[2023-06-30 23:03:02,328] [INFO] DFAST_QC pipeline started.
[2023-06-30 23:03:02,331] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 23:03:02,331] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f9297ae-2aa5-4f75-8ad4-4af99be5f9f2/dqc_reference
[2023-06-30 23:03:04,382] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 23:03:04,383] [INFO] Task started: Prodigal
[2023-06-30 23:03:04,384] [INFO] Running command: gunzip -c /var/lib/cwl/stgef0f8239-90c4-4218-a03e-2027c01f6d51/GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna.gz | prodigal -d GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/cds.fna -a GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 23:03:05,609] [INFO] Task succeeded: Prodigal
[2023-06-30 23:03:05,610] [INFO] Task started: HMMsearch
[2023-06-30 23:03:05,610] [INFO] Running command: hmmsearch --tblout GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f9297ae-2aa5-4f75-8ad4-4af99be5f9f2/dqc_reference/reference_markers.hmm GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/protein.faa > /dev/null
[2023-06-30 23:03:05,783] [INFO] Task succeeded: HMMsearch
[2023-06-30 23:03:05,785] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgef0f8239-90c4-4218-a03e-2027c01f6d51/GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna.gz]
[2023-06-30 23:03:05,817] [INFO] Query marker FASTA was written to GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/markers.fasta
[2023-06-30 23:03:05,818] [INFO] Task started: Blastn
[2023-06-30 23:03:05,818] [INFO] Running command: blastn -query GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f9297ae-2aa5-4f75-8ad4-4af99be5f9f2/dqc_reference/reference_markers.fasta -out GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:03:08,384] [INFO] Task succeeded: Blastn
[2023-06-30 23:03:08,389] [INFO] Selected 15 target genomes.
[2023-06-30 23:03:08,390] [INFO] Target genome list was writen to GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/target_genomes.txt
[2023-06-30 23:03:08,391] [INFO] Task started: fastANI
[2023-06-30 23:03:08,392] [INFO] Running command: fastANI --query /var/lib/cwl/stgef0f8239-90c4-4218-a03e-2027c01f6d51/GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna.gz --refList GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/target_genomes.txt --output GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 23:03:16,019] [INFO] Task succeeded: fastANI
[2023-06-30 23:03:16,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f9297ae-2aa5-4f75-8ad4-4af99be5f9f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 23:03:16,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f9297ae-2aa5-4f75-8ad4-4af99be5f9f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 23:03:16,021] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 23:03:16,021] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 23:03:16,021] [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
--------------------------------------------------------------------------------
[2023-06-30 23:03:16,024] [INFO] DFAST Taxonomy check result was written to GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/tc_result.tsv
[2023-06-30 23:03:16,024] [INFO] ===== Taxonomy check completed =====
[2023-06-30 23:03:16,025] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 23:03:16,025] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f9297ae-2aa5-4f75-8ad4-4af99be5f9f2/dqc_reference/checkm_data
[2023-06-30 23:03:16,028] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 23:03:16,043] [INFO] Task started: CheckM
[2023-06-30 23:03:16,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/checkm_input GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/checkm_result
[2023-06-30 23:03:28,226] [INFO] Task succeeded: CheckM
[2023-06-30 23:03:28,227] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-30 23:03:28,250] [INFO] ===== Completeness check finished =====
[2023-06-30 23:03:28,250] [INFO] ===== Start GTDB Search =====
[2023-06-30 23:03:28,251] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/markers.fasta)
[2023-06-30 23:03:28,251] [INFO] Task started: Blastn
[2023-06-30 23:03:28,252] [INFO] Running command: blastn -query GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f9297ae-2aa5-4f75-8ad4-4af99be5f9f2/dqc_reference/reference_markers_gtdb.fasta -out GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:03:28,737] [INFO] Task succeeded: Blastn
[2023-06-30 23:03:28,742] [INFO] Selected 11 target genomes.
[2023-06-30 23:03:28,742] [INFO] Target genome list was writen to GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 23:03:28,749] [INFO] Task started: fastANI
[2023-06-30 23:03:28,750] [INFO] Running command: fastANI --query /var/lib/cwl/stgef0f8239-90c4-4218-a03e-2027c01f6d51/GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna.gz --refList GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 23:03:30,634] [INFO] Task succeeded: fastANI
[2023-06-30 23:03:30,637] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 23:03:30,637] [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_000168995.1	s__BACL14 sp000168995	98.7182	190	190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	98.71	98.43	0.97	0.92	10	conclusive
GCA_002384685.1	s__BACL14 sp002384685	81.9276	150	190	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__BACL14	95.0	99.54	99.37	0.90	0.88	8	-
--------------------------------------------------------------------------------
[2023-06-30 23:03:30,640] [INFO] GTDB search result was written to GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/result_gtdb.tsv
[2023-06-30 23:03:30,640] [INFO] ===== GTDB Search completed =====
[2023-06-30 23:03:30,643] [INFO] DFAST_QC result json was written to GCA_943845005.1_20200506_Bin_Bin_17_sub_1-contigs.fa_genomic.fna/dqc_result.json
[2023-06-30 23:03:30,643] [INFO] DFAST_QC completed!
[2023-06-30 23:03:30,643] [INFO] Total running time: 0h0m28s