[2023-06-18 23:17:57,005] [INFO] DFAST_QC pipeline started.
[2023-06-18 23:17:57,008] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 23:17:57,009] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9ffc71a-e1e0-474f-8a0f-3b6376f4a4fa/dqc_reference
[2023-06-18 23:17:58,584] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 23:17:58,585] [INFO] Task started: Prodigal
[2023-06-18 23:17:58,585] [INFO] Running command: gunzip -c /var/lib/cwl/stg99c2a086-0751-4b55-980e-a57b71dcfeaa/GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 23:18:05,100] [INFO] Task succeeded: Prodigal
[2023-06-18 23:18:05,100] [INFO] Task started: HMMsearch
[2023-06-18 23:18:05,100] [INFO] Running command: hmmsearch --tblout GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9ffc71a-e1e0-474f-8a0f-3b6376f4a4fa/dqc_reference/reference_markers.hmm GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-18 23:18:05,276] [INFO] Task succeeded: HMMsearch
[2023-06-18 23:18:05,277] [INFO] Found 6/6 markers.
[2023-06-18 23:18:05,299] [INFO] Query marker FASTA was written to GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-18 23:18:05,300] [INFO] Task started: Blastn
[2023-06-18 23:18:05,300] [INFO] Running command: blastn -query GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9ffc71a-e1e0-474f-8a0f-3b6376f4a4fa/dqc_reference/reference_markers.fasta -out GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:18:06,016] [INFO] Task succeeded: Blastn
[2023-06-18 23:18:06,020] [INFO] Selected 17 target genomes.
[2023-06-18 23:18:06,020] [INFO] Target genome list was writen to GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-18 23:18:06,021] [INFO] Task started: fastANI
[2023-06-18 23:18:06,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg99c2a086-0751-4b55-980e-a57b71dcfeaa/GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 23:18:13,339] [INFO] Task succeeded: fastANI
[2023-06-18 23:18:13,340] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9ffc71a-e1e0-474f-8a0f-3b6376f4a4fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 23:18:13,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9ffc71a-e1e0-474f-8a0f-3b6376f4a4fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 23:18:13,352] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 23:18:13,352] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 23:18:13,352] [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	94.1756	585	701	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	94.1345	591	701	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	94.1087	595	701	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.3242	232	701	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	80.2296	246	701	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	80.1326	251	701	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	80.1059	240	701	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.8354	222	701	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.6327	219	701	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.6275	226	701	95	below_threshold
Collinsella provencensis	strain=Marseille-P3740	GCA_900199705.1	1937461	1937461	type	True	79.5634	175	701	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	79.2382	205	701	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	77.9089	141	701	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 23:18:13,354] [INFO] DFAST Taxonomy check result was written to GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-18 23:18:13,355] [INFO] ===== Taxonomy check completed =====
[2023-06-18 23:18:13,355] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 23:18:13,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9ffc71a-e1e0-474f-8a0f-3b6376f4a4fa/dqc_reference/checkm_data
[2023-06-18 23:18:13,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 23:18:13,382] [INFO] Task started: CheckM
[2023-06-18 23:18:13,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-18 23:18:37,375] [INFO] Task succeeded: CheckM
[2023-06-18 23:18:37,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 23:18:37,399] [INFO] ===== Completeness check finished =====
[2023-06-18 23:18:37,399] [INFO] ===== Start GTDB Search =====
[2023-06-18 23:18:37,400] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-18 23:18:37,400] [INFO] Task started: Blastn
[2023-06-18 23:18:37,400] [INFO] Running command: blastn -query GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9ffc71a-e1e0-474f-8a0f-3b6376f4a4fa/dqc_reference/reference_markers_gtdb.fasta -out GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:18:38,683] [INFO] Task succeeded: Blastn
[2023-06-18 23:18:38,686] [INFO] Selected 29 target genomes.
[2023-06-18 23:18:38,686] [INFO] Target genome list was writen to GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 23:18:38,694] [INFO] Task started: fastANI
[2023-06-18 23:18:38,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg99c2a086-0751-4b55-980e-a57b71dcfeaa/GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 23:18:50,640] [INFO] Task succeeded: fastANI
[2023-06-18 23:18:50,662] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 23:18:50,662] [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_900544205.1	s__Collinsella sp900544205	100.0	641	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_905208345.1	s__Collinsella sp905208345	94.477	477	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900550195.1	s__Collinsella sp900550195	94.4721	545	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1628	N/A	N/A	N/A	N/A	1	-
GCA_008671135.1	s__Collinsella aerofaciens_J	94.4671	554	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2147	97.21	95.28	0.90	0.82	6	-
GCA_900545875.1	s__Collinsella sp900545875	94.3328	389	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.98	0.98	2	-
GCA_900540895.1	s__Collinsella sp900540895	94.2721	552	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.25	95.25	0.87	0.87	2	-
GCA_900761615.1	s__Collinsella sp900761615	94.259	448	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.16	95.16	0.89	0.89	2	-
GCA_008668235.1	s__Collinsella aerofaciens_K	94.2278	517	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0357	97.54	95.17	0.89	0.81	5	-
GCA_900541185.1	s__Collinsella sp900541185	94.1725	508	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.043	N/A	N/A	N/A	N/A	1	-
GCA_900554325.1	s__Collinsella sp900554325	94.1164	478	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551365.1	s__Collinsella sp900551365	94.0951	468	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541025.1	s__Collinsella sp900541025	94.0834	576	701	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	94.0629	533	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015552075.1	s__Collinsella aerofaciens_Y	94.0372	551	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541235.1	s__Collinsella sp900541235	93.9387	557	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.02	95.02	0.86	0.86	2	-
GCA_900542125.1	s__Collinsella sp900542125	93.9036	560	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544865.1	s__Collinsella sp900544865	93.8594	539	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543615.1	s__Collinsella sp900543615	93.8378	460	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549355.1	s__Collinsella sp900549355	93.8307	413	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.84	99.84	0.83	0.83	2	-
GCA_900759565.1	s__Collinsella sp900759565	93.8267	506	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.12	95.02	0.84	0.84	3	-
GCA_900543025.1	s__Collinsella sp900543025	93.7042	522	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551635.1	s__Collinsella sp900551635	93.6286	331	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.56	99.56	0.78	0.78	2	-
GCA_900552295.1	s__Collinsella sp900552295	93.6041	368	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760325.1	s__Collinsella sp900760325	93.57	485	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905210085.1	s__Collinsella sp905210085	93.3924	481	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900754075.1	s__Collinsella sp900754075	92.9318	485	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.97	99.97	0.96	0.96	2	-
GCA_905209765.1	s__Collinsella sp905209765	92.7155	465	701	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	92.0728	515	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.98	99.98	0.96	0.96	2	-
GCA_900549275.1	s__Collinsella sp900549275	91.0604	319	701	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.23	96.21	0.86	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-18 23:18:50,664] [INFO] GTDB search result was written to GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-18 23:18:50,665] [INFO] ===== GTDB Search completed =====
[2023-06-18 23:18:50,669] [INFO] DFAST_QC result json was written to GCA_937925175.1_SRR2912799_bin.21_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-18 23:18:50,670] [INFO] DFAST_QC completed!
[2023-06-18 23:18:50,670] [INFO] Total running time: 0h0m54s