[2023-06-07 22:55:18,645] [INFO] DFAST_QC pipeline started.
[2023-06-07 22:55:18,647] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 22:55:18,647] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f3d94f7-b174-424f-bc87-7dcb44bae7ab/dqc_reference
[2023-06-07 22:55:19,952] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 22:55:19,953] [INFO] Task started: Prodigal
[2023-06-07 22:55:19,953] [INFO] Running command: gunzip -c /var/lib/cwl/stg51a2f5dc-c2a5-4e97-a812-8d185a6b10bc/GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 22:55:37,229] [INFO] Task succeeded: Prodigal
[2023-06-07 22:55:37,229] [INFO] Task started: HMMsearch
[2023-06-07 22:55:37,229] [INFO] Running command: hmmsearch --tblout GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f3d94f7-b174-424f-bc87-7dcb44bae7ab/dqc_reference/reference_markers.hmm GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 22:55:37,499] [INFO] Task succeeded: HMMsearch
[2023-06-07 22:55:37,501] [INFO] Found 6/6 markers.
[2023-06-07 22:55:37,531] [INFO] Query marker FASTA was written to GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 22:55:37,531] [INFO] Task started: Blastn
[2023-06-07 22:55:37,531] [INFO] Running command: blastn -query GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f3d94f7-b174-424f-bc87-7dcb44bae7ab/dqc_reference/reference_markers.fasta -out GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:55:38,137] [INFO] Task succeeded: Blastn
[2023-06-07 22:55:38,140] [INFO] Selected 18 target genomes.
[2023-06-07 22:55:38,141] [INFO] Target genome list was writen to GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 22:55:38,142] [INFO] Task started: fastANI
[2023-06-07 22:55:38,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg51a2f5dc-c2a5-4e97-a812-8d185a6b10bc/GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 22:55:47,721] [INFO] Task succeeded: fastANI
[2023-06-07 22:55:47,722] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f3d94f7-b174-424f-bc87-7dcb44bae7ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 22:55:47,722] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f3d94f7-b174-424f-bc87-7dcb44bae7ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 22:55:47,733] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 22:55:47,733] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 22:55:47,733] [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
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	77.8201	256	1064	95	below_threshold
Heminiphilus faecis	strain=AM35	GCA_008728965.1	2601703	2601703	type	True	77.7317	202	1064	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	77.5295	146	1064	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	77.4782	147	1064	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	77.466	143	1064	95	below_threshold
Duncaniella freteri	strain=TLL-A3	GCA_004766125.1	2530391	2530391	type	True	77.2396	80	1064	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	77.0517	99	1064	95	below_threshold
Barnesiella viscericola	strain=C46, DSM 18177	GCA_000512915.1	397865	397865	type	True	76.5948	52	1064	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 22:55:47,735] [INFO] DFAST Taxonomy check result was written to GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 22:55:47,736] [INFO] ===== Taxonomy check completed =====
[2023-06-07 22:55:47,736] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 22:55:47,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f3d94f7-b174-424f-bc87-7dcb44bae7ab/dqc_reference/checkm_data
[2023-06-07 22:55:47,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 22:55:47,771] [INFO] Task started: CheckM
[2023-06-07 22:55:47,771] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 22:56:40,020] [INFO] Task succeeded: CheckM
[2023-06-07 22:56:40,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.77%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-07 22:56:40,042] [INFO] ===== Completeness check finished =====
[2023-06-07 22:56:40,042] [INFO] ===== Start GTDB Search =====
[2023-06-07 22:56:40,042] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 22:56:40,043] [INFO] Task started: Blastn
[2023-06-07 22:56:40,043] [INFO] Running command: blastn -query GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f3d94f7-b174-424f-bc87-7dcb44bae7ab/dqc_reference/reference_markers_gtdb.fasta -out GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:56:40,938] [INFO] Task succeeded: Blastn
[2023-06-07 22:56:40,943] [INFO] Selected 10 target genomes.
[2023-06-07 22:56:40,943] [INFO] Target genome list was writen to GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 22:56:40,945] [INFO] Task started: fastANI
[2023-06-07 22:56:40,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg51a2f5dc-c2a5-4e97-a812-8d185a6b10bc/GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 22:56:46,748] [INFO] Task succeeded: fastANI
[2023-06-07 22:56:46,762] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 22:56:46,763] [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_003150235.1	s__Muribaculum sp003150235	99.2042	967	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	97.90	96.97	0.85	0.80	6	conclusive
GCA_910578835.1	s__Muribaculum sp910578835	82.6514	654	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570975.1	s__Muribaculum sp001701195	80.9341	576	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	97.86	97.86	0.92	0.92	2	-
GCA_910587665.1	s__Muribaculum sp910587665	80.5752	572	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009775095.1	s__Muribaculum sp009775095	77.9663	219	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.95	99.95	0.97	0.97	2	-
GCA_014801235.1	s__Muribaculum sp014801235	77.9263	115	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001689405.1	s__Muribaculum arabinoxylanisolvens	77.8384	231	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.46	99.01	0.94	0.92	3	-
GCF_008728965.1	s__Muribaculum faecis	77.7522	202	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	99.62	99.32	0.94	0.91	9	-
GCA_009177195.1	s__Muribaculum sp009177195	77.7501	150	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Muribaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003762715.1	s__Paramuribaculum sp001689565	77.0388	80	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Paramuribaculum	95.0	98.89	98.71	0.85	0.83	3	-
--------------------------------------------------------------------------------
[2023-06-07 22:56:46,778] [INFO] GTDB search result was written to GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 22:56:46,778] [INFO] ===== GTDB Search completed =====
[2023-06-07 22:56:46,786] [INFO] DFAST_QC result json was written to GCA_947426175.1_SRR12506363_bin.4_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 22:56:46,786] [INFO] DFAST_QC completed!
[2023-06-07 22:56:46,787] [INFO] Total running time: 0h1m28s