[2023-06-05 00:38:03,245] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:38:03,248] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:38:03,248] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4ae3411-7353-4a78-9eca-3f4f52d70de4/dqc_reference
[2023-06-05 00:38:05,545] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:38:05,547] [INFO] Task started: Prodigal
[2023-06-05 00:38:05,547] [INFO] Running command: gunzip -c /var/lib/cwl/stgef20b6b3-c957-4e01-a4c9-15b78a362752/GCA_934457425.1_ERR7738147_bin.59_genomic.fna.gz | prodigal -d GCA_934457425.1_ERR7738147_bin.59_genomic.fna/cds.fna -a GCA_934457425.1_ERR7738147_bin.59_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:38:09,428] [INFO] Task succeeded: Prodigal
[2023-06-05 00:38:09,428] [INFO] Task started: HMMsearch
[2023-06-05 00:38:09,429] [INFO] Running command: hmmsearch --tblout GCA_934457425.1_ERR7738147_bin.59_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4ae3411-7353-4a78-9eca-3f4f52d70de4/dqc_reference/reference_markers.hmm GCA_934457425.1_ERR7738147_bin.59_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:38:09,667] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:38:09,669] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgef20b6b3-c957-4e01-a4c9-15b78a362752/GCA_934457425.1_ERR7738147_bin.59_genomic.fna.gz]
[2023-06-05 00:38:09,689] [INFO] Query marker FASTA was written to GCA_934457425.1_ERR7738147_bin.59_genomic.fna/markers.fasta
[2023-06-05 00:38:09,690] [INFO] Task started: Blastn
[2023-06-05 00:38:09,690] [INFO] Running command: blastn -query GCA_934457425.1_ERR7738147_bin.59_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4ae3411-7353-4a78-9eca-3f4f52d70de4/dqc_reference/reference_markers.fasta -out GCA_934457425.1_ERR7738147_bin.59_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:38:10,794] [INFO] Task succeeded: Blastn
[2023-06-05 00:38:10,798] [INFO] Selected 14 target genomes.
[2023-06-05 00:38:10,799] [INFO] Target genome list was writen to GCA_934457425.1_ERR7738147_bin.59_genomic.fna/target_genomes.txt
[2023-06-05 00:38:10,832] [INFO] Task started: fastANI
[2023-06-05 00:38:10,832] [INFO] Running command: fastANI --query /var/lib/cwl/stgef20b6b3-c957-4e01-a4c9-15b78a362752/GCA_934457425.1_ERR7738147_bin.59_genomic.fna.gz --refList GCA_934457425.1_ERR7738147_bin.59_genomic.fna/target_genomes.txt --output GCA_934457425.1_ERR7738147_bin.59_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:38:18,491] [INFO] Task succeeded: fastANI
[2023-06-05 00:38:18,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4ae3411-7353-4a78-9eca-3f4f52d70de4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:38:18,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4ae3411-7353-4a78-9eca-3f4f52d70de4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:38:18,493] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:38:18,493] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 00:38:18,493] [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
--------------------------------------------------------------------------------
[2023-06-05 00:38:18,495] [INFO] DFAST Taxonomy check result was written to GCA_934457425.1_ERR7738147_bin.59_genomic.fna/tc_result.tsv
[2023-06-05 00:38:18,495] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:38:18,496] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:38:18,496] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4ae3411-7353-4a78-9eca-3f4f52d70de4/dqc_reference/checkm_data
[2023-06-05 00:38:18,499] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:38:18,518] [INFO] Task started: CheckM
[2023-06-05 00:38:18,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934457425.1_ERR7738147_bin.59_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934457425.1_ERR7738147_bin.59_genomic.fna/checkm_input GCA_934457425.1_ERR7738147_bin.59_genomic.fna/checkm_result
[2023-06-05 00:38:36,880] [INFO] Task succeeded: CheckM
[2023-06-05 00:38:36,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:38:36,901] [INFO] ===== Completeness check finished =====
[2023-06-05 00:38:36,901] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:38:36,902] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934457425.1_ERR7738147_bin.59_genomic.fna/markers.fasta)
[2023-06-05 00:38:36,902] [INFO] Task started: Blastn
[2023-06-05 00:38:36,902] [INFO] Running command: blastn -query GCA_934457425.1_ERR7738147_bin.59_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4ae3411-7353-4a78-9eca-3f4f52d70de4/dqc_reference/reference_markers_gtdb.fasta -out GCA_934457425.1_ERR7738147_bin.59_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:38:37,633] [INFO] Task succeeded: Blastn
[2023-06-05 00:38:37,639] [INFO] Selected 20 target genomes.
[2023-06-05 00:38:37,639] [INFO] Target genome list was writen to GCA_934457425.1_ERR7738147_bin.59_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:38:37,683] [INFO] Task started: fastANI
[2023-06-05 00:38:37,684] [INFO] Running command: fastANI --query /var/lib/cwl/stgef20b6b3-c957-4e01-a4c9-15b78a362752/GCA_934457425.1_ERR7738147_bin.59_genomic.fna.gz --refList GCA_934457425.1_ERR7738147_bin.59_genomic.fna/target_genomes_gtdb.txt --output GCA_934457425.1_ERR7738147_bin.59_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:38:44,531] [INFO] Task succeeded: fastANI
[2023-06-05 00:38:44,542] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 00:38:44,543] [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_900548305.1	s__UMGS1071 sp900548305	78.1862	85	443	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS1071	95.0	99.95	99.95	0.99	0.99	2	-
GCA_900541905.1	s__UMGS1071 sp900541905	77.963	101	443	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS1071	95.0	98.83	97.35	0.91	0.87	4	-
--------------------------------------------------------------------------------
[2023-06-05 00:38:44,545] [INFO] GTDB search result was written to GCA_934457425.1_ERR7738147_bin.59_genomic.fna/result_gtdb.tsv
[2023-06-05 00:38:44,546] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:38:44,548] [INFO] DFAST_QC result json was written to GCA_934457425.1_ERR7738147_bin.59_genomic.fna/dqc_result.json
[2023-06-05 00:38:44,549] [INFO] DFAST_QC completed!
[2023-06-05 00:38:44,549] [INFO] Total running time: 0h0m41s