[2023-06-28 12:01:00,787] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:01:00,789] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:01:00,789] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc156909-69e6-4620-a893-d77fff9c5783/dqc_reference
[2023-06-28 12:01:02,082] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:01:02,083] [INFO] Task started: Prodigal
[2023-06-28 12:01:02,083] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5e038ed-3a11-4dfe-a5ea-0e5d71c6c301/GCA_015062925.1_ASM1506292v1_genomic.fna.gz | prodigal -d GCA_015062925.1_ASM1506292v1_genomic.fna/cds.fna -a GCA_015062925.1_ASM1506292v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:01:05,714] [INFO] Task succeeded: Prodigal
[2023-06-28 12:01:05,716] [INFO] Task started: HMMsearch
[2023-06-28 12:01:05,716] [INFO] Running command: hmmsearch --tblout GCA_015062925.1_ASM1506292v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc156909-69e6-4620-a893-d77fff9c5783/dqc_reference/reference_markers.hmm GCA_015062925.1_ASM1506292v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:01:06,105] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:01:06,106] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb5e038ed-3a11-4dfe-a5ea-0e5d71c6c301/GCA_015062925.1_ASM1506292v1_genomic.fna.gz]
[2023-06-28 12:01:06,132] [INFO] Query marker FASTA was written to GCA_015062925.1_ASM1506292v1_genomic.fna/markers.fasta
[2023-06-28 12:01:06,132] [INFO] Task started: Blastn
[2023-06-28 12:01:06,132] [INFO] Running command: blastn -query GCA_015062925.1_ASM1506292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc156909-69e6-4620-a893-d77fff9c5783/dqc_reference/reference_markers.fasta -out GCA_015062925.1_ASM1506292v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:01:06,638] [INFO] Task succeeded: Blastn
[2023-06-28 12:01:06,642] [INFO] Selected 2 target genomes.
[2023-06-28 12:01:06,642] [INFO] Target genome list was writen to GCA_015062925.1_ASM1506292v1_genomic.fna/target_genomes.txt
[2023-06-28 12:01:06,644] [INFO] Task started: fastANI
[2023-06-28 12:01:06,644] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5e038ed-3a11-4dfe-a5ea-0e5d71c6c301/GCA_015062925.1_ASM1506292v1_genomic.fna.gz --refList GCA_015062925.1_ASM1506292v1_genomic.fna/target_genomes.txt --output GCA_015062925.1_ASM1506292v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:01:07,567] [INFO] Task succeeded: fastANI
[2023-06-28 12:01:07,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc156909-69e6-4620-a893-d77fff9c5783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:01:07,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc156909-69e6-4620-a893-d77fff9c5783/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:01:07,572] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:01:07,573] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:01:07,573] [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
Methanobrevibacter gottschalkii	strain=DSM 11977	GCA_003814835.1	190974	190974	type	True	79.7579	298	648	95	below_threshold
Methanobrevibacter millerae	strain=DSM 16643	GCA_900103415.1	230361	230361	type	True	78.0018	139	648	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:01:07,575] [INFO] DFAST Taxonomy check result was written to GCA_015062925.1_ASM1506292v1_genomic.fna/tc_result.tsv
[2023-06-28 12:01:07,575] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:01:07,576] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:01:07,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc156909-69e6-4620-a893-d77fff9c5783/dqc_reference/checkm_data
[2023-06-28 12:01:07,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:01:07,609] [INFO] Task started: CheckM
[2023-06-28 12:01:07,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015062925.1_ASM1506292v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015062925.1_ASM1506292v1_genomic.fna/checkm_input GCA_015062925.1_ASM1506292v1_genomic.fna/checkm_result
[2023-06-28 12:01:26,245] [INFO] Task succeeded: CheckM
[2023-06-28 12:01:26,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:01:26,268] [INFO] ===== Completeness check finished =====
[2023-06-28 12:01:26,268] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:01:26,269] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015062925.1_ASM1506292v1_genomic.fna/markers.fasta)
[2023-06-28 12:01:26,269] [INFO] Task started: Blastn
[2023-06-28 12:01:26,269] [INFO] Running command: blastn -query GCA_015062925.1_ASM1506292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc156909-69e6-4620-a893-d77fff9c5783/dqc_reference/reference_markers_gtdb.fasta -out GCA_015062925.1_ASM1506292v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:01:26,822] [INFO] Task succeeded: Blastn
[2023-06-28 12:01:26,829] [INFO] Selected 9 target genomes.
[2023-06-28 12:01:26,829] [INFO] Target genome list was writen to GCA_015062925.1_ASM1506292v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:01:26,836] [INFO] Task started: fastANI
[2023-06-28 12:01:26,836] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5e038ed-3a11-4dfe-a5ea-0e5d71c6c301/GCA_015062925.1_ASM1506292v1_genomic.fna.gz --refList GCA_015062925.1_ASM1506292v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015062925.1_ASM1506292v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:01:31,236] [INFO] Task succeeded: fastANI
[2023-06-28 12:01:31,250] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:01:31,250] [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_015062925.1	s__Methanobrevibacter_A thaueri_C	100.0	644	648	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902785855.1	s__Methanobrevibacter_A sp902785855	81.1613	303	648	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	97.27	97.27	0.75	0.75	2	-
GCA_900769095.1	s__Methanobrevibacter_A sp900769095	80.1258	191	648	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	99.12	98.84	0.74	0.68	3	-
GCA_017431965.1	s__Methanobrevibacter_A sp017431965	79.7684	241	648	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902764455.1	s__Methanobrevibacter_A sp902764455	79.7321	308	648	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017406825.1	s__Methanobrevibacter_A sp017406825	79.7144	221	648	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017427765.1	s__Methanobrevibacter_A sp017427765	79.6568	284	648	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782595.1	s__Methanobrevibacter_A sp902782595	78.8279	243	648	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017434555.1	s__Methanobrevibacter_A sp017434555	78.7383	221	648	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	98.09	97.80	0.83	0.83	3	-
--------------------------------------------------------------------------------
[2023-06-28 12:01:31,252] [INFO] GTDB search result was written to GCA_015062925.1_ASM1506292v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:01:31,253] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:01:31,256] [INFO] DFAST_QC result json was written to GCA_015062925.1_ASM1506292v1_genomic.fna/dqc_result.json
[2023-06-28 12:01:31,256] [INFO] DFAST_QC completed!
[2023-06-28 12:01:31,256] [INFO] Total running time: 0h0m30s