[2024-01-24 12:27:19,894] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:27:19,920] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:27:19,920] [INFO] DQC Reference Directory: /var/lib/cwl/stgf347cab4-8036-48c8-8100-4e9802b1082d/dqc_reference
[2024-01-24 12:27:21,131] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:27:21,132] [INFO] Task started: Prodigal
[2024-01-24 12:27:21,133] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb036408-c83f-438f-a0d0-55fa5f61d9f8/GCF_000147715.2_ASM14771v3_genomic.fna.gz | prodigal -d GCF_000147715.2_ASM14771v3_genomic.fna/cds.fna -a GCF_000147715.2_ASM14771v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:27:28,029] [INFO] Task succeeded: Prodigal
[2024-01-24 12:27:28,030] [INFO] Task started: HMMsearch
[2024-01-24 12:27:28,030] [INFO] Running command: hmmsearch --tblout GCF_000147715.2_ASM14771v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf347cab4-8036-48c8-8100-4e9802b1082d/dqc_reference/reference_markers.hmm GCF_000147715.2_ASM14771v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:27:28,277] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:27:28,279] [INFO] Found 6/6 markers.
[2024-01-24 12:27:28,307] [INFO] Query marker FASTA was written to GCF_000147715.2_ASM14771v3_genomic.fna/markers.fasta
[2024-01-24 12:27:28,308] [INFO] Task started: Blastn
[2024-01-24 12:27:28,308] [INFO] Running command: blastn -query GCF_000147715.2_ASM14771v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgf347cab4-8036-48c8-8100-4e9802b1082d/dqc_reference/reference_markers.fasta -out GCF_000147715.2_ASM14771v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:27:28,878] [INFO] Task succeeded: Blastn
[2024-01-24 12:27:28,882] [INFO] Selected 8 target genomes.
[2024-01-24 12:27:28,883] [INFO] Target genome list was writen to GCF_000147715.2_ASM14771v3_genomic.fna/target_genomes.txt
[2024-01-24 12:27:28,918] [INFO] Task started: fastANI
[2024-01-24 12:27:28,918] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb036408-c83f-438f-a0d0-55fa5f61d9f8/GCF_000147715.2_ASM14771v3_genomic.fna.gz --refList GCF_000147715.2_ASM14771v3_genomic.fna/target_genomes.txt --output GCF_000147715.2_ASM14771v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:27:33,707] [INFO] Task succeeded: fastANI
[2024-01-24 12:27:33,708] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf347cab4-8036-48c8-8100-4e9802b1082d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:27:33,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf347cab4-8036-48c8-8100-4e9802b1082d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:27:33,715] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:27:33,716] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:27:33,716] [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
Mesotoga prima	strain=MesG1.Ag.4.2	GCA_000147715.3	1184387	1184387	type	True	100.0	974	991	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:27:33,717] [INFO] DFAST Taxonomy check result was written to GCF_000147715.2_ASM14771v3_genomic.fna/tc_result.tsv
[2024-01-24 12:27:33,718] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:27:33,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:27:33,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf347cab4-8036-48c8-8100-4e9802b1082d/dqc_reference/checkm_data
[2024-01-24 12:27:33,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:27:33,753] [INFO] Task started: CheckM
[2024-01-24 12:27:33,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000147715.2_ASM14771v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000147715.2_ASM14771v3_genomic.fna/checkm_input GCF_000147715.2_ASM14771v3_genomic.fna/checkm_result
[2024-01-24 12:28:00,460] [INFO] Task succeeded: CheckM
[2024-01-24 12:28:00,461] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:28:00,490] [INFO] ===== Completeness check finished =====
[2024-01-24 12:28:00,490] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:28:00,491] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000147715.2_ASM14771v3_genomic.fna/markers.fasta)
[2024-01-24 12:28:00,491] [INFO] Task started: Blastn
[2024-01-24 12:28:00,491] [INFO] Running command: blastn -query GCF_000147715.2_ASM14771v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgf347cab4-8036-48c8-8100-4e9802b1082d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000147715.2_ASM14771v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:01,307] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:01,311] [INFO] Selected 13 target genomes.
[2024-01-24 12:28:01,311] [INFO] Target genome list was writen to GCF_000147715.2_ASM14771v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:28:01,448] [INFO] Task started: fastANI
[2024-01-24 12:28:01,448] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb036408-c83f-438f-a0d0-55fa5f61d9f8/GCF_000147715.2_ASM14771v3_genomic.fna.gz --refList GCF_000147715.2_ASM14771v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000147715.2_ASM14771v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:28:07,983] [INFO] Task succeeded: fastANI
[2024-01-24 12:28:07,995] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:28:07,995] [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_000147715.2	s__Mesotoga prima	100.0	978	991	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga	95.0	97.16	96.75	0.87	0.85	6	conclusive
GCA_016933635.1	s__Mesotoga sp016933635	89.9066	474	991	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664995.1	s__Mesotoga sp003664995	85.3187	536	991	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga	95.0	98.98	98.98	0.91	0.91	2	-
GCA_011045915.1	s__Mesotoga infera_D	81.6212	347	991	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002752635.1	s__Mesotoga sp002752635	80.7419	409	991	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga	95.0	98.07	97.29	0.90	0.81	15	-
GCA_002305955.1	s__Mesotoga sp002305955	78.0739	104	991	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Kosmotogaceae;g__Mesotoga	95.0	99.56	99.32	0.86	0.77	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:28:07,997] [INFO] GTDB search result was written to GCF_000147715.2_ASM14771v3_genomic.fna/result_gtdb.tsv
[2024-01-24 12:28:07,998] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:28:08,001] [INFO] DFAST_QC result json was written to GCF_000147715.2_ASM14771v3_genomic.fna/dqc_result.json
[2024-01-24 12:28:08,001] [INFO] DFAST_QC completed!
[2024-01-24 12:28:08,001] [INFO] Total running time: 0h0m48s