19,367] [INFO] Task started: fastANI
[2023-06-30 14:27:19,367] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc1c9140-f887-4b54-a0fc-58b6189103b8/GCA_900752235.1_ERS235563_53_genomic.fna.gz --refList GCA_900752235.1_ERS235563_53_genomic.fna/target_genomes.txt --output GCA_900752235.1_ERS235563_53_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:27:26,616] [INFO] Task succeeded: fastANI
[2023-06-30 14:27:26,616] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e73914b-3f84-4bab-a0e9-eb4ec8e3080b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:27:26,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e73914b-3f84-4bab-a0e9-eb4ec8e3080b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:27:26,627] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:27:26,627] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 14:27:26,627] [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=JCM 10188	GCA_010509075.1	74426	74426	type	True	92.7637	525	623	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	92.7462	528	623	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	92.6371	533	623	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.1912	216	623	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.9149	228	623	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.8014	234	623	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.7186	213	623	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.4792	220	623	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.311	211	623	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.2894	222	623	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.8724	193	623	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 14:27:26,629] [INFO] DFAST Taxonomy check result was written to GCA_900752235.1_ERS235563_53_genomic.fna/tc_result.tsv
[2023-06-30 14:27:26,630] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:27:26,630] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:27:26,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e73914b-3f84-4bab-a0e9-eb4ec8e3080b/dqc_reference/checkm_data
[2023-06-30 14:27:26,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:27:26,653] [INFO] Task started: CheckM
[2023-06-30 14:27:26,654] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900752235.1_ERS235563_53_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900752235.1_ERS235563_53_genomic.fna/checkm_input GCA_900752235.1_ERS235563_53_genomic.fna/checkm_result
[2023-06-30 14:27:48,450] [INFO] Task succeeded: CheckM
[2023-06-30 14:27:48,451] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 14:27:48,469] [INFO] ===== Completeness check finished =====
[2023-06-30 14:27:48,469] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:27:48,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900752235.1_ERS235563_53_genomic.fna/markers.fasta)
[2023-06-30 14:27:48,470] [INFO] Task started: Blastn
[2023-06-30 14:27:48,470] [INFO] Running command: blastn -query GCA_900752235.1_ERS235563_53_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e73914b-3f84-4bab-a0e9-eb4ec8e3080b/dqc_reference/reference_markers_gtdb.fasta -out GCA_900752235.1_ERS235563_53_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:27:49,769] [INFO] Task succeeded: Blastn
[2023-06-30 14:27:49,773] [INFO] Selected 31 target genomes.
[2023-06-30 14:27:49,773] [INFO] Target genome list was writen to GCA_900752235.1_ERS235563_53_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:27:49,780] [INFO] Task started: fastANI
[2023-06-30 14:27:49,780] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc1c9140-f887-4b54-a0fc-58b6189103b8/GCA_900752235.1_ERS235563_53_genomic.fna.gz --refList GCA_900752235.1_ERS235563_53_genomic.fna/target_genomes_gtdb.txt --output GCA_900752235.1_ERS235563_53_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:28:02,293] [INFO] Task succeeded: fastANI
[2023-06-30 14:28:02,317] [INFO] Found 31 fastANI hits (3 hits with ANI > circumscription radius)
[2023-06-30 14:28:02,318] [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_900540945.1	s__Collinsella sp900540945	95.8526	525	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.51	95.33	0.85	0.84	5	inconclusive
GCA_900758375.1	s__Collinsella sp900758375	95.1139	494	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.25	95.06	0.83	0.78	8	inconclusive
GCA_900541695.1	s__Collinsella sp900541695	95.0797	525	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.64	95.64	0.91	0.91	2	inconclusive
GCA_900759045.1	s__Collinsella sp900759045	94.9743	520	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900752345.1	s__Collinsella sp900752345	94.8808	375	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551625.1	s__Collinsella sp900551625	94.8706	364	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900557455.1	s__Collinsella sp900557455	94.7927	215	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542085.1	s__Collinsella sp900542085	94.7914	521	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.98	99.98	0.96	0.96	2	-
GCF_003469185.1	s__Collinsella sp003469185	94.699	527	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.87	95.38	0.90	0.84	5	-
GCA_900544225.1	s__Collinsella sp900544225	94.6089	467	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.82	95.63	0.93	0.89	3	-
GCA_900756725.1	s__Collinsella sp900756725	94.571	435	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.39	95.39	0.81	0.81	2	-
GCA_008680965.1	s__Collinsella aerofaciens_L	94.5342	547	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.14	95.14	0.89	0.89	2	-
GCA_900549555.1	s__Collinsella sp900549555	94.4678	467	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.46	95.44	0.81	0.77	3	-
GCA_900550595.1	s__Collinsella sp900550595	94.2587	318	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541045.1	s__Collinsella sp900541045	94.2305	524	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555955.1	s__Collinsella sp900555955	93.8683	283	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.54	99.54	0.80	0.80	2	-
GCA_900541475.1	s__Collinsella sp900541475	93.7498	488	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.73	95.01	0.89	0.85	4	-
GCA_900540985.1	s__Collinsella sp900540985	93.1385	509	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0011	97.54	95.11	0.88	0.81	3	-
GCA_018380015.1	s__Collinsella sp018380015	93.0709	532	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1883	96.09	95.27	0.89	0.86	8	-
GCA_900543845.1	s__Collinsella sp900543845	93.0355	492	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.60	95.22	0.88	0.81	3	-
GCA_900550785.1	s__Collinsella sp900550785	92.9337	424	623	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	92.7951	483	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541135.1	s__Collinsella sp900541135	92.7309	502	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542635.1	s__Collinsella sp900542635	92.7217	483	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0787	N/A	N/A	N/A	N/A	1	-
GCA_900752475.1	s__Collinsella sp900752475	92.6119	382	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.66	99.66	0.82	0.82	2	-
GCA_900551635.1	s__Collinsella sp900551635	92.3797	332	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.56	99.56	0.78	0.78	2	-
GCA_900540995.1	s__Collinsella sp900540995	92.3364	506	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.96	99.96	0.96	0.96	2	-
GCA_900756765.1	s__Collinsella sp900756765	92.1877	462	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545875.1	s__Collinsella sp900545875	92.1033	352	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.98	0.98	2	-
GCA_900554645.1	s__Collinsella sp900554645	91.9752	261	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545055.1	s__Collinsella sp900545055	91.8284	441	623	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 14:28:02,320] [INFO] GTDB search result was written to GCA_900752235.1_ERS235563_53_genomic.fna/result_gtdb.tsv
[2023-06-30 14:28:02,320] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:28:02,325] [INFO] DFAST_QC result json was written to GCA_900752235.1_ERS235563_53_genomic.fna/dqc_result.json
[2023-06-30 14:28:02,325] [INFO] DFAST_QC completed!
[2023-06-30 14:28:02,325] [INFO] Total running time: 0h0m51s