[2024-01-24 13:32:42,458] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:42,459] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:42,460] [INFO] DQC Reference Directory: /var/lib/cwl/stgf13e7154-6fb8-47c2-8778-cdd87151365d/dqc_reference
[2024-01-24 13:32:43,794] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:43,795] [INFO] Task started: Prodigal
[2024-01-24 13:32:43,796] [INFO] Running command: gunzip -c /var/lib/cwl/stgefa209be-3c65-4959-ac56-549f67c764c8/GCF_000320505.1_ASM32050v2_genomic.fna.gz | prodigal -d GCF_000320505.1_ASM32050v2_genomic.fna/cds.fna -a GCF_000320505.1_ASM32050v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:47,168] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:47,168] [INFO] Task started: HMMsearch
[2024-01-24 13:32:47,168] [INFO] Running command: hmmsearch --tblout GCF_000320505.1_ASM32050v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf13e7154-6fb8-47c2-8778-cdd87151365d/dqc_reference/reference_markers.hmm GCF_000320505.1_ASM32050v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:47,321] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:47,323] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgefa209be-3c65-4959-ac56-549f67c764c8/GCF_000320505.1_ASM32050v2_genomic.fna.gz]
[2024-01-24 13:32:47,346] [INFO] Query marker FASTA was written to GCF_000320505.1_ASM32050v2_genomic.fna/markers.fasta
[2024-01-24 13:32:47,346] [INFO] Task started: Blastn
[2024-01-24 13:32:47,347] [INFO] Running command: blastn -query GCF_000320505.1_ASM32050v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf13e7154-6fb8-47c2-8778-cdd87151365d/dqc_reference/reference_markers.fasta -out GCF_000320505.1_ASM32050v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:47,836] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:47,839] [INFO] Selected 3 target genomes.
[2024-01-24 13:32:47,839] [INFO] Target genome list was writen to GCF_000320505.1_ASM32050v2_genomic.fna/target_genomes.txt
[2024-01-24 13:32:47,866] [INFO] Task started: fastANI
[2024-01-24 13:32:47,866] [INFO] Running command: fastANI --query /var/lib/cwl/stgefa209be-3c65-4959-ac56-549f67c764c8/GCF_000320505.1_ASM32050v2_genomic.fna.gz --refList GCF_000320505.1_ASM32050v2_genomic.fna/target_genomes.txt --output GCF_000320505.1_ASM32050v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:49,505] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:49,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf13e7154-6fb8-47c2-8778-cdd87151365d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:49,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf13e7154-6fb8-47c2-8778-cdd87151365d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:49,512] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:49,512] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:49,512] [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 boviskoreani	strain=JH1	GCA_000320505.2	1348249	1348249	type	True	100.0	657	659	95	conclusive
Methanobrevibacter wolinii	strain=SH	GCA_000621965.1	190977	190977	type	True	80.1069	343	659	95	below_threshold
Methanobrevibacter cuticularis	strain=DSM 11139	GCA_001639285.1	47311	47311	type	True	76.1365	79	659	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:49,514] [INFO] DFAST Taxonomy check result was written to GCF_000320505.1_ASM32050v2_genomic.fna/tc_result.tsv
[2024-01-24 13:32:49,514] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:49,514] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:49,514] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf13e7154-6fb8-47c2-8778-cdd87151365d/dqc_reference/checkm_data
[2024-01-24 13:32:49,515] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:49,537] [INFO] Task started: CheckM
[2024-01-24 13:32:49,537] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000320505.1_ASM32050v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000320505.1_ASM32050v2_genomic.fna/checkm_input GCF_000320505.1_ASM32050v2_genomic.fna/checkm_result
[2024-01-24 13:33:06,615] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:06,617] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:06,633] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:06,633] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:06,634] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000320505.1_ASM32050v2_genomic.fna/markers.fasta)
[2024-01-24 13:33:06,634] [INFO] Task started: Blastn
[2024-01-24 13:33:06,634] [INFO] Running command: blastn -query GCF_000320505.1_ASM32050v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf13e7154-6fb8-47c2-8778-cdd87151365d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000320505.1_ASM32050v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:07,156] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:07,167] [INFO] Selected 8 target genomes.
[2024-01-24 13:33:07,167] [INFO] Target genome list was writen to GCF_000320505.1_ASM32050v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:07,175] [INFO] Task started: fastANI
[2024-01-24 13:33:07,175] [INFO] Running command: fastANI --query /var/lib/cwl/stgefa209be-3c65-4959-ac56-549f67c764c8/GCF_000320505.1_ASM32050v2_genomic.fna.gz --refList GCF_000320505.1_ASM32050v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000320505.1_ASM32050v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:10,447] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:10,454] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:10,455] [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_000320505.1	s__Methanobrevibacter_B boviskoreani	100.0	657	659	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_B	95.0	98.28	97.74	0.94	0.93	6	conclusive
GCF_000621965.1	s__Methanobrevibacter_B wolinii	80.1401	340	659	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002208625.1	s__Methanobrevibacter_B sp002208625	79.9803	268	659	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314605.1	s__Methanobrevibacter_B sp900314605	78.7114	252	659	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_B	95.0	99.22	98.80	0.88	0.84	11	-
GCA_015062915.1	s__Methanobrevibacter_A thaueri_B	77.1061	67	659	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_900313645.1	s__Methanobrevibacter_A sp900313645	76.6114	57	659	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	98.96	97.91	0.87	0.75	3	-
GCA_017410345.1	s__Methanobrevibacter sp017410345	76.4625	88	659	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:10,456] [INFO] GTDB search result was written to GCF_000320505.1_ASM32050v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:10,457] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:10,459] [INFO] DFAST_QC result json was written to GCF_000320505.1_ASM32050v2_genomic.fna/dqc_result.json
[2024-01-24 13:33:10,459] [INFO] DFAST_QC completed!
[2024-01-24 13:33:10,459] [INFO] Total running time: 0h0m28s