[2023-07-01 02:57:00,622] [INFO] DFAST_QC pipeline started.
[2023-07-01 02:57:00,624] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 02:57:00,625] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb6281dc-0cdd-4328-b3c8-abf72f371b50/dqc_reference
[2023-07-01 02:57:01,859] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 02:57:01,860] [INFO] Task started: Prodigal
[2023-07-01 02:57:01,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg5505bb47-2f5e-4297-a889-1a5497bbe896/GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 02:57:05,573] [INFO] Task succeeded: Prodigal
[2023-07-01 02:57:05,574] [INFO] Task started: HMMsearch
[2023-07-01 02:57:05,574] [INFO] Running command: hmmsearch --tblout GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb6281dc-0cdd-4328-b3c8-abf72f371b50/dqc_reference/reference_markers.hmm GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-07-01 02:57:05,780] [INFO] Task succeeded: HMMsearch
[2023-07-01 02:57:05,782] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg5505bb47-2f5e-4297-a889-1a5497bbe896/GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-07-01 02:57:05,807] [INFO] Query marker FASTA was written to GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-07-01 02:57:05,808] [INFO] Task started: Blastn
[2023-07-01 02:57:05,808] [INFO] Running command: blastn -query GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb6281dc-0cdd-4328-b3c8-abf72f371b50/dqc_reference/reference_markers.fasta -out GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:57:06,343] [INFO] Task succeeded: Blastn
[2023-07-01 02:57:06,347] [INFO] Selected 6 target genomes.
[2023-07-01 02:57:06,348] [INFO] Target genome list was writen to GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-07-01 02:57:06,349] [INFO] Task started: fastANI
[2023-07-01 02:57:06,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg5505bb47-2f5e-4297-a889-1a5497bbe896/GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 02:57:10,133] [INFO] Task succeeded: fastANI
[2023-07-01 02:57:10,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb6281dc-0cdd-4328-b3c8-abf72f371b50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 02:57:10,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb6281dc-0cdd-4328-b3c8-abf72f371b50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 02:57:10,138] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 02:57:10,139] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 02:57:10,139] [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
Ruminococcus flavefaciens	strain=ATCC 19208	GCA_000518765.1	1265	1265	suspected-type	True	81.9708	324	475	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 02:57:10,141] [INFO] DFAST Taxonomy check result was written to GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-07-01 02:57:10,141] [INFO] ===== Taxonomy check completed =====
[2023-07-01 02:57:10,141] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 02:57:10,141] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb6281dc-0cdd-4328-b3c8-abf72f371b50/dqc_reference/checkm_data
[2023-07-01 02:57:10,142] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 02:57:10,168] [INFO] Task started: CheckM
[2023-07-01 02:57:10,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-07-01 02:57:28,574] [INFO] Task succeeded: CheckM
[2023-07-01 02:57:28,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.47%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-07-01 02:57:28,596] [INFO] ===== Completeness check finished =====
[2023-07-01 02:57:28,597] [INFO] ===== Start GTDB Search =====
[2023-07-01 02:57:28,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-07-01 02:57:28,597] [INFO] Task started: Blastn
[2023-07-01 02:57:28,598] [INFO] Running command: blastn -query GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb6281dc-0cdd-4328-b3c8-abf72f371b50/dqc_reference/reference_markers_gtdb.fasta -out GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:57:29,263] [INFO] Task succeeded: Blastn
[2023-07-01 02:57:29,268] [INFO] Selected 8 target genomes.
[2023-07-01 02:57:29,268] [INFO] Target genome list was writen to GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 02:57:29,271] [INFO] Task started: fastANI
[2023-07-01 02:57:29,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg5505bb47-2f5e-4297-a889-1a5497bbe896/GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 02:57:34,605] [INFO] Task succeeded: fastANI
[2023-07-01 02:57:34,618] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 02:57:34,619] [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
GCF_000621845.1	s__Ruminococcus flavefaciens_E	97.8582	451	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	97.76	97.66	0.87	0.87	4	conclusive
GCF_900119075.1	s__Ruminococcus flavefaciens_Q	94.771	451	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.02	98.02	0.91	0.91	2	-
GCF_000526795.1	s__Ruminococcus flavefaciens_D	86.6171	432	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004554385.1	s__Ruminococcus flavefaciens_T	85.0145	374	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.08	98.08	0.79	0.79	2	-
GCA_017549005.1	s__Ruminococcus sp017549005	82.8271	345	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621785.1	s__Ruminococcus flavefaciens_C	82.0463	331	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518765.1	s__Ruminococcus flavefaciens	82.0102	322	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016283395.1	s__Ruminococcus sp016283395	81.8685	320	475	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 02:57:34,623] [INFO] GTDB search result was written to GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-07-01 02:57:34,623] [INFO] ===== GTDB Search completed =====
[2023-07-01 02:57:34,626] [INFO] DFAST_QC result json was written to GCA_946413345.1_SRR12081293_bin.10_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-07-01 02:57:34,626] [INFO] DFAST_QC completed!
[2023-07-01 02:57:34,626] [INFO] Total running time: 0h0m34s