[2023-06-08 02:20:21,994] [INFO] DFAST_QC pipeline started.
[2023-06-08 02:20:21,999] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 02:20:21,999] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb1672b6-3416-4ca5-a019-f2350c97809d/dqc_reference
[2023-06-08 02:20:23,684] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 02:20:23,685] [INFO] Task started: Prodigal
[2023-06-08 02:20:23,686] [INFO] Running command: gunzip -c /var/lib/cwl/stg603940f3-b796-408b-a31b-6ce1d5d68367/GCA_945897485.1_MoH-23oct19-57_genomic.fna.gz | prodigal -d GCA_945897485.1_MoH-23oct19-57_genomic.fna/cds.fna -a GCA_945897485.1_MoH-23oct19-57_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 02:20:29,590] [INFO] Task succeeded: Prodigal
[2023-06-08 02:20:29,590] [INFO] Task started: HMMsearch
[2023-06-08 02:20:29,590] [INFO] Running command: hmmsearch --tblout GCA_945897485.1_MoH-23oct19-57_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb1672b6-3416-4ca5-a019-f2350c97809d/dqc_reference/reference_markers.hmm GCA_945897485.1_MoH-23oct19-57_genomic.fna/protein.faa > /dev/null
[2023-06-08 02:20:29,851] [INFO] Task succeeded: HMMsearch
[2023-06-08 02:20:29,853] [INFO] Found 6/6 markers.
[2023-06-08 02:20:29,881] [INFO] Query marker FASTA was written to GCA_945897485.1_MoH-23oct19-57_genomic.fna/markers.fasta
[2023-06-08 02:20:29,882] [INFO] Task started: Blastn
[2023-06-08 02:20:29,882] [INFO] Running command: blastn -query GCA_945897485.1_MoH-23oct19-57_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb1672b6-3416-4ca5-a019-f2350c97809d/dqc_reference/reference_markers.fasta -out GCA_945897485.1_MoH-23oct19-57_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:20:30,447] [INFO] Task succeeded: Blastn
[2023-06-08 02:20:30,452] [INFO] Selected 11 target genomes.
[2023-06-08 02:20:30,453] [INFO] Target genome list was writen to GCA_945897485.1_MoH-23oct19-57_genomic.fna/target_genomes.txt
[2023-06-08 02:20:30,456] [INFO] Task started: fastANI
[2023-06-08 02:20:30,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg603940f3-b796-408b-a31b-6ce1d5d68367/GCA_945897485.1_MoH-23oct19-57_genomic.fna.gz --refList GCA_945897485.1_MoH-23oct19-57_genomic.fna/target_genomes.txt --output GCA_945897485.1_MoH-23oct19-57_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 02:20:37,059] [INFO] Task succeeded: fastANI
[2023-06-08 02:20:37,060] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb1672b6-3416-4ca5-a019-f2350c97809d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 02:20:37,061] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb1672b6-3416-4ca5-a019-f2350c97809d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 02:20:37,063] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 02:20:37,063] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 02:20:37,064] [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
--------------------------------------------------------------------------------
[2023-06-08 02:20:37,066] [INFO] DFAST Taxonomy check result was written to GCA_945897485.1_MoH-23oct19-57_genomic.fna/tc_result.tsv
[2023-06-08 02:20:37,067] [INFO] ===== Taxonomy check completed =====
[2023-06-08 02:20:37,067] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 02:20:37,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb1672b6-3416-4ca5-a019-f2350c97809d/dqc_reference/checkm_data
[2023-06-08 02:20:37,072] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 02:20:37,102] [INFO] Task started: CheckM
[2023-06-08 02:20:37,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945897485.1_MoH-23oct19-57_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945897485.1_MoH-23oct19-57_genomic.fna/checkm_input GCA_945897485.1_MoH-23oct19-57_genomic.fna/checkm_result
[2023-06-08 02:21:01,301] [INFO] Task succeeded: CheckM
[2023-06-08 02:21:01,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 02:21:01,326] [INFO] ===== Completeness check finished =====
[2023-06-08 02:21:01,327] [INFO] ===== Start GTDB Search =====
[2023-06-08 02:21:01,327] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945897485.1_MoH-23oct19-57_genomic.fna/markers.fasta)
[2023-06-08 02:21:01,328] [INFO] Task started: Blastn
[2023-06-08 02:21:01,328] [INFO] Running command: blastn -query GCA_945897485.1_MoH-23oct19-57_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb1672b6-3416-4ca5-a019-f2350c97809d/dqc_reference/reference_markers_gtdb.fasta -out GCA_945897485.1_MoH-23oct19-57_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:21:02,140] [INFO] Task succeeded: Blastn
[2023-06-08 02:21:02,145] [INFO] Selected 8 target genomes.
[2023-06-08 02:21:02,145] [INFO] Target genome list was writen to GCA_945897485.1_MoH-23oct19-57_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 02:21:02,146] [INFO] Task started: fastANI
[2023-06-08 02:21:02,146] [INFO] Running command: fastANI --query /var/lib/cwl/stg603940f3-b796-408b-a31b-6ce1d5d68367/GCA_945897485.1_MoH-23oct19-57_genomic.fna.gz --refList GCA_945897485.1_MoH-23oct19-57_genomic.fna/target_genomes_gtdb.txt --output GCA_945897485.1_MoH-23oct19-57_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 02:21:07,655] [INFO] Task succeeded: fastANI
[2023-06-08 02:21:07,667] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 02:21:07,667] [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_003671255.1	s__UBA969 sp003671255	98.622	622	743	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__UBA969	95.0	97.99	97.11	0.80	0.71	7	conclusive
GCA_002303765.1	s__UBA969 sp002303765	87.8224	609	743	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__UBA969	95.0	99.66	99.66	0.86	0.86	2	-
GCA_903960945.1	s__UBA969 sp903960945	87.3866	638	743	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__UBA969	95.0	98.76	98.01	0.87	0.84	7	-
GCA_009920765.1	s__UBA969 sp009920765	83.1976	649	743	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__UBA969	95.0	99.66	99.66	0.97	0.97	2	-
GCA_005786805.1	s__UBA969 sp005786805	78.1464	262	743	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__UBA969	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 02:21:07,669] [INFO] GTDB search result was written to GCA_945897485.1_MoH-23oct19-57_genomic.fna/result_gtdb.tsv
[2023-06-08 02:21:07,670] [INFO] ===== GTDB Search completed =====
[2023-06-08 02:21:07,672] [INFO] DFAST_QC result json was written to GCA_945897485.1_MoH-23oct19-57_genomic.fna/dqc_result.json
[2023-06-08 02:21:07,672] [INFO] DFAST_QC completed!
[2023-06-08 02:21:07,673] [INFO] Total running time: 0h0m46s