[2023-06-28 00:55:34,118] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:55:34,121] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:55:34,121] [INFO] DQC Reference Directory: /var/lib/cwl/stgea969621-f8d9-4a1a-8215-258a74b0db73/dqc_reference
[2023-06-28 00:55:35,315] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:55:35,316] [INFO] Task started: Prodigal
[2023-06-28 00:55:35,316] [INFO] Running command: gunzip -c /var/lib/cwl/stg256614a0-cc69-408b-a693-cb8b7d190b1b/GCA_026387875.1_ASM2638787v1_genomic.fna.gz | prodigal -d GCA_026387875.1_ASM2638787v1_genomic.fna/cds.fna -a GCA_026387875.1_ASM2638787v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:55:42,665] [INFO] Task succeeded: Prodigal
[2023-06-28 00:55:42,665] [INFO] Task started: HMMsearch
[2023-06-28 00:55:42,666] [INFO] Running command: hmmsearch --tblout GCA_026387875.1_ASM2638787v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea969621-f8d9-4a1a-8215-258a74b0db73/dqc_reference/reference_markers.hmm GCA_026387875.1_ASM2638787v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:55:42,893] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:55:42,896] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg256614a0-cc69-408b-a693-cb8b7d190b1b/GCA_026387875.1_ASM2638787v1_genomic.fna.gz]
[2023-06-28 00:55:42,933] [INFO] Query marker FASTA was written to GCA_026387875.1_ASM2638787v1_genomic.fna/markers.fasta
[2023-06-28 00:55:42,934] [INFO] Task started: Blastn
[2023-06-28 00:55:42,934] [INFO] Running command: blastn -query GCA_026387875.1_ASM2638787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea969621-f8d9-4a1a-8215-258a74b0db73/dqc_reference/reference_markers.fasta -out GCA_026387875.1_ASM2638787v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:55:43,523] [INFO] Task succeeded: Blastn
[2023-06-28 00:55:43,527] [INFO] Selected 25 target genomes.
[2023-06-28 00:55:43,528] [INFO] Target genome list was writen to GCA_026387875.1_ASM2638787v1_genomic.fna/target_genomes.txt
[2023-06-28 00:55:43,533] [INFO] Task started: fastANI
[2023-06-28 00:55:43,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg256614a0-cc69-408b-a693-cb8b7d190b1b/GCA_026387875.1_ASM2638787v1_genomic.fna.gz --refList GCA_026387875.1_ASM2638787v1_genomic.fna/target_genomes.txt --output GCA_026387875.1_ASM2638787v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:55:58,853] [INFO] Task succeeded: fastANI
[2023-06-28 00:55:58,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea969621-f8d9-4a1a-8215-258a74b0db73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:55:58,854] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea969621-f8d9-4a1a-8215-258a74b0db73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:55:58,856] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:55:58,856] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 00:55:58,856] [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 00:55:58,858] [INFO] DFAST Taxonomy check result was written to GCA_026387875.1_ASM2638787v1_genomic.fna/tc_result.tsv
[2023-06-28 00:55:58,859] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:55:58,859] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:55:58,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea969621-f8d9-4a1a-8215-258a74b0db73/dqc_reference/checkm_data
[2023-06-28 00:55:58,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:55:58,896] [INFO] Task started: CheckM
[2023-06-28 00:55:58,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026387875.1_ASM2638787v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026387875.1_ASM2638787v1_genomic.fna/checkm_input GCA_026387875.1_ASM2638787v1_genomic.fna/checkm_result
[2023-06-28 00:56:25,339] [INFO] Task succeeded: CheckM
[2023-06-28 00:56:25,341] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.57%
Contamintation: 3.45%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-28 00:56:25,365] [INFO] ===== Completeness check finished =====
[2023-06-28 00:56:25,365] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:56:25,366] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026387875.1_ASM2638787v1_genomic.fna/markers.fasta)
[2023-06-28 00:56:25,366] [INFO] Task started: Blastn
[2023-06-28 00:56:25,366] [INFO] Running command: blastn -query GCA_026387875.1_ASM2638787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea969621-f8d9-4a1a-8215-258a74b0db73/dqc_reference/reference_markers_gtdb.fasta -out GCA_026387875.1_ASM2638787v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:56:26,212] [INFO] Task succeeded: Blastn
[2023-06-28 00:56:26,217] [INFO] Selected 18 target genomes.
[2023-06-28 00:56:26,217] [INFO] Target genome list was writen to GCA_026387875.1_ASM2638787v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:56:26,228] [INFO] Task started: fastANI
[2023-06-28 00:56:26,228] [INFO] Running command: fastANI --query /var/lib/cwl/stg256614a0-cc69-408b-a693-cb8b7d190b1b/GCA_026387875.1_ASM2638787v1_genomic.fna.gz --refList GCA_026387875.1_ASM2638787v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026387875.1_ASM2638787v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:56:38,652] [INFO] Task succeeded: fastANI
[2023-06-28 00:56:38,659] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 00:56:38,660] [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_011328705.1	s__DSVR01 sp011328705	78.1233	197	493	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__SLHB01;g__DSVR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837785.1	s__CAILVY01 sp903837785	75.9694	61	493	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__CAIZGN01;g__CAILVY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018005585.1	s__JAGMZX01 sp018005585	75.9292	53	493	d__Bacteria;p__Hydrogenedentota;c__Hydrogenedentia;o__Hydrogenedentiales;f__JAGMZX01;g__JAGMZX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 00:56:38,662] [INFO] GTDB search result was written to GCA_026387875.1_ASM2638787v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:56:38,662] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:56:38,664] [INFO] DFAST_QC result json was written to GCA_026387875.1_ASM2638787v1_genomic.fna/dqc_result.json
[2023-06-28 00:56:38,665] [INFO] DFAST_QC completed!
[2023-06-28 00:56:38,665] [INFO] Total running time: 0h1m5s