[2023-07-01 03:19:15,906] [INFO] DFAST_QC pipeline started.
[2023-07-01 03:19:15,909] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 03:19:15,909] [INFO] DQC Reference Directory: /var/lib/cwl/stg9613e7df-49cb-42ae-98a7-715a61132945/dqc_reference
[2023-07-01 03:19:18,064] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 03:19:18,065] [INFO] Task started: Prodigal
[2023-07-01 03:19:18,066] [INFO] Running command: gunzip -c /var/lib/cwl/stg405db54a-3717-4d31-8d8a-40aa48174aa9/GCA_016222945.1_ASM1622294v1_genomic.fna.gz | prodigal -d GCA_016222945.1_ASM1622294v1_genomic.fna/cds.fna -a GCA_016222945.1_ASM1622294v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 03:19:22,256] [INFO] Task succeeded: Prodigal
[2023-07-01 03:19:22,256] [INFO] Task started: HMMsearch
[2023-07-01 03:19:22,256] [INFO] Running command: hmmsearch --tblout GCA_016222945.1_ASM1622294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9613e7df-49cb-42ae-98a7-715a61132945/dqc_reference/reference_markers.hmm GCA_016222945.1_ASM1622294v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 03:19:22,459] [INFO] Task succeeded: HMMsearch
[2023-07-01 03:19:22,461] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg405db54a-3717-4d31-8d8a-40aa48174aa9/GCA_016222945.1_ASM1622294v1_genomic.fna.gz]
[2023-07-01 03:19:22,507] [INFO] Query marker FASTA was written to GCA_016222945.1_ASM1622294v1_genomic.fna/markers.fasta
[2023-07-01 03:19:22,508] [INFO] Task started: Blastn
[2023-07-01 03:19:22,508] [INFO] Running command: blastn -query GCA_016222945.1_ASM1622294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9613e7df-49cb-42ae-98a7-715a61132945/dqc_reference/reference_markers.fasta -out GCA_016222945.1_ASM1622294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:19:23,580] [INFO] Task succeeded: Blastn
[2023-07-01 03:19:23,584] [INFO] Selected 1 target genomes.
[2023-07-01 03:19:23,585] [INFO] Target genome list was writen to GCA_016222945.1_ASM1622294v1_genomic.fna/target_genomes.txt
[2023-07-01 03:19:23,588] [INFO] Task started: fastANI
[2023-07-01 03:19:23,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg405db54a-3717-4d31-8d8a-40aa48174aa9/GCA_016222945.1_ASM1622294v1_genomic.fna.gz --refList GCA_016222945.1_ASM1622294v1_genomic.fna/target_genomes.txt --output GCA_016222945.1_ASM1622294v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 03:19:24,404] [INFO] Task succeeded: fastANI
[2023-07-01 03:19:24,405] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9613e7df-49cb-42ae-98a7-715a61132945/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 03:19:24,405] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9613e7df-49cb-42ae-98a7-715a61132945/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 03:19:24,411] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 03:19:24,411] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 03:19:24,411] [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 bryantii	strain=M.o.H.	GCA_002287175.1	2161	2161	type	True	78.7917	323	748	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 03:19:24,414] [INFO] DFAST Taxonomy check result was written to GCA_016222945.1_ASM1622294v1_genomic.fna/tc_result.tsv
[2023-07-01 03:19:24,415] [INFO] ===== Taxonomy check completed =====
[2023-07-01 03:19:24,415] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 03:19:24,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9613e7df-49cb-42ae-98a7-715a61132945/dqc_reference/checkm_data
[2023-07-01 03:19:24,417] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 03:19:24,443] [INFO] Task started: CheckM
[2023-07-01 03:19:24,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016222945.1_ASM1622294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016222945.1_ASM1622294v1_genomic.fna/checkm_input GCA_016222945.1_ASM1622294v1_genomic.fna/checkm_result
[2023-07-01 03:19:46,826] [INFO] Task succeeded: CheckM
[2023-07-01 03:19:46,828] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 03:19:46,848] [INFO] ===== Completeness check finished =====
[2023-07-01 03:19:46,849] [INFO] ===== Start GTDB Search =====
[2023-07-01 03:19:46,849] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016222945.1_ASM1622294v1_genomic.fna/markers.fasta)
[2023-07-01 03:19:46,849] [INFO] Task started: Blastn
[2023-07-01 03:19:46,849] [INFO] Running command: blastn -query GCA_016222945.1_ASM1622294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9613e7df-49cb-42ae-98a7-715a61132945/dqc_reference/reference_markers_gtdb.fasta -out GCA_016222945.1_ASM1622294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:19:47,411] [INFO] Task succeeded: Blastn
[2023-07-01 03:19:47,416] [INFO] Selected 6 target genomes.
[2023-07-01 03:19:47,416] [INFO] Target genome list was writen to GCA_016222945.1_ASM1622294v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 03:19:47,422] [INFO] Task started: fastANI
[2023-07-01 03:19:47,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg405db54a-3717-4d31-8d8a-40aa48174aa9/GCA_016222945.1_ASM1622294v1_genomic.fna.gz --refList GCA_016222945.1_ASM1622294v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016222945.1_ASM1622294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 03:19:50,614] [INFO] Task succeeded: fastANI
[2023-07-01 03:19:50,625] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 03:19:50,625] [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_016222945.1	s__Methanobacterium_D sp016222945	100.0	747	748	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002287175.1	s__Methanobacterium_D bryantii	78.7917	323	748	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_D	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002509665.1	s__Methanobacterium_D sp002509665	78.2549	255	748	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002839705.1	s__UBA349 sp002839705	77.3852	95	748	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__UBA349	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744455.1	s__Methanobacterium_B sp000744455	76.7776	108	748	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_B	95.0	97.99	97.99	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-07-01 03:19:50,627] [INFO] GTDB search result was written to GCA_016222945.1_ASM1622294v1_genomic.fna/result_gtdb.tsv
[2023-07-01 03:19:50,628] [INFO] ===== GTDB Search completed =====
[2023-07-01 03:19:50,631] [INFO] DFAST_QC result json was written to GCA_016222945.1_ASM1622294v1_genomic.fna/dqc_result.json
[2023-07-01 03:19:50,631] [INFO] DFAST_QC completed!
[2023-07-01 03:19:50,632] [INFO] Total running time: 0h0m35s