[2023-06-13 14:46:09,770] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:46:09,773] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:46:09,773] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4dae846-635d-4c3b-a04b-9f5651bf59cb/dqc_reference
[2023-06-13 14:46:11,000] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:46:11,001] [INFO] Task started: Prodigal
[2023-06-13 14:46:11,001] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b40532d-2540-4d4b-b7d9-3f557c17c398/GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:46:19,280] [INFO] Task succeeded: Prodigal
[2023-06-13 14:46:19,280] [INFO] Task started: HMMsearch
[2023-06-13 14:46:19,281] [INFO] Running command: hmmsearch --tblout GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4dae846-635d-4c3b-a04b-9f5651bf59cb/dqc_reference/reference_markers.hmm GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:46:19,502] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:46:19,503] [INFO] Found 6/6 markers.
[2023-06-13 14:46:19,533] [INFO] Query marker FASTA was written to GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 14:46:19,534] [INFO] Task started: Blastn
[2023-06-13 14:46:19,534] [INFO] Running command: blastn -query GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4dae846-635d-4c3b-a04b-9f5651bf59cb/dqc_reference/reference_markers.fasta -out GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:46:20,102] [INFO] Task succeeded: Blastn
[2023-06-13 14:46:20,105] [INFO] Selected 29 target genomes.
[2023-06-13 14:46:20,106] [INFO] Target genome list was writen to GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 14:46:20,109] [INFO] Task started: fastANI
[2023-06-13 14:46:20,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b40532d-2540-4d4b-b7d9-3f557c17c398/GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:46:35,607] [INFO] Task succeeded: fastANI
[2023-06-13 14:46:35,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4dae846-635d-4c3b-a04b-9f5651bf59cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:46:35,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4dae846-635d-4c3b-a04b-9f5651bf59cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:46:35,616] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:46:35,616] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 14:46:35,616] [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
Butyrivibrio crossotus	strain=DSM 2876	GCA_025148445.1	45851	45851	type	True	81.2294	66	1200	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	78.3727	93	1200	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	77.7269	80	1200	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	76.8268	66	1200	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.7299	53	1200	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.6327	60	1200	95	below_threshold
Anaerostipes hadrus	strain=DSM 3319	GCA_000332875.2	649756	649756	type	True	76.6269	51	1200	95	below_threshold
Butyrivibrio hungatei	strain=DSM 14810	GCA_900143205.1	185008	185008	type	True	76.256	58	1200	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:46:35,618] [INFO] DFAST Taxonomy check result was written to GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 14:46:35,619] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:46:35,619] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:46:35,619] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4dae846-635d-4c3b-a04b-9f5651bf59cb/dqc_reference/checkm_data
[2023-06-13 14:46:35,620] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:46:35,655] [INFO] Task started: CheckM
[2023-06-13 14:46:35,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 14:47:04,845] [INFO] Task succeeded: CheckM
[2023-06-13 14:47:04,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 4.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:47:04,865] [INFO] ===== Completeness check finished =====
[2023-06-13 14:47:04,865] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:47:04,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 14:47:04,866] [INFO] Task started: Blastn
[2023-06-13 14:47:04,866] [INFO] Running command: blastn -query GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4dae846-635d-4c3b-a04b-9f5651bf59cb/dqc_reference/reference_markers_gtdb.fasta -out GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:47:05,677] [INFO] Task succeeded: Blastn
[2023-06-13 14:47:05,681] [INFO] Selected 27 target genomes.
[2023-06-13 14:47:05,681] [INFO] Target genome list was writen to GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:47:05,706] [INFO] Task started: fastANI
[2023-06-13 14:47:05,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b40532d-2540-4d4b-b7d9-3f557c17c398/GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:47:19,317] [INFO] Task succeeded: fastANI
[2023-06-13 14:47:19,335] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 14:47:19,336] [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_900753305.1	s__COE1 sp900753305	99.9547	982	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	99.96	99.96	0.93	0.93	2	conclusive
GCA_001916965.1	s__COE1 sp001916965	85.0911	785	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	98.52	98.34	0.88	0.83	8	-
GCF_000156015.1	s__Butyrivibrio_A crossotus	81.3597	64	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	98.48	97.83	0.85	0.60	12	-
GCA_017436865.1	s__COE1 sp017436865	78.3112	228	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	98.13	98.13	0.76	0.76	2	-
GCA_015056925.1	s__COE1 sp015056925	77.8218	193	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003584705.1	s__Acetatifactor sp900066565	77.7804	116	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	98.01	97.56	0.88	0.80	26	-
GCA_014804345.1	s__COE1 sp014804345	77.7665	50	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017440575.1	s__COE1 sp017440575	77.5726	192	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017622845.1	s__COE1 sp017622845	77.5506	159	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	98.75	98.75	0.86	0.86	2	-
GCF_003458705.1	s__Lachnospira sp003537285	77.484	65	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.4867	98.01	96.87	0.87	0.80	8	-
GCA_017437065.1	s__RGIG3002 sp017437065	77.4651	104	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG3002	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017520425.1	s__Acetatifactor sp017520425	77.3583	66	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003464165.1	s__Lachnospira sp003451515	77.3375	52	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	97.95	97.44	0.88	0.84	9	-
GCA_017463255.1	s__RGIG4034 sp017463255	77.0807	82	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG4034	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586585.1	s__COE1 sp910586585	76.9753	117	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774375.1	s__COE1 sp009774375	76.9522	72	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	99.47	99.47	0.88	0.88	2	-
GCA_014804225.1	s__COE1 sp014804225	76.8505	59	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239155.1	s__COE1 sp014239155	76.8289	98	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	99.30	99.30	0.91	0.91	2	-
GCA_002490665.1	s__COE1 sp002490665	76.825	80	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	95.75	95.74	0.79	0.79	3	-
GCA_017621815.1	s__CAG-95 sp017621815	76.8127	83	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017521985.1	s__RGIG6307 sp017521985	76.7062	55	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG6307	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578555.1	s__UBA3282 sp910578555	76.5113	56	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017468395.1	s__SIG332 sp017468395	76.1139	65	1200	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG332	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 14:47:19,338] [INFO] GTDB search result was written to GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 14:47:19,338] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:47:19,342] [INFO] DFAST_QC result json was written to GCA_938016375.1_ERR414302_bin.110_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 14:47:19,342] [INFO] DFAST_QC completed!
[2023-06-13 14:47:19,342] [INFO] Total running time: 0h1m10s