[2023-06-28 12:02:02,368] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:02:02,371] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:02:02,372] [INFO] DQC Reference Directory: /var/lib/cwl/stg916bdbc5-d53d-4730-85c4-7a3f1ba6c9e7/dqc_reference
[2023-06-28 12:02:03,628] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:02:03,629] [INFO] Task started: Prodigal
[2023-06-28 12:02:03,629] [INFO] Running command: gunzip -c /var/lib/cwl/stg62722abb-8c3c-4ac8-828b-d7467ec20b16/GCA_005504395.1_ASM550439v1_genomic.fna.gz | prodigal -d GCA_005504395.1_ASM550439v1_genomic.fna/cds.fna -a GCA_005504395.1_ASM550439v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:02:06,252] [INFO] Task succeeded: Prodigal
[2023-06-28 12:02:06,253] [INFO] Task started: HMMsearch
[2023-06-28 12:02:06,253] [INFO] Running command: hmmsearch --tblout GCA_005504395.1_ASM550439v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg916bdbc5-d53d-4730-85c4-7a3f1ba6c9e7/dqc_reference/reference_markers.hmm GCA_005504395.1_ASM550439v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:02:06,467] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:02:06,469] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg62722abb-8c3c-4ac8-828b-d7467ec20b16/GCA_005504395.1_ASM550439v1_genomic.fna.gz]
[2023-06-28 12:02:06,491] [INFO] Query marker FASTA was written to GCA_005504395.1_ASM550439v1_genomic.fna/markers.fasta
[2023-06-28 12:02:06,491] [INFO] Task started: Blastn
[2023-06-28 12:02:06,491] [INFO] Running command: blastn -query GCA_005504395.1_ASM550439v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg916bdbc5-d53d-4730-85c4-7a3f1ba6c9e7/dqc_reference/reference_markers.fasta -out GCA_005504395.1_ASM550439v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:02:06,989] [INFO] Task succeeded: Blastn
[2023-06-28 12:02:06,994] [INFO] Selected 10 target genomes.
[2023-06-28 12:02:06,995] [INFO] Target genome list was writen to GCA_005504395.1_ASM550439v1_genomic.fna/target_genomes.txt
[2023-06-28 12:02:07,007] [INFO] Task started: fastANI
[2023-06-28 12:02:07,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg62722abb-8c3c-4ac8-828b-d7467ec20b16/GCA_005504395.1_ASM550439v1_genomic.fna.gz --refList GCA_005504395.1_ASM550439v1_genomic.fna/target_genomes.txt --output GCA_005504395.1_ASM550439v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:02:11,933] [INFO] Task succeeded: fastANI
[2023-06-28 12:02:11,934] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg916bdbc5-d53d-4730-85c4-7a3f1ba6c9e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:02:11,934] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg916bdbc5-d53d-4730-85c4-7a3f1ba6c9e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:02:11,935] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:02:11,936] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:02:11,936] [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
--------------------------------------------------------------------------------
[2023-06-28 12:02:11,938] [INFO] DFAST Taxonomy check result was written to GCA_005504395.1_ASM550439v1_genomic.fna/tc_result.tsv
[2023-06-28 12:02:11,938] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:02:11,938] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:02:11,939] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg916bdbc5-d53d-4730-85c4-7a3f1ba6c9e7/dqc_reference/checkm_data
[2023-06-28 12:02:11,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:02:11,961] [INFO] Task started: CheckM
[2023-06-28 12:02:11,962] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005504395.1_ASM550439v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005504395.1_ASM550439v1_genomic.fna/checkm_input GCA_005504395.1_ASM550439v1_genomic.fna/checkm_result
[2023-06-28 12:02:28,776] [INFO] Task succeeded: CheckM
[2023-06-28 12:02:28,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:02:28,792] [INFO] ===== Completeness check finished =====
[2023-06-28 12:02:28,793] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:02:28,793] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005504395.1_ASM550439v1_genomic.fna/markers.fasta)
[2023-06-28 12:02:28,793] [INFO] Task started: Blastn
[2023-06-28 12:02:28,794] [INFO] Running command: blastn -query GCA_005504395.1_ASM550439v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg916bdbc5-d53d-4730-85c4-7a3f1ba6c9e7/dqc_reference/reference_markers_gtdb.fasta -out GCA_005504395.1_ASM550439v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:02:29,275] [INFO] Task succeeded: Blastn
[2023-06-28 12:02:29,278] [INFO] Selected 9 target genomes.
[2023-06-28 12:02:29,279] [INFO] Target genome list was writen to GCA_005504395.1_ASM550439v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:02:29,291] [INFO] Task started: fastANI
[2023-06-28 12:02:29,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg62722abb-8c3c-4ac8-828b-d7467ec20b16/GCA_005504395.1_ASM550439v1_genomic.fna.gz --refList GCA_005504395.1_ASM550439v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005504395.1_ASM550439v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:02:32,431] [INFO] Task succeeded: fastANI
[2023-06-28 12:02:32,435] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:02:32,435] [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
GCA_002926195.1	s__Methanomarinus sp002926195	97.7562	250	328	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanocomedenaceae;g__Methanomarinus	95.0	97.97	97.92	0.72	0.69	4	conclusive
--------------------------------------------------------------------------------
[2023-06-28 12:02:32,438] [INFO] GTDB search result was written to GCA_005504395.1_ASM550439v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:02:32,439] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:02:32,441] [INFO] DFAST_QC result json was written to GCA_005504395.1_ASM550439v1_genomic.fna/dqc_result.json
[2023-06-28 12:02:32,442] [INFO] DFAST_QC completed!
[2023-06-28 12:02:32,442] [INFO] Total running time: 0h0m30s