[2023-06-07 18:15:05,400] [INFO] DFAST_QC pipeline started.
[2023-06-07 18:15:05,403] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 18:15:05,403] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9726a89-5233-43a4-b12f-6538754a3cdb/dqc_reference
[2023-06-07 18:15:06,863] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 18:15:06,864] [INFO] Task started: Prodigal
[2023-06-07 18:15:06,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg6eb26068-bc6f-4de4-a460-7be49a0f7d78/GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 18:15:13,305] [INFO] Task succeeded: Prodigal
[2023-06-07 18:15:13,306] [INFO] Task started: HMMsearch
[2023-06-07 18:15:13,306] [INFO] Running command: hmmsearch --tblout GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9726a89-5233-43a4-b12f-6538754a3cdb/dqc_reference/reference_markers.hmm GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 18:15:13,550] [INFO] Task succeeded: HMMsearch
[2023-06-07 18:15:13,551] [INFO] Found 6/6 markers.
[2023-06-07 18:15:13,576] [INFO] Query marker FASTA was written to GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 18:15:13,577] [INFO] Task started: Blastn
[2023-06-07 18:15:13,577] [INFO] Running command: blastn -query GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9726a89-5233-43a4-b12f-6538754a3cdb/dqc_reference/reference_markers.fasta -out GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:15:14,253] [INFO] Task succeeded: Blastn
[2023-06-07 18:15:14,257] [INFO] Selected 14 target genomes.
[2023-06-07 18:15:14,257] [INFO] Target genome list was writen to GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 18:15:14,262] [INFO] Task started: fastANI
[2023-06-07 18:15:14,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg6eb26068-bc6f-4de4-a460-7be49a0f7d78/GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 18:15:21,531] [INFO] Task succeeded: fastANI
[2023-06-07 18:15:21,532] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9726a89-5233-43a4-b12f-6538754a3cdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 18:15:21,532] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9726a89-5233-43a4-b12f-6538754a3cdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 18:15:21,542] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 18:15:21,542] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 18:15:21,542] [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=NCTC11838	GCA_900461335.1	74426	74426	type	True	94.6527	595	691	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	94.6338	592	691	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	94.6296	587	691	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.3717	234	691	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	79.7459	220	691	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.6691	267	691	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	79.5893	239	691	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.5471	234	691	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.3885	226	691	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.8603	210	691	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 18:15:21,544] [INFO] DFAST Taxonomy check result was written to GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 18:15:21,545] [INFO] ===== Taxonomy check completed =====
[2023-06-07 18:15:21,545] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 18:15:21,545] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9726a89-5233-43a4-b12f-6538754a3cdb/dqc_reference/checkm_data
[2023-06-07 18:15:21,546] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 18:15:21,576] [INFO] Task started: CheckM
[2023-06-07 18:15:21,576] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 18:15:46,354] [INFO] Task succeeded: CheckM
[2023-06-07 18:15:46,355] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 18:15:46,380] [INFO] ===== Completeness check finished =====
[2023-06-07 18:15:46,380] [INFO] ===== Start GTDB Search =====
[2023-06-07 18:15:46,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 18:15:46,381] [INFO] Task started: Blastn
[2023-06-07 18:15:46,381] [INFO] Running command: blastn -query GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9726a89-5233-43a4-b12f-6538754a3cdb/dqc_reference/reference_markers_gtdb.fasta -out GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:15:47,363] [INFO] Task succeeded: Blastn
[2023-06-07 18:15:47,368] [INFO] Selected 35 target genomes.
