[2023-06-13 20:23:33,393] [INFO] DFAST_QC pipeline started.
[2023-06-13 20:23:33,395] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 20:23:33,395] [INFO] DQC Reference Directory: /var/lib/cwl/stg88fdcf80-aaf5-42e9-af77-796c88eacf4e/dqc_reference
[2023-06-13 20:23:35,993] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 20:23:35,994] [INFO] Task started: Prodigal
[2023-06-13 20:23:35,994] [INFO] Running command: gunzip -c /var/lib/cwl/stg40535b36-483e-49c1-bdca-4d4a403e33a8/GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 20:23:40,997] [INFO] Task succeeded: Prodigal
[2023-06-13 20:23:40,997] [INFO] Task started: HMMsearch
[2023-06-13 20:23:40,997] [INFO] Running command: hmmsearch --tblout GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88fdcf80-aaf5-42e9-af77-796c88eacf4e/dqc_reference/reference_markers.hmm GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 20:23:41,211] [INFO] Task succeeded: HMMsearch
[2023-06-13 20:23:41,213] [INFO] Found 6/6 markers.
[2023-06-13 20:23:41,235] [INFO] Query marker FASTA was written to GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 20:23:41,236] [INFO] Task started: Blastn
[2023-06-13 20:23:41,236] [INFO] Running command: blastn -query GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg88fdcf80-aaf5-42e9-af77-796c88eacf4e/dqc_reference/reference_markers.fasta -out GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:23:41,986] [INFO] Task succeeded: Blastn
[2023-06-13 20:23:41,991] [INFO] Selected 21 target genomes.
[2023-06-13 20:23:41,991] [INFO] Target genome list was writen to GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 20:23:41,996] [INFO] Task started: fastANI
[2023-06-13 20:23:41,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg40535b36-483e-49c1-bdca-4d4a403e33a8/GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 20:23:50,866] [INFO] Task succeeded: fastANI
[2023-06-13 20:23:50,866] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88fdcf80-aaf5-42e9-af77-796c88eacf4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 20:23:50,866] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88fdcf80-aaf5-42e9-af77-796c88eacf4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 20:23:50,877] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 20:23:50,877] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 20:23:50,877] [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	94.668	392	444	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	94.5787	393	444	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	94.5002	395	444	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.1398	149	444	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.9266	141	444	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.7381	153	444	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.7048	155	444	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.3637	131	444	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.0515	138	444	95	below_threshold
Collinsella provencensis	strain=Marseille-P3740	GCA_900199705.1	1937461	1937461	type	True	78.9703	105	444	95	below_threshold
Enorma shizhengliae	strain=HF-1365	GCA_009676995.1	2606615	2606615	type	True	78.8583	110	444	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.6256	139	444	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 20:23:50,880] [INFO] DFAST Taxonomy check result was written to GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 20:23:50,880] [INFO] ===== Taxonomy check completed =====
[2023-06-13 20:23:50,881] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 20:23:50,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88fdcf80-aaf5-42e9-af77-796c88eacf4e/dqc_reference/checkm_data
[2023-06-13 20:23:50,883] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 20:23:50,911] [INFO] Task started: CheckM
[2023-06-13 20:23:50,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 20:24:12,551] [INFO] Task succeeded: CheckM
[2023-06-13 20:24:12,553] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.41%
Contamintation: 6.25%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 20:24:12,577] [INFO] ===== Completeness check finished =====
[2023-06-13 20:24:12,578] [INFO] ===== Start GTDB Search =====
[2023-06-13 20:24:12,578] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 20:24:12,579] [INFO] Task started: Blastn
[2023-06-13 20:24:12,579] [INFO] Running command: blastn -query GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg88fdcf80-aaf5-42e9-af77-796c88eacf4e/dqc_reference/reference_markers_gtdb.fasta -out GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:24:13,892] [INFO] Task succeeded: Blastn
[2023-06-13 20:24:13,896] [INFO] Selected 35 target genomes.
