[2024-01-24 11:43:50,649] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:50,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:50,652] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7c4d2e9-cd41-472f-86cb-0c77f710d9bf/dqc_reference
[2024-01-24 11:43:51,871] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:51,872] [INFO] Task started: Prodigal
[2024-01-24 11:43:51,872] [INFO] Running command: gunzip -c /var/lib/cwl/stg58aeee03-61d1-4c05-8dad-d7821c0b5df7/GCF_004363215.1_ASM436321v1_genomic.fna.gz | prodigal -d GCF_004363215.1_ASM436321v1_genomic.fna/cds.fna -a GCF_004363215.1_ASM436321v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:56,588] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:56,589] [INFO] Task started: HMMsearch
[2024-01-24 11:43:56,589] [INFO] Running command: hmmsearch --tblout GCF_004363215.1_ASM436321v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7c4d2e9-cd41-472f-86cb-0c77f710d9bf/dqc_reference/reference_markers.hmm GCF_004363215.1_ASM436321v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:56,752] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:56,754] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg58aeee03-61d1-4c05-8dad-d7821c0b5df7/GCF_004363215.1_ASM436321v1_genomic.fna.gz]
[2024-01-24 11:43:56,773] [INFO] Query marker FASTA was written to GCF_004363215.1_ASM436321v1_genomic.fna/markers.fasta
[2024-01-24 11:43:56,773] [INFO] Task started: Blastn
[2024-01-24 11:43:56,773] [INFO] Running command: blastn -query GCF_004363215.1_ASM436321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7c4d2e9-cd41-472f-86cb-0c77f710d9bf/dqc_reference/reference_markers.fasta -out GCF_004363215.1_ASM436321v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:57,241] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:57,244] [INFO] Selected 7 target genomes.
[2024-01-24 11:43:57,244] [INFO] Target genome list was writen to GCF_004363215.1_ASM436321v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:57,341] [INFO] Task started: fastANI
[2024-01-24 11:43:57,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg58aeee03-61d1-4c05-8dad-d7821c0b5df7/GCF_004363215.1_ASM436321v1_genomic.fna.gz --refList GCF_004363215.1_ASM436321v1_genomic.fna/target_genomes.txt --output GCF_004363215.1_ASM436321v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:01,960] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:01,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7c4d2e9-cd41-472f-86cb-0c77f710d9bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:01,961] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7c4d2e9-cd41-472f-86cb-0c77f710d9bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:01,965] [INFO] Found 3 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:44:01,966] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:01,966] [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=DSM 13328	GCA_004363215.1	91560	91560	type	True	100.0	587	588	95	conclusive
Methanimicrococcus blatticola	strain=DSM 13328	GCA_020011555.1	91560	91560	type	True	99.9963	587	588	95	conclusive
Methanimicrococcus blatticola	strain=PA	GCA_020685265.1	91560	91560	type	True	99.9818	582	588	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 11:44:01,967] [INFO] DFAST Taxonomy check result was written to GCF_004363215.1_ASM436321v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:01,968] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:01,968] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:01,968] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7c4d2e9-cd41-472f-86cb-0c77f710d9bf/dqc_reference/checkm_data
[2024-01-24 11:44:01,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:01,988] [INFO] Task started: CheckM
[2024-01-24 11:44:01,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004363215.1_ASM436321v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004363215.1_ASM436321v1_genomic.fna/checkm_input GCF_004363215.1_ASM436321v1_genomic.fna/checkm_result
[2024-01-24 11:44:21,248] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:21,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:21,264] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:21,264] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:21,264] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004363215.1_ASM436321v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:21,264] [INFO] Task started: Blastn
[2024-01-24 11:44:21,264] [INFO] Running command: blastn -query GCF_004363215.1_ASM436321v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7c4d2e9-cd41-472f-86cb-0c77f710d9bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_004363215.1_ASM436321v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:21,688] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:21,691] [INFO] Selected 9 target genomes.
[2024-01-24 11:44:21,691] [INFO] Target genome list was writen to GCF_004363215.1_ASM436321v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:21,697] [INFO] Task started: fastANI
[2024-01-24 11:44:21,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg58aeee03-61d1-4c05-8dad-d7821c0b5df7/GCF_004363215.1_ASM436321v1_genomic.fna.gz --refList GCF_004363215.1_ASM436321v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004363215.1_ASM436321v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:26,127] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:26,130] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:26,130] [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	100.0	587	588	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	78.5162	234	588	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 11:44:26,132] [INFO] GTDB search result was written to GCF_004363215.1_ASM436321v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:26,133] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:26,135] [INFO] DFAST_QC result json was written to GCF_004363215.1_ASM436321v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:26,135] [INFO] DFAST_QC completed!
[2024-01-24 11:44:26,135] [INFO] Total running time: 0h0m35s