[2024-01-24 11:59:35,515] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:35,517] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:35,517] [INFO] DQC Reference Directory: /var/lib/cwl/stg86f6fdf1-027e-4a6c-8b24-a2da72acb8b8/dqc_reference
[2024-01-24 11:59:36,738] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:36,739] [INFO] Task started: Prodigal
[2024-01-24 11:59:36,740] [INFO] Running command: gunzip -c /var/lib/cwl/stg3bdedb4f-1b10-4820-905a-a9c7240e2575/GCF_002072215.1_ASM207221v1_genomic.fna.gz | prodigal -d GCF_002072215.1_ASM207221v1_genomic.fna/cds.fna -a GCF_002072215.1_ASM207221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:40,179] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:40,180] [INFO] Task started: HMMsearch
[2024-01-24 11:59:40,180] [INFO] Running command: hmmsearch --tblout GCF_002072215.1_ASM207221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86f6fdf1-027e-4a6c-8b24-a2da72acb8b8/dqc_reference/reference_markers.hmm GCF_002072215.1_ASM207221v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:40,435] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:40,436] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg3bdedb4f-1b10-4820-905a-a9c7240e2575/GCF_002072215.1_ASM207221v1_genomic.fna.gz]
[2024-01-24 11:59:40,459] [INFO] Query marker FASTA was written to GCF_002072215.1_ASM207221v1_genomic.fna/markers.fasta
[2024-01-24 11:59:40,460] [INFO] Task started: Blastn
[2024-01-24 11:59:40,460] [INFO] Running command: blastn -query GCF_002072215.1_ASM207221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86f6fdf1-027e-4a6c-8b24-a2da72acb8b8/dqc_reference/reference_markers.fasta -out GCF_002072215.1_ASM207221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:41,056] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:41,060] [INFO] Selected 6 target genomes.
[2024-01-24 11:59:41,060] [INFO] Target genome list was writen to GCF_002072215.1_ASM207221v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:41,084] [INFO] Task started: fastANI
[2024-01-24 11:59:41,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bdedb4f-1b10-4820-905a-a9c7240e2575/GCF_002072215.1_ASM207221v1_genomic.fna.gz --refList GCF_002072215.1_ASM207221v1_genomic.fna/target_genomes.txt --output GCF_002072215.1_ASM207221v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:45,026] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:45,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86f6fdf1-027e-4a6c-8b24-a2da72acb8b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:45,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86f6fdf1-027e-4a6c-8b24-a2da72acb8b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:45,036] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:59:45,036] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:45,037] [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 arboriphilus	strain=DH1	GCA_002072215.1	39441	39441	type	True	100.0	794	795	95	conclusive
Methanobrevibacter arboriphilus	strain=JCM 13429	GCA_001316345.1	39441	39441	type	True	99.4435	543	795	95	conclusive
Methanobrevibacter cuticularis	strain=DSM 11139	GCA_001639285.1	47311	47311	type	True	78.2981	336	795	95	below_threshold
Methanobrevibacter filiformis	strain=DSM 11501	GCA_001639265.1	55758	55758	type	True	76.9978	231	795	95	below_threshold
Methanobrevibacter woesei	strain=DSM 11979	GCA_003111605.1	190976	190976	type	True	76.3799	156	795	95	below_threshold
Methanobrevibacter gottschalkii	strain=DSM 11977	GCA_003814835.1	190974	190974	type	True	76.2403	136	795	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:45,038] [INFO] DFAST Taxonomy check result was written to GCF_002072215.1_ASM207221v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:45,039] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:45,039] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:45,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86f6fdf1-027e-4a6c-8b24-a2da72acb8b8/dqc_reference/checkm_data
[2024-01-24 11:59:45,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:45,065] [INFO] Task started: CheckM
[2024-01-24 11:59:45,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002072215.1_ASM207221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002072215.1_ASM207221v1_genomic.fna/checkm_input GCF_002072215.1_ASM207221v1_genomic.fna/checkm_result
[2024-01-24 12:00:05,547] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:05,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:05,568] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:05,568] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:05,568] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002072215.1_ASM207221v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:05,569] [INFO] Task started: Blastn
[2024-01-24 12:00:05,569] [INFO] Running command: blastn -query GCF_002072215.1_ASM207221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86f6fdf1-027e-4a6c-8b24-a2da72acb8b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002072215.1_ASM207221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:06,088] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:06,092] [INFO] Selected 7 target genomes.
[2024-01-24 12:00:06,092] [INFO] Target genome list was writen to GCF_002072215.1_ASM207221v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:06,101] [INFO] Task started: fastANI
[2024-01-24 12:00:06,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bdedb4f-1b10-4820-905a-a9c7240e2575/GCF_002072215.1_ASM207221v1_genomic.fna.gz --refList GCF_002072215.1_ASM207221v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002072215.1_ASM207221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:10,604] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:10,614] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:10,615] [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_002072215.1	s__Methanobrevibacter_C arboriphilus	100.0	794	795	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_C	95.0	99.72	99.72	0.99	0.99	2	conclusive
GCF_000513315.1	s__Methanobrevibacter_C arboriphilus_A	94.385	653	795	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_C	95.0	98.28	97.35	0.85	0.82	3	-
GCA_003315655.1	s__Methanobrevibacter_C sp003315655	80.3256	407	795	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009784145.1	s__Methanobrevibacter_C sp009784145	79.3148	258	795	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001639285.1	s__Methanobrevibacter_C cuticularis	78.3663	331	795	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009776495.1	s__Methanobrevibacter_C sp009776495	77.5535	156	795	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009777005.1	s__Methanobrevibacter_C sp009777005	77.1704	285	795	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:10,616] [INFO] GTDB search result was written to GCF_002072215.1_ASM207221v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:10,617] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:10,619] [INFO] DFAST_QC result json was written to GCF_002072215.1_ASM207221v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:10,619] [INFO] DFAST_QC completed!
[2024-01-24 12:00:10,619] [INFO] Total running time: 0h0m35s