[2023-06-19 05:51:43,432] [INFO] DFAST_QC pipeline started.
[2023-06-19 05:51:43,439] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 05:51:43,440] [INFO] DQC Reference Directory: /var/lib/cwl/stgd34de4ca-5117-4f55-8284-0a02999cb9b1/dqc_reference
[2023-06-19 05:51:44,827] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 05:51:44,828] [INFO] Task started: Prodigal
[2023-06-19 05:51:44,828] [INFO] Running command: gunzip -c /var/lib/cwl/stg853bb5d3-02f2-4f4a-add2-bc3300ecf2c9/GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 05:51:50,634] [INFO] Task succeeded: Prodigal
[2023-06-19 05:51:50,635] [INFO] Task started: HMMsearch
[2023-06-19 05:51:50,635] [INFO] Running command: hmmsearch --tblout GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd34de4ca-5117-4f55-8284-0a02999cb9b1/dqc_reference/reference_markers.hmm GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 05:51:50,895] [INFO] Task succeeded: HMMsearch
[2023-06-19 05:51:50,897] [INFO] Found 6/6 markers.
[2023-06-19 05:51:50,930] [INFO] Query marker FASTA was written to GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 05:51:50,930] [INFO] Task started: Blastn
[2023-06-19 05:51:50,931] [INFO] Running command: blastn -query GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd34de4ca-5117-4f55-8284-0a02999cb9b1/dqc_reference/reference_markers.fasta -out GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:51:51,671] [INFO] Task succeeded: Blastn
[2023-06-19 05:51:51,677] [INFO] Selected 21 target genomes.
[2023-06-19 05:51:51,677] [INFO] Target genome list was writen to GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 05:51:51,679] [INFO] Task started: fastANI
[2023-06-19 05:51:51,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg853bb5d3-02f2-4f4a-add2-bc3300ecf2c9/GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:52:00,785] [INFO] Task succeeded: fastANI
[2023-06-19 05:52:00,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd34de4ca-5117-4f55-8284-0a02999cb9b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:52:00,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd34de4ca-5117-4f55-8284-0a02999cb9b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:52:00,800] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 05:52:00,800] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 05:52:00,800] [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	94.4803	488	565	95	below_threshold
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	94.4342	489	565	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	94.3869	497	565	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.0598	186	565	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	79.6838	202	565	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.4425	214	565	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.3882	181	565	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.3221	189	565	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.3066	179	565	95	below_threshold
Collinsella provencensis	strain=Marseille-P3740	GCA_900199705.1	1937461	1937461	type	True	79.053	148	565	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.0183	175	565	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.8853	166	565	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	76.5237	65	565	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 05:52:00,811] [INFO] DFAST Taxonomy check result was written to GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 05:52:00,814] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:52:00,814] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:52:00,814] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd34de4ca-5117-4f55-8284-0a02999cb9b1/dqc_reference/checkm_data
[2023-06-19 05:52:00,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:52:00,860] [INFO] Task started: CheckM
[2023-06-19 05:52:00,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 05:52:26,671] [INFO] Task succeeded: CheckM
[2023-06-19 05:52:26,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 20.50%
Strain heterogeneity: 18.42%
--------------------------------------------------------------------------------
[2023-06-19 05:52:26,724] [INFO] ===== Completeness check finished =====
[2023-06-19 05:52:26,724] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:52:26,725] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 05:52:26,725] [INFO] Task started: Blastn
[2023-06-19 05:52:26,725] [INFO] Running command: blastn -query GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd34de4ca-5117-4f55-8284-0a02999cb9b1/dqc_reference/reference_markers_gtdb.fasta -out GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:52:27,773] [INFO] Task succeeded: Blastn
[2023-06-19 05:52:27,777] [INFO] Selected 37 target genomes.
[2023-06-19 05:52:27,777] [INFO] Target genome list was writen to GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:52:27,786] [INFO] Task started: fastANI
[2023-06-19 05:52:27,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg853bb5d3-02f2-4f4a-add2-bc3300ecf2c9/GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:52:42,032] [INFO] Task succeeded: fastANI
[2023-06-19 05:52:42,060] [INFO] Found 32 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 05:52:42,061] [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_015553355.1	s__Collinsella aerofaciens_V	94.8089	474	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.92	96.92	0.91	0.91	2	-
GCF_015558785.1	s__Collinsella aerofaciens_P	94.6441	468	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1792	95.28	95.25	0.89	0.89	3	-
GCA_900542905.1	s__Collinsella sp900542905	94.4844	458	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540095.1	s__Collinsella sp900540095	94.3316	411	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.82	99.82	0.89	0.89	2	-
GCA_900552385.1	s__Collinsella sp900552385	94.2923	360	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1029	95.27	95.27	0.73	0.73	2	-
GCA_900758885.1	s__Collinsella sp900758885	94.277	409	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0066	N/A	N/A	N/A	N/A	1	-
GCF_019131995.1	s__Collinsella aerofaciens_S	94.1124	486	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.99	99.99	0.99	0.99	2	-
GCA_900541205.1	s__Collinsella sp900541205	94.0883	467	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.97	99.97	0.98	0.98	2	-
GCA_900542305.1	s__Collinsella sp900542305	94.079	440	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544205.1	s__Collinsella sp900544205	94.0736	420	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000434535.1	s__Collinsella sp000434535	94.0213	398	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900754525.1	s__Collinsella sp900754525	93.9924	416	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0709	95.23	95.09	0.81	0.78	4	-
GCA_900554325.1	s__Collinsella sp900554325	93.9909	386	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018376905.1	s__Collinsella sp018376905	93.9898	454	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543025.1	s__Collinsella sp900543025	93.987	446	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761615.1	s__Collinsella sp900761615	93.9574	390	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.16	95.16	0.89	0.89	2	-
GCA_900549185.1	s__Collinsella sp900549185	93.9137	409	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542125.1	s__Collinsella sp900542125	93.8702	453	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905216145.1	s__Collinsella sp905216145	93.8113	475	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545615.1	s__Collinsella sp900545615	93.7668	425	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.94	99.94	0.92	0.92	2	-
GCA_900555515.1	s__Collinsella sp900555515	93.609	343	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546455.1	s__Collinsella sp900546455	93.5856	434	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554655.1	s__Collinsella sp900554655	93.5273	294	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.98	0.98	2	-
GCA_900555745.1	s__Collinsella sp900555745	93.4658	254	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550415.1	s__Collinsella sp900550415	93.1156	410	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900554465.1	s__Collinsella sp900554465	92.8192	327	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541745.1	s__Collinsella sp900541745	92.79	450	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.25	95.02	0.88	0.85	9	-
GCA_900758475.1	s__Collinsella sp900758475	92.7707	425	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.39	95.09	0.82	0.79	4	-
GCA_900543845.1	s__Collinsella sp900543845	92.7054	434	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.60	95.22	0.88	0.81	3	-
GCF_003466125.1	s__Collinsella sp003466125	92.5079	447	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.79	97.08	0.91	0.86	19	-
GCA_900759435.1	s__Collinsella sp900759435	92.3034	339	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549455.1	s__Collinsella sp900549455	92.1067	381	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.06	95.06	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-19 05:52:42,064] [INFO] GTDB search result was written to GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 05:52:42,065] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:52:42,071] [INFO] DFAST_QC result json was written to GCA_937945015.1_ERR912041_bin.89_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 05:52:42,071] [INFO] DFAST_QC completed!
[2023-06-19 05:52:42,071] [INFO] Total running time: 0h0m59s