[2023-06-07 21:27:10,007] [INFO] DFAST_QC pipeline started.
[2023-06-07 21:27:10,011] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 21:27:10,011] [INFO] DQC Reference Directory: /var/lib/cwl/stg41131bb4-a2cb-4e1f-add9-7c79fa7e1032/dqc_reference
[2023-06-07 21:27:11,335] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 21:27:11,336] [INFO] Task started: Prodigal
[2023-06-07 21:27:11,336] [INFO] Running command: gunzip -c /var/lib/cwl/stg3891bd31-cfab-42fa-a4c5-b0b1911f8244/GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 21:27:22,369] [INFO] Task succeeded: Prodigal
[2023-06-07 21:27:22,369] [INFO] Task started: HMMsearch
[2023-06-07 21:27:22,370] [INFO] Running command: hmmsearch --tblout GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41131bb4-a2cb-4e1f-add9-7c79fa7e1032/dqc_reference/reference_markers.hmm GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 21:27:22,524] [INFO] Task succeeded: HMMsearch
[2023-06-07 21:27:22,526] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3891bd31-cfab-42fa-a4c5-b0b1911f8244/GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-07 21:27:22,546] [INFO] Query marker FASTA was written to GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 21:27:22,546] [INFO] Task started: Blastn
[2023-06-07 21:27:22,546] [INFO] Running command: blastn -query GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg41131bb4-a2cb-4e1f-add9-7c79fa7e1032/dqc_reference/reference_markers.fasta -out GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:27:23,017] [INFO] Task succeeded: Blastn
[2023-06-07 21:27:23,021] [INFO] Selected 12 target genomes.
[2023-06-07 21:27:23,021] [INFO] Target genome list was writen to GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 21:27:23,022] [INFO] Task started: fastANI
[2023-06-07 21:27:23,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg3891bd31-cfab-42fa-a4c5-b0b1911f8244/GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 21:27:28,734] [INFO] Task succeeded: fastANI
[2023-06-07 21:27:28,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41131bb4-a2cb-4e1f-add9-7c79fa7e1032/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 21:27:28,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41131bb4-a2cb-4e1f-add9-7c79fa7e1032/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 21:27:28,740] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 21:27:28,740] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 21:27:28,741] [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
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	76.7876	52	538	95	below_threshold
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	76.4347	53	538	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 21:27:28,754] [INFO] DFAST Taxonomy check result was written to GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 21:27:28,755] [INFO] ===== Taxonomy check completed =====
[2023-06-07 21:27:28,755] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 21:27:28,755] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41131bb4-a2cb-4e1f-add9-7c79fa7e1032/dqc_reference/checkm_data
[2023-06-07 21:27:28,757] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 21:27:28,780] [INFO] Task started: CheckM
[2023-06-07 21:27:28,781] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 21:28:03,368] [INFO] Task succeeded: CheckM
[2023-06-07 21:28:03,369] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-07 21:28:03,395] [INFO] ===== Completeness check finished =====
[2023-06-07 21:28:03,395] [INFO] ===== Start GTDB Search =====
[2023-06-07 21:28:03,395] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 21:28:03,395] [INFO] Task started: Blastn
[2023-06-07 21:28:03,396] [INFO] Running command: blastn -query GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg41131bb4-a2cb-4e1f-add9-7c79fa7e1032/dqc_reference/reference_markers_gtdb.fasta -out GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:28:03,897] [INFO] Task succeeded: Blastn
[2023-06-07 21:28:03,901] [INFO] Selected 11 target genomes.
[2023-06-07 21:28:03,901] [INFO] Target genome list was writen to GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 21:28:03,907] [INFO] Task started: fastANI
[2023-06-07 21:28:03,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg3891bd31-cfab-42fa-a4c5-b0b1911f8244/GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 21:28:08,393] [INFO] Task succeeded: fastANI
[2023-06-07 21:28:08,401] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 21:28:08,401] [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_001689485.1	s__UBA7173 sp001689485	99.106	501	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	99.04	99.00	0.86	0.84	5	conclusive
GCA_910586565.1	s__UBA7173 sp910586565	78.9156	212	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013316535.1	s__UBA7173 sp013316535	78.3948	159	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	97.52	97.52	0.95	0.95	2	-
GCA_900540205.1	s__UBA7173 sp900540205	78.2273	140	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	96.71	95.96	0.83	0.74	4	-
GCA_014800795.1	s__UBA7173 sp014800795	77.6522	88	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575545.1	s__UBA7173 sp013316675	77.6483	154	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	99.44	98.97	0.94	0.91	3	-
GCA_902836725.1	s__UBA7173 sp902836725	77.3792	90	538	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 21:28:08,403] [INFO] GTDB search result was written to GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 21:28:08,403] [INFO] ===== GTDB Search completed =====
[2023-06-07 21:28:08,406] [INFO] DFAST_QC result json was written to GCA_947646665.1_SRR15633981_bin.21_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 21:28:08,407] [INFO] DFAST_QC completed!
[2023-06-07 21:28:08,407] [INFO] Total running time: 0h0m58s