[2023-06-13 20:24:13,896] [INFO] Target genome list was writen to GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 20:24:13,904] [INFO] Task started: fastANI
[2023-06-13 20:24:13,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg40535b36-483e-49c1-bdca-4d4a403e33a8/GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 20:24:26,265] [INFO] Task succeeded: fastANI
[2023-06-13 20:24:26,304] [INFO] Found 35 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 20:24:26,304] [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
GCF_000763055.1	s__Collinsella sp000763055	94.6563	392	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_014871665.1	s__Collinsella sp014871665	94.6263	356	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1702	95.19	95.19	0.85	0.85	2	-
GCA_900540985.1	s__Collinsella sp900540985	94.4836	370	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0011	97.54	95.11	0.88	0.81	3	-
GCA_900545665.1	s__Collinsella sp900545665	94.4641	381	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1787	95.41	95.41	0.86	0.86	2	-
GCF_015553355.1	s__Collinsella aerofaciens_V	94.4108	380	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.92	96.92	0.91	0.91	2	-
GCF_015670795.1	s__Collinsella aerofaciens_Q	94.4087	399	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1438	95.30	95.30	0.93	0.92	3	-
GCA_900751755.1	s__Collinsella sp900751755	94.3706	359	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.91	99.91	0.92	0.92	2	-
GCA_900547345.1	s__Collinsella sp900547345	94.3567	341	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0188	95.15	95.15	0.87	0.87	2	-
GCA_900541065.1	s__Collinsella sp900541065	94.326	386	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0334	N/A	N/A	N/A	N/A	1	-
GCA_900544995.1	s__Collinsella sp900544995	94.3043	344	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.98	99.98	0.93	0.93	2	-
GCA_008668235.1	s__Collinsella aerofaciens_K	94.2912	359	444	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	94.2633	354	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.043	N/A	N/A	N/A	N/A	1	-
GCA_900548495.1	s__Collinsella sp900548495	94.2276	356	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0367	N/A	N/A	N/A	N/A	1	-
GCA_905215835.1	s__Collinsella sp905215835	94.1393	337	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0274	N/A	N/A	N/A	N/A	1	-
GCA_900542555.1	s__Collinsella sp900542555	94.087	361	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540995.1	s__Collinsella sp900540995	94.0309	368	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.96	99.96	0.96	0.96	2	-
GCA_900757505.1	s__Collinsella sp900757505	93.9851	365	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540935.1	s__Collinsella sp900540935	93.933	365	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.34	95.21	0.87	0.87	3	-
GCA_900552185.1	s__Collinsella sp900552185	93.9009	306	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1905	N/A	N/A	N/A	N/A	1	-
GCA_900752475.1	s__Collinsella sp900752475	93.8799	292	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.66	99.66	0.82	0.82	2	-
GCA_900550355.1	s__Collinsella sp900550355	93.6682	320	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.039	N/A	N/A	N/A	N/A	1	-
GCA_900548515.1	s__Collinsella sp900548515	93.6571	339	444	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	93.4459	368	444	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	93.3318	335	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554645.1	s__Collinsella sp900554645	93.2847	158	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018368345.1	s__Collinsella sp018368345	93.268	376	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555515.1	s__Collinsella sp900555515	93.1299	287	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215225.1	s__Collinsella sp905215225	93.0062	274	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556205.1	s__Collinsella sp900556205	92.9853	258	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900757595.1	s__Collinsella sp900757595	92.8427	343	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545445.1	s__Collinsella sp900545445	92.7695	355	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.18	95.16	0.86	0.84	3	-
GCA_900547805.1	s__Collinsella sp900547805	92.7528	331	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900756765.1	s__Collinsella sp900756765	92.2453	330	444	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	92.2021	360	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.98	99.98	0.96	0.96	2	-
GCA_900542825.1	s__Collinsella sp900542825	91.8171	360	444	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 20:24:26,306] [INFO] GTDB search result was written to GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 20:24:26,307] [INFO] ===== GTDB Search completed =====
[2023-06-13 20:24:26,313] [INFO] DFAST_QC result json was written to GCA_938014285.1_SRR3313068_bin.2_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 20:24:26,313] [INFO] DFAST_QC completed!
[2023-06-13 20:24:26,313] [INFO] Total running time: 0h0m53s