[2023-06-04 20:23:58,321] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:23:58,322] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:23:58,323] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6eb685a-7227-44f9-9339-80e18fd202d9/dqc_reference
[2023-06-04 20:23:59,568] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:23:59,569] [INFO] Task started: Prodigal
[2023-06-04 20:23:59,569] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c03397a-f94d-4daf-b2d1-995c673ccc9e/GCA_934149105.1_ERR7747615_bin.105_genomic.fna.gz | prodigal -d GCA_934149105.1_ERR7747615_bin.105_genomic.fna/cds.fna -a GCA_934149105.1_ERR7747615_bin.105_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:24:01,200] [INFO] Task succeeded: Prodigal
[2023-06-04 20:24:01,200] [INFO] Task started: HMMsearch
[2023-06-04 20:24:01,200] [INFO] Running command: hmmsearch --tblout GCA_934149105.1_ERR7747615_bin.105_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6eb685a-7227-44f9-9339-80e18fd202d9/dqc_reference/reference_markers.hmm GCA_934149105.1_ERR7747615_bin.105_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:24:01,413] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:24:01,415] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1c03397a-f94d-4daf-b2d1-995c673ccc9e/GCA_934149105.1_ERR7747615_bin.105_genomic.fna.gz]
[2023-06-04 20:24:01,431] [INFO] Query marker FASTA was written to GCA_934149105.1_ERR7747615_bin.105_genomic.fna/markers.fasta
[2023-06-04 20:24:01,431] [INFO] Task started: Blastn
[2023-06-04 20:24:01,432] [INFO] Running command: blastn -query GCA_934149105.1_ERR7747615_bin.105_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6eb685a-7227-44f9-9339-80e18fd202d9/dqc_reference/reference_markers.fasta -out GCA_934149105.1_ERR7747615_bin.105_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:24:03,072] [INFO] Task succeeded: Blastn
[2023-06-04 20:24:03,077] [INFO] Selected 27 target genomes.
[2023-06-04 20:24:03,077] [INFO] Target genome list was writen to GCA_934149105.1_ERR7747615_bin.105_genomic.fna/target_genomes.txt
[2023-06-04 20:24:03,112] [INFO] Task started: fastANI
[2023-06-04 20:24:03,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c03397a-f94d-4daf-b2d1-995c673ccc9e/GCA_934149105.1_ERR7747615_bin.105_genomic.fna.gz --refList GCA_934149105.1_ERR7747615_bin.105_genomic.fna/target_genomes.txt --output GCA_934149105.1_ERR7747615_bin.105_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:24:15,377] [INFO] Task succeeded: fastANI
[2023-06-04 20:24:15,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6eb685a-7227-44f9-9339-80e18fd202d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:24:15,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6eb685a-7227-44f9-9339-80e18fd202d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:24:15,381] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 20:24:15,381] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 20:24:15,381] [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
--------------------------------------------------------------------------------
[2023-06-04 20:24:15,383] [INFO] DFAST Taxonomy check result was written to GCA_934149105.1_ERR7747615_bin.105_genomic.fna/tc_result.tsv
[2023-06-04 20:24:15,384] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:24:15,384] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:24:15,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6eb685a-7227-44f9-9339-80e18fd202d9/dqc_reference/checkm_data
[2023-06-04 20:24:15,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:24:15,407] [INFO] Task started: CheckM
[2023-06-04 20:24:15,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934149105.1_ERR7747615_bin.105_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934149105.1_ERR7747615_bin.105_genomic.fna/checkm_input GCA_934149105.1_ERR7747615_bin.105_genomic.fna/checkm_result
[2023-06-04 20:24:29,077] [INFO] Task succeeded: CheckM
[2023-06-04 20:24:29,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:24:29,101] [INFO] ===== Completeness check finished =====
[2023-06-04 20:24:29,101] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:24:29,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934149105.1_ERR7747615_bin.105_genomic.fna/markers.fasta)
[2023-06-04 20:24:29,102] [INFO] Task started: Blastn
[2023-06-04 20:24:29,102] [INFO] Running command: blastn -query GCA_934149105.1_ERR7747615_bin.105_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6eb685a-7227-44f9-9339-80e18fd202d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_934149105.1_ERR7747615_bin.105_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:24:29,968] [INFO] Task succeeded: Blastn
[2023-06-04 20:24:29,975] [INFO] Selected 26 target genomes.
[2023-06-04 20:24:29,975] [INFO] Target genome list was writen to GCA_934149105.1_ERR7747615_bin.105_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:24:30,007] [INFO] Task started: fastANI
[2023-06-04 20:24:30,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c03397a-f94d-4daf-b2d1-995c673ccc9e/GCA_934149105.1_ERR7747615_bin.105_genomic.fna.gz --refList GCA_934149105.1_ERR7747615_bin.105_genomic.fna/target_genomes_gtdb.txt --output GCA_934149105.1_ERR7747615_bin.105_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:24:34,780] [INFO] Task succeeded: fastANI
[2023-06-04 20:24:34,785] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 20:24:34,786] [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_902766875.1	s__RUG11215 sp902766875	78.2401	111	378	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548425.1	s__CAG-302 sp900548425	77.0529	56	378	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	99.47	98.99	0.91	0.87	3	-
GCA_905211265.1	s__HGM10818 sp905211265	76.9192	68	378	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__HGM10818	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432825.1	s__RUG11198 sp017432825	76.8368	59	378	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11198	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001916775.1	s__CAG-302 sp001916775	76.6735	68	378	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-302	95.0	95.82	95.12	0.84	0.77	8	-
--------------------------------------------------------------------------------
[2023-06-04 20:24:34,787] [INFO] GTDB search result was written to GCA_934149105.1_ERR7747615_bin.105_genomic.fna/result_gtdb.tsv
[2023-06-04 20:24:34,788] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:24:34,791] [INFO] DFAST_QC result json was written to GCA_934149105.1_ERR7747615_bin.105_genomic.fna/dqc_result.json
[2023-06-04 20:24:34,791] [INFO] DFAST_QC completed!
[2023-06-04 20:24:34,791] [INFO] Total running time: 0h0m36s