[2023-06-29 19:13:39,595] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:13:39,597] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:13:39,597] [INFO] DQC Reference Directory: /var/lib/cwl/stg538d5475-d2d3-48d3-ac0a-a9a4eab86ec8/dqc_reference
[2023-06-29 19:13:40,819] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:13:40,820] [INFO] Task started: Prodigal
[2023-06-29 19:13:40,820] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b9c8f24-acb5-4416-b0e8-e337492a6afb/GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:13:46,670] [INFO] Task succeeded: Prodigal
[2023-06-29 19:13:46,671] [INFO] Task started: HMMsearch
[2023-06-29 19:13:46,671] [INFO] Running command: hmmsearch --tblout GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg538d5475-d2d3-48d3-ac0a-a9a4eab86ec8/dqc_reference/reference_markers.hmm GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:13:46,845] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:13:46,846] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9b9c8f24-acb5-4416-b0e8-e337492a6afb/GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-29 19:13:46,869] [INFO] Query marker FASTA was written to GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 19:13:46,869] [INFO] Task started: Blastn
[2023-06-29 19:13:46,869] [INFO] Running command: blastn -query GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg538d5475-d2d3-48d3-ac0a-a9a4eab86ec8/dqc_reference/reference_markers.fasta -out GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:13:47,566] [INFO] Task succeeded: Blastn
[2023-06-29 19:13:47,570] [INFO] Selected 13 target genomes.
[2023-06-29 19:13:47,570] [INFO] Target genome list was writen to GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 19:13:47,572] [INFO] Task started: fastANI
[2023-06-29 19:13:47,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b9c8f24-acb5-4416-b0e8-e337492a6afb/GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:13:54,112] [INFO] Task succeeded: fastANI
[2023-06-29 19:13:54,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg538d5475-d2d3-48d3-ac0a-a9a4eab86ec8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:13:54,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg538d5475-d2d3-48d3-ac0a-a9a4eab86ec8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:13:54,120] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:13:54,121] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 19:13:54,121] [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
Butyricicoccus faecihominis	strain=JCM 31056	GCA_014648015.1	1712515	1712515	type	True	83.6182	418	727	95	below_threshold
Butyricicoccus faecihominis	strain=JCM 31056	GCA_016586375.1	1712515	1712515	type	True	83.5795	415	727	95	below_threshold
Agathobaculum desmolans	strain=ATCC 43058	GCA_000701665.1	39484	39484	type	True	79.4673	261	727	95	below_threshold
Intestinibacillus massiliensis	strain=type strain: Marseille-P3216	GCA_900155735.1	1871029	1871029	type	True	78.756	197	727	95	below_threshold
Butyricicoccus pullicaecorum	strain=DSM 23266	GCA_900167005.1	501571	501571	type	True	78.7158	170	727	95	below_threshold
Butyricicoccus porcorum	strain=BB10	GCA_002157465.1	1945634	1945634	type	True	77.6846	105	727	95	below_threshold
Butyricicoccus intestinisimiae	strain=MSJd-7	GCA_018918345.1	2841509	2841509	type	True	77.4574	91	727	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	76.6182	54	727	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:13:54,122] [INFO] DFAST Taxonomy check result was written to GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 19:13:54,123] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:13:54,123] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:13:54,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg538d5475-d2d3-48d3-ac0a-a9a4eab86ec8/dqc_reference/checkm_data
[2023-06-29 19:13:54,124] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:13:54,149] [INFO] Task started: CheckM
[2023-06-29 19:13:54,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 19:14:17,024] [INFO] Task succeeded: CheckM
[2023-06-29 19:14:17,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:14:17,042] [INFO] ===== Completeness check finished =====
[2023-06-29 19:14:17,042] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:14:17,042] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 19:14:17,043] [INFO] Task started: Blastn
[2023-06-29 19:14:17,043] [INFO] Running command: blastn -query GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg538d5475-d2d3-48d3-ac0a-a9a4eab86ec8/dqc_reference/reference_markers_gtdb.fasta -out GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:14:18,273] [INFO] Task succeeded: Blastn
[2023-06-29 19:14:18,276] [INFO] Selected 13 target genomes.
[2023-06-29 19:14:18,277] [INFO] Target genome list was writen to GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:14:18,282] [INFO] Task started: fastANI
[2023-06-29 19:14:18,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b9c8f24-acb5-4416-b0e8-e337492a6afb/GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:14:23,990] [INFO] Task succeeded: fastANI
[2023-06-29 19:14:24,000] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:14:24,000] [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_900544475.1	s__Agathobaculum sp900544475	98.2611	463	727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	97.90	97.82	0.89	0.86	3	conclusive
GCF_003481705.1	s__Agathobaculum sp003481705	89.8203	586	727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.33	96.26	0.92	0.82	8	-
GCA_003096535.1	s__Agathobaculum butyriciproducens	83.8211	421	727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	96.66	95.68	0.85	0.79	34	-
GCA_900555465.1	s__Agathobaculum intestinigallinarum	81.3997	220	727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	97.06	97.06	0.83	0.83	2	-
GCF_900625105.1	s__Agathobaculum sp900625105	81.3042	338	727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113065.1	s__Agathobaculum stercoravium	81.0443	282	727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.25	98.25	0.89	0.89	2	-
GCA_019115615.1	s__Agathobaculum merdavium	80.4874	276	727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900557315.1	s__Agathobaculum sp900557315	80.2907	201	727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	100.00	100.00	0.98	0.98	2	-
GCA_019114345.1	s__Agathobaculum pullistercoris	80.2024	264	727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.72	98.13	0.86	0.78	4	-
GCA_019115085.1	s__Agathobaculum pullicola	79.4594	218	727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155735.1	s__Intestinibacillus massiliensis	78.756	197	727	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Intestinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 19:14:24,002] [INFO] GTDB search result was written to GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 19:14:24,003] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:14:24,006] [INFO] DFAST_QC result json was written to GCA_937941075.1_ERR1430402_bin.85_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 19:14:24,006] [INFO] DFAST_QC completed!
[2023-06-29 19:14:24,006] [INFO] Total running time: 0h0m44s