[2024-01-24 11:13:49,258] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:49,261] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:49,261] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9d2f52b-a325-4b1f-ad42-0c3c961a6eef/dqc_reference
[2024-01-24 11:13:50,476] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:50,476] [INFO] Task started: Prodigal
[2024-01-24 11:13:50,477] [INFO] Running command: gunzip -c /var/lib/cwl/stgb505f50f-a8ed-4369-8a21-ebcbf2dcb343/GCF_019931065.1_ASM1993106v1_genomic.fna.gz | prodigal -d GCF_019931065.1_ASM1993106v1_genomic.fna/cds.fna -a GCF_019931065.1_ASM1993106v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:55,503] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:55,503] [INFO] Task started: HMMsearch
[2024-01-24 11:13:55,503] [INFO] Running command: hmmsearch --tblout GCF_019931065.1_ASM1993106v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9d2f52b-a325-4b1f-ad42-0c3c961a6eef/dqc_reference/reference_markers.hmm GCF_019931065.1_ASM1993106v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:55,714] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:55,716] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb505f50f-a8ed-4369-8a21-ebcbf2dcb343/GCF_019931065.1_ASM1993106v1_genomic.fna.gz]
[2024-01-24 11:13:55,741] [INFO] Query marker FASTA was written to GCF_019931065.1_ASM1993106v1_genomic.fna/markers.fasta
[2024-01-24 11:13:55,742] [INFO] Task started: Blastn
[2024-01-24 11:13:55,742] [INFO] Running command: blastn -query GCF_019931065.1_ASM1993106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9d2f52b-a325-4b1f-ad42-0c3c961a6eef/dqc_reference/reference_markers.fasta -out GCF_019931065.1_ASM1993106v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:56,242] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:56,245] [INFO] Selected 3 target genomes.
[2024-01-24 11:13:56,246] [INFO] Target genome list was writen to GCF_019931065.1_ASM1993106v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:56,248] [INFO] Task started: fastANI
[2024-01-24 11:13:56,249] [INFO] Running command: fastANI --query /var/lib/cwl/stgb505f50f-a8ed-4369-8a21-ebcbf2dcb343/GCF_019931065.1_ASM1993106v1_genomic.fna.gz --refList GCF_019931065.1_ASM1993106v1_genomic.fna/target_genomes.txt --output GCF_019931065.1_ASM1993106v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:57,732] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:57,733] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9d2f52b-a325-4b1f-ad42-0c3c961a6eef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:57,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9d2f52b-a325-4b1f-ad42-0c3c961a6eef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:57,742] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:57,743] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:57,743] [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
Methanobacterium aggregans	strain=DSM 29428	GCA_017874455.1	1615586	1615586	type	True	77.7689	149	876	95	below_threshold
Methanobacterium bryantii	strain=M.o.H.	GCA_002287175.1	2161	2161	type	True	76.6245	116	876	95	below_threshold
Methanobrevibacter arboriphilus	strain=DH1	GCA_002072215.1	39441	39441	type	True	75.6361	52	876	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:57,745] [INFO] DFAST Taxonomy check result was written to GCF_019931065.1_ASM1993106v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:57,746] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:57,746] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:57,746] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9d2f52b-a325-4b1f-ad42-0c3c961a6eef/dqc_reference/checkm_data
[2024-01-24 11:13:57,748] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:57,781] [INFO] Task started: CheckM
[2024-01-24 11:13:57,781] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019931065.1_ASM1993106v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019931065.1_ASM1993106v1_genomic.fna/checkm_input GCF_019931065.1_ASM1993106v1_genomic.fna/checkm_result
[2024-01-24 11:14:19,351] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:19,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:19,366] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:19,367] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:19,367] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019931065.1_ASM1993106v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:19,367] [INFO] Task started: Blastn
[2024-01-24 11:14:19,368] [INFO] Running command: blastn -query GCF_019931065.1_ASM1993106v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9d2f52b-a325-4b1f-ad42-0c3c961a6eef/dqc_reference/reference_markers_gtdb.fasta -out GCF_019931065.1_ASM1993106v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:19,886] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:19,890] [INFO] Selected 6 target genomes.
[2024-01-24 11:14:19,890] [INFO] Target genome list was writen to GCF_019931065.1_ASM1993106v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:19,896] [INFO] Task started: fastANI
[2024-01-24 11:14:19,897] [INFO] Running command: fastANI --query /var/lib/cwl/stgb505f50f-a8ed-4369-8a21-ebcbf2dcb343/GCF_019931065.1_ASM1993106v1_genomic.fna.gz --refList GCF_019931065.1_ASM1993106v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019931065.1_ASM1993106v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:23,070] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:23,082] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:23,082] [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_000744455.1	s__Methanobacterium_B sp000744455	95.0391	685	876	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_B	95.0	97.99	97.99	0.89	0.89	2	conclusive
GCA_003162655.1	s__Methanobacterium_B sp003162655	80.7066	233	876	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151535.1	s__Methanobacterium_B sp003151535	80.145	401	876	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003162115.1	s__Methanobacterium_B sp003162115	80.1379	349	876	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_B	95.0	99.36	99.21	0.89	0.88	3	-
GCA_003158115.1	s__Methanobacterium_B sp003158115	80.0949	344	876	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_B	95.0	99.56	99.27	0.91	0.90	5	-
GCA_003164415.1	s__Methanobacterium_B sp003164415	78.776	275	876	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:23,084] [INFO] GTDB search result was written to GCF_019931065.1_ASM1993106v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:23,085] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:23,089] [INFO] DFAST_QC result json was written to GCF_019931065.1_ASM1993106v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:23,089] [INFO] DFAST_QC completed!
[2024-01-24 11:14:23,090] [INFO] Total running time: 0h0m34s