[2023-06-28 17:23:50,380] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:23:50,382] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:23:50,382] [INFO] DQC Reference Directory: /var/lib/cwl/stg6316bffe-86c6-4609-92fe-bf81e971731c/dqc_reference
[2023-06-28 17:23:51,605] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:23:51,609] [INFO] Task started: Prodigal
[2023-06-28 17:23:51,609] [INFO] Running command: gunzip -c /var/lib/cwl/stge32946ad-7fb2-48df-93e6-91505e89cdc6/GCA_002708145.1_ASM270814v1_genomic.fna.gz | prodigal -d GCA_002708145.1_ASM270814v1_genomic.fna/cds.fna -a GCA_002708145.1_ASM270814v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:23:53,802] [INFO] Task succeeded: Prodigal
[2023-06-28 17:23:53,802] [INFO] Task started: HMMsearch
[2023-06-28 17:23:53,802] [INFO] Running command: hmmsearch --tblout GCA_002708145.1_ASM270814v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6316bffe-86c6-4609-92fe-bf81e971731c/dqc_reference/reference_markers.hmm GCA_002708145.1_ASM270814v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:23:54,050] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:23:54,052] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge32946ad-7fb2-48df-93e6-91505e89cdc6/GCA_002708145.1_ASM270814v1_genomic.fna.gz]
[2023-06-28 17:23:54,076] [INFO] Query marker FASTA was written to GCA_002708145.1_ASM270814v1_genomic.fna/markers.fasta
[2023-06-28 17:23:54,076] [INFO] Task started: Blastn
[2023-06-28 17:23:54,076] [INFO] Running command: blastn -query GCA_002708145.1_ASM270814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6316bffe-86c6-4609-92fe-bf81e971731c/dqc_reference/reference_markers.fasta -out GCA_002708145.1_ASM270814v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:23:54,643] [INFO] Task succeeded: Blastn
[2023-06-28 17:23:54,647] [INFO] Selected 9 target genomes.
[2023-06-28 17:23:54,648] [INFO] Target genome list was writen to GCA_002708145.1_ASM270814v1_genomic.fna/target_genomes.txt
[2023-06-28 17:23:54,651] [INFO] Task started: fastANI
[2023-06-28 17:23:54,651] [INFO] Running command: fastANI --query /var/lib/cwl/stge32946ad-7fb2-48df-93e6-91505e89cdc6/GCA_002708145.1_ASM270814v1_genomic.fna.gz --refList GCA_002708145.1_ASM270814v1_genomic.fna/target_genomes.txt --output GCA_002708145.1_ASM270814v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:23:58,681] [INFO] Task succeeded: fastANI
[2023-06-28 17:23:58,681] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6316bffe-86c6-4609-92fe-bf81e971731c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:23:58,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6316bffe-86c6-4609-92fe-bf81e971731c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:23:58,684] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:23:58,684] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 17:23:58,684] [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
--------------------------------------------------------------------------------
[2023-06-28 17:23:58,687] [INFO] DFAST Taxonomy check result was written to GCA_002708145.1_ASM270814v1_genomic.fna/tc_result.tsv
[2023-06-28 17:23:58,688] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:23:58,688] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:23:58,689] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6316bffe-86c6-4609-92fe-bf81e971731c/dqc_reference/checkm_data
[2023-06-28 17:23:58,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:23:58,715] [INFO] Task started: CheckM
[2023-06-28 17:23:58,716] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708145.1_ASM270814v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708145.1_ASM270814v1_genomic.fna/checkm_input GCA_002708145.1_ASM270814v1_genomic.fna/checkm_result
[2023-06-28 17:24:13,981] [INFO] Task succeeded: CheckM
[2023-06-28 17:24:13,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.64%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 17:24:14,009] [INFO] ===== Completeness check finished =====
[2023-06-28 17:24:14,010] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:24:14,010] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708145.1_ASM270814v1_genomic.fna/markers.fasta)
[2023-06-28 17:24:14,011] [INFO] Task started: Blastn
[2023-06-28 17:24:14,011] [INFO] Running command: blastn -query GCA_002708145.1_ASM270814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6316bffe-86c6-4609-92fe-bf81e971731c/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708145.1_ASM270814v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:24:14,762] [INFO] Task succeeded: Blastn
[2023-06-28 17:24:14,767] [INFO] Selected 14 target genomes.
[2023-06-28 17:24:14,767] [INFO] Target genome list was writen to GCA_002708145.1_ASM270814v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:24:14,776] [INFO] Task started: fastANI
[2023-06-28 17:24:14,776] [INFO] Running command: fastANI --query /var/lib/cwl/stge32946ad-7fb2-48df-93e6-91505e89cdc6/GCA_002708145.1_ASM270814v1_genomic.fna.gz --refList GCA_002708145.1_ASM270814v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708145.1_ASM270814v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:24:19,549] [INFO] Task succeeded: fastANI
[2023-06-28 17:24:19,557] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 17:24:19,557] [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_002708145.1	s__GCA-002708145 sp002708145	100.0	430	435	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002708145	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002714425.1	s__GCA-002708145 sp002714425	82.1697	296	435	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002708145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002728715.1	s__GCA-002708145 sp002728715	81.8398	291	435	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002708145	95.0	98.77	97.83	0.89	0.87	3	-
GCA_002712125.1	s__GCA-002708145 sp002712125	81.4871	267	435	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002708145	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 17:24:19,559] [INFO] GTDB search result was written to GCA_002708145.1_ASM270814v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:24:19,560] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:24:19,562] [INFO] DFAST_QC result json was written to GCA_002708145.1_ASM270814v1_genomic.fna/dqc_result.json
[2023-06-28 17:24:19,563] [INFO] DFAST_QC completed!
[2023-06-28 17:24:19,563] [INFO] Total running time: 0h0m29s