[2023-06-07 18:15:47,368] [INFO] Target genome list was writen to GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 18:15:47,411] [INFO] Task started: fastANI
[2023-06-07 18:15:47,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg6eb26068-bc6f-4de4-a460-7be49a0f7d78/GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 18:16:03,775] [INFO] Task succeeded: fastANI
[2023-06-07 18:16:03,812] [INFO] Found 32 fastANI hits (5 hits with ANI > circumscription radius)
[2023-06-07 18:16:03,813] [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_005844325.1	s__Collinsella aerofaciens_G	96.0413	581	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.009	96.00	95.07	0.90	0.86	20	inconclusive
GCF_015560765.1	s__Collinsella aerofaciens_M	95.6792	579	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1158	96.04	95.15	0.86	0.78	15	inconclusive
GCA_008671135.1	s__Collinsella aerofaciens_J	95.2191	579	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2147	97.21	95.28	0.90	0.82	6	inconclusive
GCA_900541235.1	s__Collinsella sp900541235	95.1311	563	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.02	95.02	0.86	0.86	2	inconclusive
GCA_900551365.1	s__Collinsella sp900551365	95.0193	480	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_018373675.1	s__Collinsella sp018373675	95.0153	564	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0912	N/A	N/A	N/A	N/A	1	-
GCF_015558785.1	s__Collinsella aerofaciens_P	94.9802	573	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1792	95.28	95.25	0.89	0.89	3	-
GCF_015670795.1	s__Collinsella aerofaciens_Q	94.9311	580	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1438	95.30	95.30	0.93	0.92	3	-
GCA_900754275.1	s__Collinsella sp900754275	94.8894	495	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	97.49	95.11	0.84	0.77	3	-
GCA_900544865.1	s__Collinsella sp900544865	94.8843	540	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541065.1	s__Collinsella sp900541065	94.8664	580	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0334	N/A	N/A	N/A	N/A	1	-
GCA_900541135.1	s__Collinsella sp900541135	94.8447	543	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018382295.1	s__Collinsella sp018382295	94.8389	538	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548495.1	s__Collinsella sp900548495	94.7887	496	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0367	N/A	N/A	N/A	N/A	1	-
GCA_900542165.1	s__Collinsella sp900542165	94.6731	549	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0912	95.41	95.20	0.86	0.82	3	-
GCA_900762015.1	s__Collinsella sp900762015	94.6179	481	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1172	N/A	N/A	N/A	N/A	1	-
GCA_018376905.1	s__Collinsella sp018376905	94.5485	558	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540895.1	s__Collinsella sp900540895	94.5465	574	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.25	95.25	0.87	0.87	2	-
GCA_905216145.1	s__Collinsella sp905216145	94.5448	564	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548515.1	s__Collinsella sp900548515	94.3639	484	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552755.1	s__Collinsella sp900552755	94.342	430	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014871545.1	s__Collinsella sp014871545	94.2573	368	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0116	N/A	N/A	N/A	N/A	1	-
GCA_905215195.1	s__Collinsella sp905215195	94.246	397	691	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	94.2124	538	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760245.1	s__Collinsella sp900760245	94.0908	479	691	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	94.0735	339	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.98	0.98	2	-
GCA_900552295.1	s__Collinsella sp900552295	94.0585	379	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544135.1	s__Collinsella sp900544135	93.9816	551	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.96	99.96	0.98	0.98	2	-
GCF_015554145.1	s__Collinsella aerofaciens_AA	93.1073	592	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761145.1	s__Collinsella sp900761145	93.0522	493	691	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	93.0474	508	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.18	95.16	0.86	0.84	3	-
GCF_003459505.1	s__Collinsella sp003459505	92.632	582	691	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	96.69	95.03	0.91	0.87	4	-
--------------------------------------------------------------------------------
[2023-06-07 18:16:03,817] [INFO] GTDB search result was written to GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 18:16:03,819] [INFO] ===== GTDB Search completed =====
[2023-06-07 18:16:03,825] [INFO] DFAST_QC result json was written to GCA_947003005.1_SRR19721630_bin.5_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 18:16:03,825] [INFO] DFAST_QC completed!
[2023-06-07 18:16:03,826] [INFO] Total running time: 0h0m58s