[2023-06-05 15:05:22,484] [INFO] DFAST_QC pipeline started.
[2023-06-05 15:05:22,486] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 15:05:22,486] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc8e1808-cd19-4765-b2f3-7de7af60bd3f/dqc_reference
[2023-06-05 15:05:23,666] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 15:05:23,667] [INFO] Task started: Prodigal
[2023-06-05 15:05:23,667] [INFO] Running command: gunzip -c /var/lib/cwl/stg91335531-c884-4f3d-8980-b151a0b687a6/GCA_004367355.1_ASM436735v1_genomic.fna.gz | prodigal -d GCA_004367355.1_ASM436735v1_genomic.fna/cds.fna -a GCA_004367355.1_ASM436735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 15:05:28,121] [INFO] Task succeeded: Prodigal
[2023-06-05 15:05:28,122] [INFO] Task started: HMMsearch
[2023-06-05 15:05:28,122] [INFO] Running command: hmmsearch --tblout GCA_004367355.1_ASM436735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc8e1808-cd19-4765-b2f3-7de7af60bd3f/dqc_reference/reference_markers.hmm GCA_004367355.1_ASM436735v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 15:05:28,311] [INFO] Task succeeded: HMMsearch
[2023-06-05 15:05:28,312] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg91335531-c884-4f3d-8980-b151a0b687a6/GCA_004367355.1_ASM436735v1_genomic.fna.gz]
[2023-06-05 15:05:28,338] [INFO] Query marker FASTA was written to GCA_004367355.1_ASM436735v1_genomic.fna/markers.fasta
[2023-06-05 15:05:28,339] [INFO] Task started: Blastn
[2023-06-05 15:05:28,339] [INFO] Running command: blastn -query GCA_004367355.1_ASM436735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc8e1808-cd19-4765-b2f3-7de7af60bd3f/dqc_reference/reference_markers.fasta -out GCA_004367355.1_ASM436735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 15:05:28,956] [INFO] Task succeeded: Blastn
[2023-06-05 15:05:28,960] [INFO] Selected 17 target genomes.
[2023-06-05 15:05:28,961] [INFO] Target genome list was writen to GCA_004367355.1_ASM436735v1_genomic.fna/target_genomes.txt
[2023-06-05 15:05:28,964] [INFO] Task started: fastANI
[2023-06-05 15:05:28,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg91335531-c884-4f3d-8980-b151a0b687a6/GCA_004367355.1_ASM436735v1_genomic.fna.gz --refList GCA_004367355.1_ASM436735v1_genomic.fna/target_genomes.txt --output GCA_004367355.1_ASM436735v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 15:05:41,346] [INFO] Task succeeded: fastANI
[2023-06-05 15:05:41,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc8e1808-cd19-4765-b2f3-7de7af60bd3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 15:05:41,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc8e1808-cd19-4765-b2f3-7de7af60bd3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 15:05:41,348] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 15:05:41,349] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 15:05:41,349] [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
--------------------------------------------------------------------------------
[2023-06-05 15:05:41,351] [INFO] DFAST Taxonomy check result was written to GCA_004367355.1_ASM436735v1_genomic.fna/tc_result.tsv
[2023-06-05 15:05:41,351] [INFO] ===== Taxonomy check completed =====
[2023-06-05 15:05:41,351] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 15:05:41,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc8e1808-cd19-4765-b2f3-7de7af60bd3f/dqc_reference/checkm_data
[2023-06-05 15:05:41,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 15:05:41,380] [INFO] Task started: CheckM
[2023-06-05 15:05:41,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004367355.1_ASM436735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004367355.1_ASM436735v1_genomic.fna/checkm_input GCA_004367355.1_ASM436735v1_genomic.fna/checkm_result
[2023-06-05 15:06:01,054] [INFO] Task succeeded: CheckM
[2023-06-05 15:06:01,055] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 8.80%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-05 15:06:01,076] [INFO] ===== Completeness check finished =====
[2023-06-05 15:06:01,076] [INFO] ===== Start GTDB Search =====
[2023-06-05 15:06:01,076] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004367355.1_ASM436735v1_genomic.fna/markers.fasta)
[2023-06-05 15:06:01,076] [INFO] Task started: Blastn
[2023-06-05 15:06:01,077] [INFO] Running command: blastn -query GCA_004367355.1_ASM436735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc8e1808-cd19-4765-b2f3-7de7af60bd3f/dqc_reference/reference_markers_gtdb.fasta -out GCA_004367355.1_ASM436735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 15:06:01,903] [INFO] Task succeeded: Blastn
[2023-06-05 15:06:01,909] [INFO] Selected 13 target genomes.
[2023-06-05 15:06:01,909] [INFO] Target genome list was writen to GCA_004367355.1_ASM436735v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 15:06:02,010] [INFO] Task started: fastANI
[2023-06-05 15:06:02,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg91335531-c884-4f3d-8980-b151a0b687a6/GCA_004367355.1_ASM436735v1_genomic.fna.gz --refList GCA_004367355.1_ASM436735v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004367355.1_ASM436735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 15:06:08,613] [INFO] Task succeeded: fastANI
[2023-06-05 15:06:08,618] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 15:06:08,618] [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_003530255.1	s__UBA9673 sp003530255	99.2979	314	372	d__Bacteria;p__Firmicutes_E;c__DTU015;o__UBA9673;f__UBA9673;g__UBA9673	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003541445.1	s__UBA9673 sp003541445	93.1302	255	372	d__Bacteria;p__Firmicutes_E;c__DTU015;o__UBA9673;f__UBA9673;g__UBA9673	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599345.1	s__SURF-36 sp003599345	77.1099	80	372	d__Bacteria;p__Firmicutes_E;c__DTU015;o__UBA9673;f__UBA9673;g__SURF-36	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 15:06:08,621] [INFO] GTDB search result was written to GCA_004367355.1_ASM436735v1_genomic.fna/result_gtdb.tsv
[2023-06-05 15:06:08,621] [INFO] ===== GTDB Search completed =====
[2023-06-05 15:06:08,624] [INFO] DFAST_QC result json was written to GCA_004367355.1_ASM436735v1_genomic.fna/dqc_result.json
[2023-06-05 15:06:08,625] [INFO] DFAST_QC completed!
[2023-06-05 15:06:08,625] [INFO] Total running time: 0h0m46s