[2023-06-13 01:53:05,930] [INFO] DFAST_QC pipeline started.
[2023-06-13 01:53:05,934] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 01:53:05,935] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d069eea-c85a-49e7-9971-3fc13f029b63/dqc_reference
[2023-06-13 01:53:07,412] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 01:53:07,413] [INFO] Task started: Prodigal
[2023-06-13 01:53:07,414] [INFO] Running command: gunzip -c /var/lib/cwl/stg149de6b1-fd0c-4393-8332-89ee420e27ad/GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna.gz | prodigal -d GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/cds.fna -a GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 01:53:14,612] [INFO] Task succeeded: Prodigal
[2023-06-13 01:53:14,612] [INFO] Task started: HMMsearch
[2023-06-13 01:53:14,612] [INFO] Running command: hmmsearch --tblout GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d069eea-c85a-49e7-9971-3fc13f029b63/dqc_reference/reference_markers.hmm GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/protein.faa > /dev/null
[2023-06-13 01:53:14,880] [INFO] Task succeeded: HMMsearch
[2023-06-13 01:53:14,881] [INFO] Found 6/6 markers.
[2023-06-13 01:53:14,903] [INFO] Query marker FASTA was written to GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/markers.fasta
[2023-06-13 01:53:14,903] [INFO] Task started: Blastn
[2023-06-13 01:53:14,903] [INFO] Running command: blastn -query GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d069eea-c85a-49e7-9971-3fc13f029b63/dqc_reference/reference_markers.fasta -out GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:53:15,580] [INFO] Task succeeded: Blastn
[2023-06-13 01:53:15,586] [INFO] Selected 11 target genomes.
[2023-06-13 01:53:15,587] [INFO] Target genome list was writen to GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/target_genomes.txt
[2023-06-13 01:53:15,592] [INFO] Task started: fastANI
[2023-06-13 01:53:15,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg149de6b1-fd0c-4393-8332-89ee420e27ad/GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna.gz --refList GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/target_genomes.txt --output GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 01:53:25,191] [INFO] Task succeeded: fastANI
[2023-06-13 01:53:25,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d069eea-c85a-49e7-9971-3fc13f029b63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 01:53:25,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d069eea-c85a-49e7-9971-3fc13f029b63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 01:53:25,194] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 01:53:25,194] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 01:53:25,194] [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
--------------------------------------------------------------------------------
[2023-06-13 01:53:25,197] [INFO] DFAST Taxonomy check result was written to GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/tc_result.tsv
[2023-06-13 01:53:25,198] [INFO] ===== Taxonomy check completed =====
[2023-06-13 01:53:25,198] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 01:53:25,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d069eea-c85a-49e7-9971-3fc13f029b63/dqc_reference/checkm_data
[2023-06-13 01:53:25,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 01:53:25,221] [INFO] Task started: CheckM
[2023-06-13 01:53:25,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/checkm_input GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/checkm_result
[2023-06-13 01:53:51,981] [INFO] Task succeeded: CheckM
[2023-06-13 01:53:51,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 01:53:52,016] [INFO] ===== Completeness check finished =====
[2023-06-13 01:53:52,016] [INFO] ===== Start GTDB Search =====
[2023-06-13 01:53:52,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/markers.fasta)
[2023-06-13 01:53:52,017] [INFO] Task started: Blastn
[2023-06-13 01:53:52,017] [INFO] Running command: blastn -query GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d069eea-c85a-49e7-9971-3fc13f029b63/dqc_reference/reference_markers_gtdb.fasta -out GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:53:52,809] [INFO] Task succeeded: Blastn
[2023-06-13 01:53:52,815] [INFO] Selected 14 target genomes.
[2023-06-13 01:53:52,815] [INFO] Target genome list was writen to GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 01:53:52,824] [INFO] Task started: fastANI
[2023-06-13 01:53:52,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg149de6b1-fd0c-4393-8332-89ee420e27ad/GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna.gz --refList GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/target_genomes_gtdb.txt --output GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 01:53:57,786] [INFO] Task succeeded: fastANI
[2023-06-13 01:53:57,794] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 01:53:57,794] [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
GCF_011006175.1	s__UBA11096 sp011006175	78.3892	158	460	d__Bacteria;p__Aquificota;c__Aquificae;o__Aquificales;f__Aquificaceae;g__UBA11096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011054805.1	s__UBA11096 sp011054805	77.9811	202	460	d__Bacteria;p__Aquificota;c__Aquificae;o__Aquificales;f__Aquificaceae;g__UBA11096	95.0	99.69	99.59	0.93	0.91	3	-
GCA_018771605.1	s__UBA11096 sp003534055	77.9584	206	460	d__Bacteria;p__Aquificota;c__Aquificae;o__Aquificales;f__Aquificaceae;g__UBA11096	95.0	98.57	98.52	0.97	0.96	3	-
GCA_003696155.1	s__UBA11096 sp003696155	76.9271	81	460	d__Bacteria;p__Aquificota;c__Aquificae;o__Aquificales;f__Aquificaceae;g__UBA11096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011375435.1	s__Thermocrinis ruber_A	76.1313	65	460	d__Bacteria;p__Aquificota;c__Aquificae;o__Aquificales;f__Aquificaceae;g__Thermocrinis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 01:53:57,798] [INFO] GTDB search result was written to GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/result_gtdb.tsv
[2023-06-13 01:53:57,799] [INFO] ===== GTDB Search completed =====
[2023-06-13 01:53:57,803] [INFO] DFAST_QC result json was written to GCA_938048815.1_S1_Bin_MAXBIN_048_sub_1_genomic.fna/dqc_result.json
[2023-06-13 01:53:57,803] [INFO] DFAST_QC completed!
[2023-06-13 01:53:57,803] [INFO] Total running time: 0h0m52s