[2023-06-08 13:52:03,129] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:52:03,132] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:52:03,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg587c1622-959e-4a15-93d6-a594f8540b93/dqc_reference
[2023-06-08 13:52:04,435] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:52:04,436] [INFO] Task started: Prodigal
[2023-06-08 13:52:04,436] [INFO] Running command: gunzip -c /var/lib/cwl/stgec49ae91-8a74-4409-b1a6-1914284f30a5/GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:52:13,058] [INFO] Task succeeded: Prodigal
[2023-06-08 13:52:13,058] [INFO] Task started: HMMsearch
[2023-06-08 13:52:13,058] [INFO] Running command: hmmsearch --tblout GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg587c1622-959e-4a15-93d6-a594f8540b93/dqc_reference/reference_markers.hmm GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:52:13,311] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:52:13,313] [INFO] Found 6/6 markers.
[2023-06-08 13:52:13,343] [INFO] Query marker FASTA was written to GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 13:52:13,344] [INFO] Task started: Blastn
[2023-06-08 13:52:13,344] [INFO] Running command: blastn -query GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg587c1622-959e-4a15-93d6-a594f8540b93/dqc_reference/reference_markers.fasta -out GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:52:13,924] [INFO] Task succeeded: Blastn
[2023-06-08 13:52:13,929] [INFO] Selected 24 target genomes.
[2023-06-08 13:52:13,929] [INFO] Target genome list was writen to GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 13:52:13,932] [INFO] Task started: fastANI
[2023-06-08 13:52:13,933] [INFO] Running command: fastANI --query /var/lib/cwl/stgec49ae91-8a74-4409-b1a6-1914284f30a5/GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:52:25,143] [INFO] Task succeeded: fastANI
[2023-06-08 13:52:25,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg587c1622-959e-4a15-93d6-a594f8540b93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:52:25,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg587c1622-959e-4a15-93d6-a594f8540b93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:52:25,152] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:52:25,152] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 13:52:25,153] [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	77.2203	67	1035	95	below_threshold
Butyricicoccus faecihominis	strain=JCM 31056	GCA_016586375.1	1712515	1712515	type	True	77.1464	70	1035	95	below_threshold
Butyricicoccus pullicaecorum	strain=DSM 23266	GCA_900167005.1	501571	501571	type	True	76.9785	76	1035	95	below_threshold
Intestinibacillus massiliensis	strain=type strain: Marseille-P3216	GCA_900155735.1	1871029	1871029	type	True	76.7844	60	1035	95	below_threshold
Agathobaculum desmolans	strain=ATCC 43058	GCA_000701665.1	39484	39484	type	True	76.6202	93	1035	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 13:52:25,154] [INFO] DFAST Taxonomy check result was written to GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 13:52:25,155] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:52:25,155] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:52:25,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg587c1622-959e-4a15-93d6-a594f8540b93/dqc_reference/checkm_data
[2023-06-08 13:52:25,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:52:25,192] [INFO] Task started: CheckM
[2023-06-08 13:52:25,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 13:52:55,916] [INFO] Task succeeded: CheckM
[2023-06-08 13:52:55,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:52:55,945] [INFO] ===== Completeness check finished =====
[2023-06-08 13:52:55,945] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:52:55,945] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 13:52:55,946] [INFO] Task started: Blastn
[2023-06-08 13:52:55,946] [INFO] Running command: blastn -query GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg587c1622-959e-4a15-93d6-a594f8540b93/dqc_reference/reference_markers_gtdb.fasta -out GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:52:56,740] [INFO] Task succeeded: Blastn
[2023-06-08 13:52:56,745] [INFO] Selected 20 target genomes.
[2023-06-08 13:52:56,745] [INFO] Target genome list was writen to GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:52:56,753] [INFO] Task started: fastANI
[2023-06-08 13:52:56,753] [INFO] Running command: fastANI --query /var/lib/cwl/stgec49ae91-8a74-4409-b1a6-1914284f30a5/GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:53:06,383] [INFO] Task succeeded: fastANI
[2023-06-08 13:53:06,398] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 13:53:06,399] [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_910589115.1	s__QXXE01 sp910589115	97.4781	788	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__QXXE01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910586105.1	s__QXXE01 sp910586105	79.8994	294	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__QXXE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586575.1	s__QXXE01 sp910586575	79.4332	353	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__QXXE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009911355.1	s__QXXE01 sp009911355	78.8276	291	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__QXXE01	95.0	98.12	98.12	0.77	0.77	2	-
GCF_900604335.1	s__Butyricicoccus sp900604335	77.4504	73	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018383195.1	s__Butyricicoccus sp018383195	77.2163	70	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus	95.0	96.96	96.96	0.89	0.89	2	-
GCF_900167005.1	s__Butyricicoccus pullicaecorum	76.9785	76	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus	95.0	98.10	95.60	0.92	0.80	7	-
GCF_000701665.1	s__Agathobaculum desmolans	76.6437	92	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.85	98.85	0.90	0.90	2	-
GCA_910584935.1	s__Butyricicoccus sp910584935	76.2861	71	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 13:53:06,408] [INFO] GTDB search result was written to GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 13:53:06,409] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:53:06,413] [INFO] DFAST_QC result json was written to GCA_947088045.1_SRR14038237_bin.73_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 13:53:06,413] [INFO] DFAST_QC completed!
[2023-06-08 13:53:06,413] [INFO] Total running time: 0h1m3s