[2024-01-24 11:05:28,286] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:28,292] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:28,292] [INFO] DQC Reference Directory: /var/lib/cwl/stgd96c0297-2757-4ee1-a70f-22fe1ec81baa/dqc_reference
[2024-01-24 11:05:29,655] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:29,655] [INFO] Task started: Prodigal
[2024-01-24 11:05:29,656] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ca14e18-fbd8-4786-b66c-bbf7b60219db/GCF_020685265.1_ASM2068526v1_genomic.fna.gz | prodigal -d GCF_020685265.1_ASM2068526v1_genomic.fna/cds.fna -a GCF_020685265.1_ASM2068526v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:34,156] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:34,156] [INFO] Task started: HMMsearch
[2024-01-24 11:05:34,157] [INFO] Running command: hmmsearch --tblout GCF_020685265.1_ASM2068526v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd96c0297-2757-4ee1-a70f-22fe1ec81baa/dqc_reference/reference_markers.hmm GCF_020685265.1_ASM2068526v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:34,366] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:34,368] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6ca14e18-fbd8-4786-b66c-bbf7b60219db/GCF_020685265.1_ASM2068526v1_genomic.fna.gz]
[2024-01-24 11:05:34,395] [INFO] Query marker FASTA was written to GCF_020685265.1_ASM2068526v1_genomic.fna/markers.fasta
[2024-01-24 11:05:34,395] [INFO] Task started: Blastn
[2024-01-24 11:05:34,396] [INFO] Running command: blastn -query GCF_020685265.1_ASM2068526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd96c0297-2757-4ee1-a70f-22fe1ec81baa/dqc_reference/reference_markers.fasta -out GCF_020685265.1_ASM2068526v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:34,917] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:34,923] [INFO] Selected 7 target genomes.
[2024-01-24 11:05:34,924] [INFO] Target genome list was writen to GCF_020685265.1_ASM2068526v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:34,927] [INFO] Task started: fastANI
[2024-01-24 11:05:34,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ca14e18-fbd8-4786-b66c-bbf7b60219db/GCF_020685265.1_ASM2068526v1_genomic.fna.gz --refList GCF_020685265.1_ASM2068526v1_genomic.fna/target_genomes.txt --output GCF_020685265.1_ASM2068526v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:39,654] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:39,655] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd96c0297-2757-4ee1-a70f-22fe1ec81baa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:39,655] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd96c0297-2757-4ee1-a70f-22fe1ec81baa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:39,660] [INFO] Found 3 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:05:39,660] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:39,660] [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
Methanimicrococcus blatticola	strain=PA	GCA_020685265.1	91560	91560	type	True	100.0	586	589	95	conclusive
Methanimicrococcus blatticola	strain=DSM 13328	GCA_004363215.1	91560	91560	type	True	99.9768	581	589	95	conclusive
Methanimicrococcus blatticola	strain=DSM 13328	GCA_020011555.1	91560	91560	type	True	99.9728	582	589	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 11:05:39,662] [INFO] DFAST Taxonomy check result was written to GCF_020685265.1_ASM2068526v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:39,662] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:39,662] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:39,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd96c0297-2757-4ee1-a70f-22fe1ec81baa/dqc_reference/checkm_data
[2024-01-24 11:05:39,664] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:39,685] [INFO] Task started: CheckM
[2024-01-24 11:05:39,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020685265.1_ASM2068526v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020685265.1_ASM2068526v1_genomic.fna/checkm_input GCF_020685265.1_ASM2068526v1_genomic.fna/checkm_result
[2024-01-24 11:06:00,417] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:00,418] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:00,478] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:00,478] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:00,478] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020685265.1_ASM2068526v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:00,479] [INFO] Task started: Blastn
[2024-01-24 11:06:00,479] [INFO] Running command: blastn -query GCF_020685265.1_ASM2068526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd96c0297-2757-4ee1-a70f-22fe1ec81baa/dqc_reference/reference_markers_gtdb.fasta -out GCF_020685265.1_ASM2068526v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:01,107] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:01,113] [INFO] Selected 9 target genomes.
[2024-01-24 11:06:01,113] [INFO] Target genome list was writen to GCF_020685265.1_ASM2068526v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:01,121] [INFO] Task started: fastANI
[2024-01-24 11:06:01,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ca14e18-fbd8-4786-b66c-bbf7b60219db/GCF_020685265.1_ASM2068526v1_genomic.fna.gz --refList GCF_020685265.1_ASM2068526v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020685265.1_ASM2068526v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:06,078] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:06,084] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:06,084] [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_004363215.1	s__Methanimicrococcus blatticola	99.9768	581	589	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanimicrococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009784005.1	s__Methanimicrococcus sp009784005	78.6738	236	589	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanimicrococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:06,085] [INFO] GTDB search result was written to GCF_020685265.1_ASM2068526v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:06,086] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:06,088] [INFO] DFAST_QC result json was written to GCF_020685265.1_ASM2068526v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:06,088] [INFO] DFAST_QC completed!
[2024-01-24 11:06:06,088] [INFO] Total running time: 0h0m38s