[2023-06-13 13:44:17,161] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:44:17,165] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:44:17,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c09beee-b073-4d8c-a321-7c82c54f6260/dqc_reference
[2023-06-13 13:44:18,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:44:18,379] [INFO] Task started: Prodigal
[2023-06-13 13:44:18,379] [INFO] Running command: gunzip -c /var/lib/cwl/stgad7272bb-a723-4490-9a6a-369187ad74f4/GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna.gz | prodigal -d GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/cds.fna -a GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:44:21,692] [INFO] Task succeeded: Prodigal
[2023-06-13 13:44:21,693] [INFO] Task started: HMMsearch
[2023-06-13 13:44:21,693] [INFO] Running command: hmmsearch --tblout GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c09beee-b073-4d8c-a321-7c82c54f6260/dqc_reference/reference_markers.hmm GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:44:21,903] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:44:21,906] [INFO] Found 6/6 markers.
[2023-06-13 13:44:21,927] [INFO] Query marker FASTA was written to GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/markers.fasta
[2023-06-13 13:44:21,928] [INFO] Task started: Blastn
[2023-06-13 13:44:21,928] [INFO] Running command: blastn -query GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c09beee-b073-4d8c-a321-7c82c54f6260/dqc_reference/reference_markers.fasta -out GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:44:22,577] [INFO] Task succeeded: Blastn
[2023-06-13 13:44:22,582] [INFO] Selected 35 target genomes.
[2023-06-13 13:44:22,582] [INFO] Target genome list was writen to GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/target_genomes.txt
[2023-06-13 13:44:22,589] [INFO] Task started: fastANI
[2023-06-13 13:44:22,590] [INFO] Running command: fastANI --query /var/lib/cwl/stgad7272bb-a723-4490-9a6a-369187ad74f4/GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna.gz --refList GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/target_genomes.txt --output GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:44:45,219] [INFO] Task succeeded: fastANI
[2023-06-13 13:44:45,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c09beee-b073-4d8c-a321-7c82c54f6260/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:44:45,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c09beee-b073-4d8c-a321-7c82c54f6260/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:44:45,222] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:44:45,223] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 13:44:45,223] [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 13:44:45,226] [INFO] DFAST Taxonomy check result was written to GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/tc_result.tsv
[2023-06-13 13:44:45,227] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:44:45,227] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:44:45,227] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c09beee-b073-4d8c-a321-7c82c54f6260/dqc_reference/checkm_data
[2023-06-13 13:44:45,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:44:45,251] [INFO] Task started: CheckM
[2023-06-13 13:44:45,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/checkm_input GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/checkm_result
[2023-06-13 13:45:02,770] [INFO] Task succeeded: CheckM
[2023-06-13 13:45:02,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 13:45:02,795] [INFO] ===== Completeness check finished =====
[2023-06-13 13:45:02,796] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:45:02,796] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/markers.fasta)
[2023-06-13 13:45:02,796] [INFO] Task started: Blastn
[2023-06-13 13:45:02,797] [INFO] Running command: blastn -query GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c09beee-b073-4d8c-a321-7c82c54f6260/dqc_reference/reference_markers_gtdb.fasta -out GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:45:03,588] [INFO] Task succeeded: Blastn
[2023-06-13 13:45:03,594] [INFO] Selected 19 target genomes.
[2023-06-13 13:45:03,594] [INFO] Target genome list was writen to GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:45:03,641] [INFO] Task started: fastANI
[2023-06-13 13:45:03,642] [INFO] Running command: fastANI --query /var/lib/cwl/stgad7272bb-a723-4490-9a6a-369187ad74f4/GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna.gz --refList GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/target_genomes_gtdb.txt --output GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:45:15,086] [INFO] Task succeeded: fastANI
[2023-06-13 13:45:15,095] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 13:45:15,095] [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_013283365.1	s__Marinobacterium sp013283365	87.9075	428	457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	98.13	97.87	0.91	0.89	16	-
GCA_018623095.1	s__Marinobacterium sp018623095	84.6132	299	457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012848475.1	s__Marinobacterium sp012848475	79.9312	159	457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373575.1	s__Marinobacterium sp013373575	78.1241	75	457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 13:45:15,097] [INFO] GTDB search result was written to GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/result_gtdb.tsv
[2023-06-13 13:45:15,098] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:45:15,101] [INFO] DFAST_QC result json was written to GCA_938091545.1_S4_Bin_Bin_5_1_genomic.fna/dqc_result.json
[2023-06-13 13:45:15,102] [INFO] DFAST_QC completed!
[2023-06-13 13:45:15,102] [INFO] Total running time: 0h0m58s