[2024-01-24 11:12:39,850] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,856] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,857] [INFO] DQC Reference Directory: /var/lib/cwl/stg35fce0ee-7ef7-4b4a-a5da-c074cb15156c/dqc_reference
[2024-01-24 11:12:41,216] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:41,217] [INFO] Task started: Prodigal
[2024-01-24 11:12:41,217] [INFO] Running command: gunzip -c /var/lib/cwl/stgf876f512-5638-4c52-917a-552962aa0d60/GCF_002072955.1_ASM207295v1_genomic.fna.gz | prodigal -d GCF_002072955.1_ASM207295v1_genomic.fna/cds.fna -a GCF_002072955.1_ASM207295v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:50,443] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:50,443] [INFO] Task started: HMMsearch
[2024-01-24 11:12:50,443] [INFO] Running command: hmmsearch --tblout GCF_002072955.1_ASM207295v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35fce0ee-7ef7-4b4a-a5da-c074cb15156c/dqc_reference/reference_markers.hmm GCF_002072955.1_ASM207295v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:50,748] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:50,749] [INFO] Found 6/6 markers.
[2024-01-24 11:12:50,787] [INFO] Query marker FASTA was written to GCF_002072955.1_ASM207295v1_genomic.fna/markers.fasta
[2024-01-24 11:12:50,787] [INFO] Task started: Blastn
[2024-01-24 11:12:50,787] [INFO] Running command: blastn -query GCF_002072955.1_ASM207295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35fce0ee-7ef7-4b4a-a5da-c074cb15156c/dqc_reference/reference_markers.fasta -out GCF_002072955.1_ASM207295v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:51,427] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:51,431] [INFO] Selected 29 target genomes.
[2024-01-24 11:12:51,432] [INFO] Target genome list was writen to GCF_002072955.1_ASM207295v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:51,450] [INFO] Task started: fastANI
[2024-01-24 11:12:51,450] [INFO] Running command: fastANI --query /var/lib/cwl/stgf876f512-5638-4c52-917a-552962aa0d60/GCF_002072955.1_ASM207295v1_genomic.fna.gz --refList GCF_002072955.1_ASM207295v1_genomic.fna/target_genomes.txt --output GCF_002072955.1_ASM207295v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:11,875] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:11,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35fce0ee-7ef7-4b4a-a5da-c074cb15156c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:11,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35fce0ee-7ef7-4b4a-a5da-c074cb15156c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:11,880] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:11,881] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:11,881] [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	100.0	1428	1428	95	conclusive
Methylobacter tundripaludum	strain=SV96	GCA_000190755.3	173365	173365	type	True	77.2824	56	1428	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:11,884] [INFO] DFAST Taxonomy check result was written to GCF_002072955.1_ASM207295v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:11,884] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:11,884] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:11,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35fce0ee-7ef7-4b4a-a5da-c074cb15156c/dqc_reference/checkm_data
[2024-01-24 11:13:11,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:11,932] [INFO] Task started: CheckM
[2024-01-24 11:13:11,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002072955.1_ASM207295v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002072955.1_ASM207295v1_genomic.fna/checkm_input GCF_002072955.1_ASM207295v1_genomic.fna/checkm_result
[2024-01-24 11:13:44,153] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:44,155] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:44,178] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:44,178] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:44,179] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002072955.1_ASM207295v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:44,180] [INFO] Task started: Blastn
[2024-01-24 11:13:44,180] [INFO] Running command: blastn -query GCF_002072955.1_ASM207295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35fce0ee-7ef7-4b4a-a5da-c074cb15156c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002072955.1_ASM207295v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:45,373] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:45,378] [INFO] Selected 13 target genomes.
[2024-01-24 11:13:45,378] [INFO] Target genome list was writen to GCF_002072955.1_ASM207295v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:45,390] [INFO] Task started: fastANI
[2024-01-24 11:13:45,390] [INFO] Running command: fastANI --query /var/lib/cwl/stgf876f512-5638-4c52-917a-552962aa0d60/GCF_002072955.1_ASM207295v1_genomic.fna.gz --refList GCF_002072955.1_ASM207295v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002072955.1_ASM207295v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:56,152] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:56,169] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:56,169] [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	100.0	1428	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002189065.1	s__Methyloprofundus sp002189065	79.6763	465	1428	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	79.4379	441	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	98.32	97.92	0.84	0.80	9	-
GCA_014859465.1	s__Methyloprofundus sp014859465	78.4467	299	1428	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	78.2388	320	1428	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	78.1836	311	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013138555.1	s__Methyloprofundus sp013138555	78.149	279	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013138595.1	s__Methyloprofundus sp013138595	76.941	195	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938485.1	s__KS41 sp903938485	76.4355	63	1428	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.68	99.39	0.94	0.91	15	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:56,171] [INFO] GTDB search result was written to GCF_002072955.1_ASM207295v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:56,172] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:56,177] [INFO] DFAST_QC result json was written to GCF_002072955.1_ASM207295v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:56,177] [INFO] DFAST_QC completed!
[2024-01-24 11:13:56,177] [INFO] Total running time: 0h1m16s