[2023-06-16 21:53:37,576] [INFO] DFAST_QC pipeline started.
[2023-06-16 21:53:37,579] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 21:53:37,579] [INFO] DQC Reference Directory: /var/lib/cwl/stgcde3e745-211a-41c0-9b8b-1e476b731e6a/dqc_reference
[2023-06-16 21:53:39,032] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 21:53:39,034] [INFO] Task started: Prodigal
[2023-06-16 21:53:39,034] [INFO] Running command: gunzip -c /var/lib/cwl/stg56509369-41f5-4b2b-bef2-79045d3ab381/GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna.gz | prodigal -d GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/cds.fna -a GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 21:53:43,225] [INFO] Task succeeded: Prodigal
[2023-06-16 21:53:43,225] [INFO] Task started: HMMsearch
[2023-06-16 21:53:43,225] [INFO] Running command: hmmsearch --tblout GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcde3e745-211a-41c0-9b8b-1e476b731e6a/dqc_reference/reference_markers.hmm GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/protein.faa > /dev/null
[2023-06-16 21:53:43,503] [INFO] Task succeeded: HMMsearch
[2023-06-16 21:53:43,505] [INFO] Found 6/6 markers.
[2023-06-16 21:53:43,533] [INFO] Query marker FASTA was written to GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/markers.fasta
[2023-06-16 21:53:43,533] [INFO] Task started: Blastn
[2023-06-16 21:53:43,533] [INFO] Running command: blastn -query GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/markers.fasta -db /var/lib/cwl/stgcde3e745-211a-41c0-9b8b-1e476b731e6a/dqc_reference/reference_markers.fasta -out GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:53:44,310] [INFO] Task succeeded: Blastn
[2023-06-16 21:53:44,314] [INFO] Selected 21 target genomes.
[2023-06-16 21:53:44,314] [INFO] Target genome list was writen to GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/target_genomes.txt
[2023-06-16 21:53:44,326] [INFO] Task started: fastANI
[2023-06-16 21:53:44,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg56509369-41f5-4b2b-bef2-79045d3ab381/GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna.gz --refList GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/target_genomes.txt --output GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 21:53:57,206] [INFO] Task succeeded: fastANI
[2023-06-16 21:53:57,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcde3e745-211a-41c0-9b8b-1e476b731e6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 21:53:57,207] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcde3e745-211a-41c0-9b8b-1e476b731e6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 21:53:57,209] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 21:53:57,209] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 21:53:57,209] [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
--------------------------------------------------------------------------------
[2023-06-16 21:53:57,211] [INFO] DFAST Taxonomy check result was written to GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/tc_result.tsv
[2023-06-16 21:53:57,212] [INFO] ===== Taxonomy check completed =====
[2023-06-16 21:53:57,212] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 21:53:57,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcde3e745-211a-41c0-9b8b-1e476b731e6a/dqc_reference/checkm_data
[2023-06-16 21:53:57,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 21:53:57,242] [INFO] Task started: CheckM
[2023-06-16 21:53:57,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/checkm_input GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/checkm_result
[2023-06-16 21:54:18,267] [INFO] Task succeeded: CheckM
[2023-06-16 21:54:18,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 21:54:18,289] [INFO] ===== Completeness check finished =====
[2023-06-16 21:54:18,290] [INFO] ===== Start GTDB Search =====
[2023-06-16 21:54:18,290] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/markers.fasta)
[2023-06-16 21:54:18,290] [INFO] Task started: Blastn
[2023-06-16 21:54:18,291] [INFO] Running command: blastn -query GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/markers.fasta -db /var/lib/cwl/stgcde3e745-211a-41c0-9b8b-1e476b731e6a/dqc_reference/reference_markers_gtdb.fasta -out GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:54:19,359] [INFO] Task succeeded: Blastn
[2023-06-16 21:54:19,363] [INFO] Selected 17 target genomes.
[2023-06-16 21:54:19,363] [INFO] Target genome list was writen to GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 21:54:19,381] [INFO] Task started: fastANI
[2023-06-16 21:54:19,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg56509369-41f5-4b2b-bef2-79045d3ab381/GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna.gz --refList GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/target_genomes_gtdb.txt --output GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 21:54:25,202] [INFO] Task succeeded: fastANI
[2023-06-16 21:54:25,209] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 21:54:25,209] [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_900552285.1	s__UMGS1484 sp900552285	98.6904	367	503	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS1484	95.0	99.13	98.75	0.83	0.79	4	conclusive
GCA_905193225.1	s__UMGS1484 sp905193225	81.7276	316	503	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS1484	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902388225.1	s__UMGS1484 sp902388225	81.2707	241	503	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS1484	95.0	99.69	99.69	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-16 21:54:25,211] [INFO] GTDB search result was written to GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/result_gtdb.tsv
[2023-06-16 21:54:25,212] [INFO] ===== GTDB Search completed =====
[2023-06-16 21:54:25,214] [INFO] DFAST_QC result json was written to GCA_905206895.1_ERR1600732-mag-bin.6_genomic.fna/dqc_result.json
[2023-06-16 21:54:25,214] [INFO] DFAST_QC completed!
[2023-06-16 21:54:25,214] [INFO] Total running time: 0h0m48s