[2024-01-25 18:54:20,564] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:20,566] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:20,566] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf3ee067-328f-48aa-ac22-63980da58209/dqc_reference
[2024-01-25 18:54:21,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:21,679] [INFO] Task started: Prodigal
[2024-01-25 18:54:21,679] [INFO] Running command: gunzip -c /var/lib/cwl/stg46f995ba-a4d4-4967-a9e8-388b60d37bf9/GCF_002287175.1_ASM228717v1_genomic.fna.gz | prodigal -d GCF_002287175.1_ASM228717v1_genomic.fna/cds.fna -a GCF_002287175.1_ASM228717v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:27,168] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:27,169] [INFO] Task started: HMMsearch
[2024-01-25 18:54:27,169] [INFO] Running command: hmmsearch --tblout GCF_002287175.1_ASM228717v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf3ee067-328f-48aa-ac22-63980da58209/dqc_reference/reference_markers.hmm GCF_002287175.1_ASM228717v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:27,363] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:27,368] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg46f995ba-a4d4-4967-a9e8-388b60d37bf9/GCF_002287175.1_ASM228717v1_genomic.fna.gz]
[2024-01-25 18:54:27,395] [INFO] Query marker FASTA was written to GCF_002287175.1_ASM228717v1_genomic.fna/markers.fasta
[2024-01-25 18:54:27,395] [INFO] Task started: Blastn
[2024-01-25 18:54:27,395] [INFO] Running command: blastn -query GCF_002287175.1_ASM228717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf3ee067-328f-48aa-ac22-63980da58209/dqc_reference/reference_markers.fasta -out GCF_002287175.1_ASM228717v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:27,843] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:27,846] [INFO] Selected 2 target genomes.
[2024-01-25 18:54:27,846] [INFO] Target genome list was writen to GCF_002287175.1_ASM228717v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:27,851] [INFO] Task started: fastANI
[2024-01-25 18:54:27,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg46f995ba-a4d4-4967-a9e8-388b60d37bf9/GCF_002287175.1_ASM228717v1_genomic.fna.gz --refList GCF_002287175.1_ASM228717v1_genomic.fna/target_genomes.txt --output GCF_002287175.1_ASM228717v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:29,581] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:29,582] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf3ee067-328f-48aa-ac22-63980da58209/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:29,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf3ee067-328f-48aa-ac22-63980da58209/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:29,586] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:54:29,586] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:54:29,586] [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	100.0	1139	1141	95	conclusive
Methanobacterium paludis	strain=SWAN1	GCA_000214725.1	868131	868131	type	True	76.9051	120	1141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:29,590] [INFO] DFAST Taxonomy check result was written to GCF_002287175.1_ASM228717v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:29,591] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:29,591] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:29,591] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf3ee067-328f-48aa-ac22-63980da58209/dqc_reference/checkm_data
[2024-01-25 18:54:29,592] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:29,626] [INFO] Task started: CheckM
[2024-01-25 18:54:29,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002287175.1_ASM228717v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002287175.1_ASM228717v1_genomic.fna/checkm_input GCF_002287175.1_ASM228717v1_genomic.fna/checkm_result
[2024-01-25 18:54:51,511] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:51,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.76%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:51,541] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:51,541] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:51,542] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002287175.1_ASM228717v1_genomic.fna/markers.fasta)
[2024-01-25 18:54:51,542] [INFO] Task started: Blastn
[2024-01-25 18:54:51,542] [INFO] Running command: blastn -query GCF_002287175.1_ASM228717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf3ee067-328f-48aa-ac22-63980da58209/dqc_reference/reference_markers_gtdb.fasta -out GCF_002287175.1_ASM228717v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:52,046] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:52,049] [INFO] Selected 6 target genomes.
[2024-01-25 18:54:52,049] [INFO] Target genome list was writen to GCF_002287175.1_ASM228717v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:52,057] [INFO] Task started: fastANI
[2024-01-25 18:54:52,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg46f995ba-a4d4-4967-a9e8-388b60d37bf9/GCF_002287175.1_ASM228717v1_genomic.fna.gz --refList GCF_002287175.1_ASM228717v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002287175.1_ASM228717v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:56,509] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:56,515] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:56,515] [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_002287175.1	s__Methanobacterium_D bryantii	100.0	1139	1141	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_D	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_000745485.1	s__Methanobacterium_D veterum	93.1544	928	1141	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobacterium_D	95.0	99.98	99.98	0.99	0.99	2	-
GCA_002509665.1	s__Methanobacterium_D sp002509665	88.7784	642	1141	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_016222945.1	s__Methanobacterium_D sp016222945	78.6442	323	1141	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_003491285.1	s__UBA117 sp002494785	76.708	109	1141	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__UBA117	95.0	99.40	99.40	0.95	0.95	2	-
GCA_016874685.1	s__VGTM01 sp016874685	76.6225	91	1141	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__VGTM01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:54:56,517] [INFO] GTDB search result was written to GCF_002287175.1_ASM228717v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:56,518] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:56,521] [INFO] DFAST_QC result json was written to GCF_002287175.1_ASM228717v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:56,521] [INFO] DFAST_QC completed!
[2024-01-25 18:54:56,521] [INFO] Total running time: 0h0m36s