[2023-06-28 10:15:47,011] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:15:47,013] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:15:47,013] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cabf0ee-190a-46d7-84df-2e3a8a54dcfd/dqc_reference
[2023-06-28 10:15:48,219] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:15:48,220] [INFO] Task started: Prodigal
[2023-06-28 10:15:48,220] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4e9616c-dc2b-49be-9bd7-938f633a1057/GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:15:50,995] [INFO] Task succeeded: Prodigal
[2023-06-28 10:15:50,995] [INFO] Task started: HMMsearch
[2023-06-28 10:15:50,996] [INFO] Running command: hmmsearch --tblout GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cabf0ee-190a-46d7-84df-2e3a8a54dcfd/dqc_reference/reference_markers.hmm GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:15:51,225] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:15:51,227] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf4e9616c-dc2b-49be-9bd7-938f633a1057/GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 10:15:51,250] [INFO] Query marker FASTA was written to GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 10:15:51,250] [INFO] Task started: Blastn
[2023-06-28 10:15:51,251] [INFO] Running command: blastn -query GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cabf0ee-190a-46d7-84df-2e3a8a54dcfd/dqc_reference/reference_markers.fasta -out GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:15:51,821] [INFO] Task succeeded: Blastn
[2023-06-28 10:15:51,826] [INFO] Selected 23 target genomes.
[2023-06-28 10:15:51,826] [INFO] Target genome list was writen to GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 10:15:51,833] [INFO] Task started: fastANI
[2023-06-28 10:15:51,833] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4e9616c-dc2b-49be-9bd7-938f633a1057/GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:16:04,290] [INFO] Task succeeded: fastANI
[2023-06-28 10:16:04,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cabf0ee-190a-46d7-84df-2e3a8a54dcfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:16:04,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cabf0ee-190a-46d7-84df-2e3a8a54dcfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:16:04,308] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:16:04,308] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:16:04,309] [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
Methyloprofundus sedimenti	strain=WF1	GCA_002072955.1	1420851	1420851	type	True	77.9483	70	440	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:16:04,311] [INFO] DFAST Taxonomy check result was written to GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 10:16:04,312] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:16:04,312] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:16:04,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cabf0ee-190a-46d7-84df-2e3a8a54dcfd/dqc_reference/checkm_data
[2023-06-28 10:16:04,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:16:04,340] [INFO] Task started: CheckM
[2023-06-28 10:16:04,341] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 10:16:20,526] [INFO] Task succeeded: CheckM
[2023-06-28 10:16:20,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.63%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:16:20,565] [INFO] ===== Completeness check finished =====
[2023-06-28 10:16:20,566] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:16:20,566] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 10:16:20,566] [INFO] Task started: Blastn
[2023-06-28 10:16:20,566] [INFO] Running command: blastn -query GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cabf0ee-190a-46d7-84df-2e3a8a54dcfd/dqc_reference/reference_markers_gtdb.fasta -out GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:16:21,337] [INFO] Task succeeded: Blastn
[2023-06-28 10:16:21,342] [INFO] Selected 14 target genomes.
[2023-06-28 10:16:21,343] [INFO] Target genome list was writen to GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:16:21,351] [INFO] Task started: fastANI
[2023-06-28 10:16:21,352] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4e9616c-dc2b-49be-9bd7-938f633a1057/GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:16:28,034] [INFO] Task succeeded: fastANI
[2023-06-28 10:16:28,048] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 10:16:28,048] [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_002072955.1	s__Methyloprofundus sedimenti	77.9483	70	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002189065.1	s__Methyloprofundus sp002189065	77.3967	71	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128525.1	s__Methyloprofundus sp900128525	77.3866	97	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859465.1	s__Methyloprofundus sp014859465	77.0794	90	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016592635.1	s__Methyloprofundus sp016592635	77.0771	112	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960135.1	s__Methyloprofundus sp012960135	76.7837	56	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	98.32	97.92	0.84	0.80	9	-
GCA_013138595.1	s__Methyloprofundus sp013138595	76.2729	77	440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:16:28,050] [INFO] GTDB search result was written to GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 10:16:28,051] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:16:28,056] [INFO] DFAST_QC result json was written to GCA_913009515.1_SRR5469033_bin.84_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 10:16:28,056] [INFO] DFAST_QC completed!
[2023-06-28 10:16:28,056] [INFO] Total running time: 0h0m41s