[2023-06-17 12:34:57,906] [INFO] DFAST_QC pipeline started.
[2023-06-17 12:34:57,936] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 12:34:57,937] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f278c03-fc44-41a9-9b52-2b5b9fd10967/dqc_reference
[2023-06-17 12:34:59,399] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 12:34:59,400] [INFO] Task started: Prodigal
[2023-06-17 12:34:59,400] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd1dd9bc-501a-479f-aea0-d1c191486013/GCA_028821465.1_ASM2882146v1_genomic.fna.gz | prodigal -d GCA_028821465.1_ASM2882146v1_genomic.fna/cds.fna -a GCA_028821465.1_ASM2882146v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 12:35:12,160] [INFO] Task succeeded: Prodigal
[2023-06-17 12:35:12,160] [INFO] Task started: HMMsearch
[2023-06-17 12:35:12,160] [INFO] Running command: hmmsearch --tblout GCA_028821465.1_ASM2882146v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f278c03-fc44-41a9-9b52-2b5b9fd10967/dqc_reference/reference_markers.hmm GCA_028821465.1_ASM2882146v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 12:35:12,483] [INFO] Task succeeded: HMMsearch
[2023-06-17 12:35:12,484] [INFO] Found 6/6 markers.
[2023-06-17 12:35:12,527] [INFO] Query marker FASTA was written to GCA_028821465.1_ASM2882146v1_genomic.fna/markers.fasta
[2023-06-17 12:35:12,528] [INFO] Task started: Blastn
[2023-06-17 12:35:12,528] [INFO] Running command: blastn -query GCA_028821465.1_ASM2882146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f278c03-fc44-41a9-9b52-2b5b9fd10967/dqc_reference/reference_markers.fasta -out GCA_028821465.1_ASM2882146v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:35:13,227] [INFO] Task succeeded: Blastn
[2023-06-17 12:35:13,232] [INFO] Selected 23 target genomes.
[2023-06-17 12:35:13,233] [INFO] Target genome list was writen to GCA_028821465.1_ASM2882146v1_genomic.fna/target_genomes.txt
[2023-06-17 12:35:13,235] [INFO] Task started: fastANI
[2023-06-17 12:35:13,236] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd1dd9bc-501a-479f-aea0-d1c191486013/GCA_028821465.1_ASM2882146v1_genomic.fna.gz --refList GCA_028821465.1_ASM2882146v1_genomic.fna/target_genomes.txt --output GCA_028821465.1_ASM2882146v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 12:35:31,912] [INFO] Task succeeded: fastANI
[2023-06-17 12:35:31,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f278c03-fc44-41a9-9b52-2b5b9fd10967/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 12:35:31,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f278c03-fc44-41a9-9b52-2b5b9fd10967/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 12:35:31,915] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 12:35:31,915] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 12:35:31,915] [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
--------------------------------------------------------------------------------
[2023-06-17 12:35:31,918] [INFO] DFAST Taxonomy check result was written to GCA_028821465.1_ASM2882146v1_genomic.fna/tc_result.tsv
[2023-06-17 12:35:31,918] [INFO] ===== Taxonomy check completed =====
[2023-06-17 12:35:31,919] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 12:35:31,919] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f278c03-fc44-41a9-9b52-2b5b9fd10967/dqc_reference/checkm_data
[2023-06-17 12:35:31,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 12:35:31,977] [INFO] Task started: CheckM
[2023-06-17 12:35:31,977] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028821465.1_ASM2882146v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028821465.1_ASM2882146v1_genomic.fna/checkm_input GCA_028821465.1_ASM2882146v1_genomic.fna/checkm_result
[2023-06-17 12:36:11,682] [INFO] Task succeeded: CheckM
[2023-06-17 12:36:11,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.21%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 12:36:11,707] [INFO] ===== Completeness check finished =====
[2023-06-17 12:36:11,708] [INFO] ===== Start GTDB Search =====
[2023-06-17 12:36:11,708] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028821465.1_ASM2882146v1_genomic.fna/markers.fasta)
[2023-06-17 12:36:11,708] [INFO] Task started: Blastn
[2023-06-17 12:36:11,708] [INFO] Running command: blastn -query GCA_028821465.1_ASM2882146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f278c03-fc44-41a9-9b52-2b5b9fd10967/dqc_reference/reference_markers_gtdb.fasta -out GCA_028821465.1_ASM2882146v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:36:12,590] [INFO] Task succeeded: Blastn
[2023-06-17 12:36:12,595] [INFO] Selected 14 target genomes.
[2023-06-17 12:36:12,595] [INFO] Target genome list was writen to GCA_028821465.1_ASM2882146v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 12:36:12,602] [INFO] Task started: fastANI
[2023-06-17 12:36:12,602] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd1dd9bc-501a-479f-aea0-d1c191486013/GCA_028821465.1_ASM2882146v1_genomic.fna.gz --refList GCA_028821465.1_ASM2882146v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028821465.1_ASM2882146v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 12:36:25,185] [INFO] Task succeeded: fastANI
[2023-06-17 12:36:25,199] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 12:36:25,199] [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_009840225.1	s__Bin5 sp009840225	95.1084	1023	1331	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	97.63	95.35	0.89	0.84	3	conclusive
GCA_011523365.1	s__Bin5 sp011523365	92.0955	1018	1331	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009841235.1	s__Bin5 sp009841235	84.3838	884	1331	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	95.53	95.53	0.91	0.91	2	-
GCA_009838625.1	s__Bin5 sp009838625	83.8275	853	1331	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	99.90	99.90	0.97	0.97	2	-
GCA_002238445.1	s__Bin5 sp002238445	81.6684	722	1331	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124945.1	s__RI-153 sp016124945	75.8261	82	1331	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__RI-153	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577005.1	s__CFX5 sp003577005	75.3989	55	1331	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__CFX5	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 12:36:25,202] [INFO] GTDB search result was written to GCA_028821465.1_ASM2882146v1_genomic.fna/result_gtdb.tsv
[2023-06-17 12:36:25,202] [INFO] ===== GTDB Search completed =====
[2023-06-17 12:36:25,206] [INFO] DFAST_QC result json was written to GCA_028821465.1_ASM2882146v1_genomic.fna/dqc_result.json
[2023-06-17 12:36:25,206] [INFO] DFAST_QC completed!
[2023-06-17 12:36:25,207] [INFO] Total running time: 0h1m27s