[2024-01-24 13:18:55,260] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:55,261] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:55,262] [INFO] DQC Reference Directory: /var/lib/cwl/stg1868f0c2-fc24-4800-b0dc-759ccf729ce4/dqc_reference
[2024-01-24 13:18:56,593] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:56,594] [INFO] Task started: Prodigal
[2024-01-24 13:18:56,594] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c9e3483-fdec-487d-aee7-89bd212222c3/GCF_000012545.1_ASM1254v1_genomic.fna.gz | prodigal -d GCF_000012545.1_ASM1254v1_genomic.fna/cds.fna -a GCF_000012545.1_ASM1254v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:59,653] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:59,654] [INFO] Task started: HMMsearch
[2024-01-24 13:18:59,654] [INFO] Running command: hmmsearch --tblout GCF_000012545.1_ASM1254v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1868f0c2-fc24-4800-b0dc-759ccf729ce4/dqc_reference/reference_markers.hmm GCF_000012545.1_ASM1254v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:59,849] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:59,851] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg6c9e3483-fdec-487d-aee7-89bd212222c3/GCF_000012545.1_ASM1254v1_genomic.fna.gz]
[2024-01-24 13:18:59,876] [INFO] Query marker FASTA was written to GCF_000012545.1_ASM1254v1_genomic.fna/markers.fasta
[2024-01-24 13:18:59,877] [INFO] Task started: Blastn
[2024-01-24 13:18:59,877] [INFO] Running command: blastn -query GCF_000012545.1_ASM1254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1868f0c2-fc24-4800-b0dc-759ccf729ce4/dqc_reference/reference_markers.fasta -out GCF_000012545.1_ASM1254v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:00,391] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:00,395] [INFO] Selected 3 target genomes.
[2024-01-24 13:19:00,396] [INFO] Target genome list was writen to GCF_000012545.1_ASM1254v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:00,401] [INFO] Task started: fastANI
[2024-01-24 13:19:00,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c9e3483-fdec-487d-aee7-89bd212222c3/GCF_000012545.1_ASM1254v1_genomic.fna.gz --refList GCF_000012545.1_ASM1254v1_genomic.fna/target_genomes.txt --output GCF_000012545.1_ASM1254v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:01,673] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:01,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1868f0c2-fc24-4800-b0dc-759ccf729ce4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:01,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1868f0c2-fc24-4800-b0dc-759ccf729ce4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:01,679] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:01,679] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:01,679] [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
Methanosphaera stadtmanae	strain=DSM 3091	GCA_000012545.1	2317	2317	type	True	100.0	589	589	95	conclusive
Methanosphaera cuniculi	strain=DSM 4103	GCA_003149675.1	1077256	1077256	type	True	79.1998	247	589	95	below_threshold
Methanosphaera cuniculi	strain=1R-7	GCA_002287195.1	1077256	1077256	type	True	79.1043	263	589	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:01,681] [INFO] DFAST Taxonomy check result was written to GCF_000012545.1_ASM1254v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:01,681] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:01,682] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:01,682] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1868f0c2-fc24-4800-b0dc-759ccf729ce4/dqc_reference/checkm_data
[2024-01-24 13:19:01,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:01,704] [INFO] Task started: CheckM
[2024-01-24 13:19:01,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000012545.1_ASM1254v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000012545.1_ASM1254v1_genomic.fna/checkm_input GCF_000012545.1_ASM1254v1_genomic.fna/checkm_result
[2024-01-24 13:19:19,662] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:19,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:19,680] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:19,680] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:19,681] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000012545.1_ASM1254v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:19,681] [INFO] Task started: Blastn
[2024-01-24 13:19:19,681] [INFO] Running command: blastn -query GCF_000012545.1_ASM1254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1868f0c2-fc24-4800-b0dc-759ccf729ce4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000012545.1_ASM1254v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:20,206] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:20,209] [INFO] Selected 6 target genomes.
[2024-01-24 13:19:20,209] [INFO] Target genome list was writen to GCF_000012545.1_ASM1254v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:20,230] [INFO] Task started: fastANI
[2024-01-24 13:19:20,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c9e3483-fdec-487d-aee7-89bd212222c3/GCF_000012545.1_ASM1254v1_genomic.fna.gz --refList GCF_000012545.1_ASM1254v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000012545.1_ASM1254v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:23,065] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:23,072] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:23,072] [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_000012545.1	s__Methanosphaera stadtmanae	100.0	589	589	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera	95.0	99.82	99.70	0.99	0.98	6	conclusive
GCF_001729965.1	s__Methanosphaera sp001729965	81.5242	340	589	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782945.1	s__Methanosphaera sp900322125	80.1641	284	589	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera	95.0	97.80	97.01	0.80	0.75	4	-
GCF_003149675.1	s__Methanosphaera cuniculi	79.1629	249	589	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera	95.0	99.96	99.96	0.98	0.98	2	-
GCA_015062825.1	s__Methanosphaera stadtmanae_A	78.9519	245	589	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017431845.1	s__Methanosphaera sp017431845	78.9301	209	589	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:23,074] [INFO] GTDB search result was written to GCF_000012545.1_ASM1254v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:23,074] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:23,076] [INFO] DFAST_QC result json was written to GCF_000012545.1_ASM1254v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:23,077] [INFO] DFAST_QC completed!
[2024-01-24 13:19:23,077] [INFO] Total running time: 0h0m28s