[2023-06-29 14:46:25,717] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:46:25,719] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:46:25,719] [INFO] DQC Reference Directory: /var/lib/cwl/stg898203d5-5845-4494-aa8a-05a04f458d33/dqc_reference
[2023-06-29 14:46:26,893] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:46:26,893] [INFO] Task started: Prodigal
[2023-06-29 14:46:26,894] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3df5506-bcd4-4ff5-9ea3-10c3a54116af/GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:46:30,668] [INFO] Task succeeded: Prodigal
[2023-06-29 14:46:30,668] [INFO] Task started: HMMsearch
[2023-06-29 14:46:30,668] [INFO] Running command: hmmsearch --tblout GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg898203d5-5845-4494-aa8a-05a04f458d33/dqc_reference/reference_markers.hmm GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:46:30,818] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:46:30,819] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgf3df5506-bcd4-4ff5-9ea3-10c3a54116af/GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-29 14:46:30,841] [INFO] Query marker FASTA was written to GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 14:46:30,841] [INFO] Task started: Blastn
[2023-06-29 14:46:30,841] [INFO] Running command: blastn -query GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg898203d5-5845-4494-aa8a-05a04f458d33/dqc_reference/reference_markers.fasta -out GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:46:31,306] [INFO] Task succeeded: Blastn
[2023-06-29 14:46:31,309] [INFO] Selected 2 target genomes.
[2023-06-29 14:46:31,310] [INFO] Target genome list was writen to GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 14:46:31,311] [INFO] Task started: fastANI
[2023-06-29 14:46:31,311] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3df5506-bcd4-4ff5-9ea3-10c3a54116af/GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:46:32,316] [INFO] Task succeeded: fastANI
[2023-06-29 14:46:32,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg898203d5-5845-4494-aa8a-05a04f458d33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:46:32,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg898203d5-5845-4494-aa8a-05a04f458d33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:46:32,321] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:46:32,321] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:46:32,321] [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	86.9787	408	496	95	below_threshold
Methanobacterium bryantii	strain=M.o.H.	GCA_002287175.1	2161	2161	type	True	76.3015	59	496	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:46:32,323] [INFO] DFAST Taxonomy check result was written to GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 14:46:32,324] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:46:32,324] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:46:32,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg898203d5-5845-4494-aa8a-05a04f458d33/dqc_reference/checkm_data
[2023-06-29 14:46:32,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:46:32,349] [INFO] Task started: CheckM
[2023-06-29 14:46:32,349] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 14:46:51,938] [INFO] Task succeeded: CheckM
[2023-06-29 14:46:51,939] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.56%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:46:51,959] [INFO] ===== Completeness check finished =====
[2023-06-29 14:46:51,959] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:46:51,960] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 14:46:51,960] [INFO] Task started: Blastn
[2023-06-29 14:46:51,960] [INFO] Running command: blastn -query GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg898203d5-5845-4494-aa8a-05a04f458d33/dqc_reference/reference_markers_gtdb.fasta -out GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:46:52,393] [INFO] Task succeeded: Blastn
[2023-06-29 14:46:52,397] [INFO] Selected 5 target genomes.
[2023-06-29 14:46:52,398] [INFO] Target genome list was writen to GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:46:52,424] [INFO] Task started: fastANI
[2023-06-29 14:46:52,425] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3df5506-bcd4-4ff5-9ea3-10c3a54116af/GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:46:55,127] [INFO] Task succeeded: fastANI
[2023-06-29 14:46:55,133] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:46:55,133] [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_900095295.1	s__Methanobacterium_C congolense	95.5103	435	496	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_C	95.0	95.90	95.90	0.92	0.92	2	conclusive
GCF_017874455.1	s__Methanobacterium_C aggregans	86.9787	408	496	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002498385.1	s__Methanobacterium_C sp002498385	77.8321	153	496	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_C	95.0	99.69	99.35	0.95	0.90	18	-
GCF_000744455.1	s__Methanobacterium_B sp000744455	77.219	76	496	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_B	95.0	97.99	97.99	0.89	0.89	2	-
GCF_000745485.1	s__Methanobacterium_D veterum	76.7559	53	496	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_D	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-29 14:46:55,135] [INFO] GTDB search result was written to GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 14:46:55,136] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:46:55,139] [INFO] DFAST_QC result json was written to GCA_937893005.1_SRR1562003_bin.96_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 14:46:55,139] [INFO] DFAST_QC completed!
[2023-06-29 14:46:55,139] [INFO] Total running time: 0h0m29s