[2023-06-05 05:15:46,779] [INFO] DFAST_QC pipeline started.
[2023-06-05 05:15:46,829] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 05:15:46,829] [INFO] DQC Reference Directory: /var/lib/cwl/stg1799e493-0ad3-4401-8ffc-b96df09d1727/dqc_reference
[2023-06-05 05:15:48,078] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 05:15:48,079] [INFO] Task started: Prodigal
[2023-06-05 05:15:48,080] [INFO] Running command: gunzip -c /var/lib/cwl/stg6157e99d-484e-4bd8-b378-79a1ee9a94a2/GCA_902624705.1_AH-287-J02_genomic.fna.gz | prodigal -d GCA_902624705.1_AH-287-J02_genomic.fna/cds.fna -a GCA_902624705.1_AH-287-J02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 05:15:49,604] [INFO] Task succeeded: Prodigal
[2023-06-05 05:15:49,605] [INFO] Task started: HMMsearch
[2023-06-05 05:15:49,605] [INFO] Running command: hmmsearch --tblout GCA_902624705.1_AH-287-J02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1799e493-0ad3-4401-8ffc-b96df09d1727/dqc_reference/reference_markers.hmm GCA_902624705.1_AH-287-J02_genomic.fna/protein.faa > /dev/null
[2023-06-05 05:15:49,763] [INFO] Task succeeded: HMMsearch
[2023-06-05 05:15:49,765] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg6157e99d-484e-4bd8-b378-79a1ee9a94a2/GCA_902624705.1_AH-287-J02_genomic.fna.gz]
[2023-06-05 05:15:49,780] [INFO] Query marker FASTA was written to GCA_902624705.1_AH-287-J02_genomic.fna/markers.fasta
[2023-06-05 05:15:49,781] [INFO] Task started: Blastn
[2023-06-05 05:15:49,781] [INFO] Running command: blastn -query GCA_902624705.1_AH-287-J02_genomic.fna/markers.fasta -db /var/lib/cwl/stg1799e493-0ad3-4401-8ffc-b96df09d1727/dqc_reference/reference_markers.fasta -out GCA_902624705.1_AH-287-J02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:15:50,278] [INFO] Task succeeded: Blastn
[2023-06-05 05:15:50,283] [INFO] Selected 5 target genomes.
[2023-06-05 05:15:50,283] [INFO] Target genome list was writen to GCA_902624705.1_AH-287-J02_genomic.fna/target_genomes.txt
[2023-06-05 05:15:50,284] [INFO] Task started: fastANI
[2023-06-05 05:15:50,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg6157e99d-484e-4bd8-b378-79a1ee9a94a2/GCA_902624705.1_AH-287-J02_genomic.fna.gz --refList GCA_902624705.1_AH-287-J02_genomic.fna/target_genomes.txt --output GCA_902624705.1_AH-287-J02_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 05:15:51,906] [INFO] Task succeeded: fastANI
[2023-06-05 05:15:51,907] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1799e493-0ad3-4401-8ffc-b96df09d1727/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 05:15:51,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1799e493-0ad3-4401-8ffc-b96df09d1727/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 05:15:51,909] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 05:15:51,909] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 05:15:51,909] [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 05:15:51,911] [INFO] DFAST Taxonomy check result was written to GCA_902624705.1_AH-287-J02_genomic.fna/tc_result.tsv
[2023-06-05 05:15:51,912] [INFO] ===== Taxonomy check completed =====
[2023-06-05 05:15:51,912] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 05:15:51,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1799e493-0ad3-4401-8ffc-b96df09d1727/dqc_reference/checkm_data
[2023-06-05 05:15:51,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 05:15:51,925] [INFO] Task started: CheckM
[2023-06-05 05:15:51,925] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902624705.1_AH-287-J02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902624705.1_AH-287-J02_genomic.fna/checkm_input GCA_902624705.1_AH-287-J02_genomic.fna/checkm_result
[2023-06-05 05:16:04,138] [INFO] Task succeeded: CheckM
[2023-06-05 05:16:04,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 05:16:04,158] [INFO] ===== Completeness check finished =====
[2023-06-05 05:16:04,158] [INFO] ===== Start GTDB Search =====
[2023-06-05 05:16:04,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902624705.1_AH-287-J02_genomic.fna/markers.fasta)
[2023-06-05 05:16:04,159] [INFO] Task started: Blastn
[2023-06-05 05:16:04,159] [INFO] Running command: blastn -query GCA_902624705.1_AH-287-J02_genomic.fna/markers.fasta -db /var/lib/cwl/stg1799e493-0ad3-4401-8ffc-b96df09d1727/dqc_reference/reference_markers_gtdb.fasta -out GCA_902624705.1_AH-287-J02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:16:04,701] [INFO] Task succeeded: Blastn
[2023-06-05 05:16:04,706] [INFO] Selected 5 target genomes.
[2023-06-05 05:16:04,706] [INFO] Target genome list was writen to GCA_902624705.1_AH-287-J02_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 05:16:04,711] [INFO] Task started: fastANI
[2023-06-05 05:16:04,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg6157e99d-484e-4bd8-b378-79a1ee9a94a2/GCA_902624705.1_AH-287-J02_genomic.fna.gz --refList GCA_902624705.1_AH-287-J02_genomic.fna/target_genomes_gtdb.txt --output GCA_902624705.1_AH-287-J02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 05:16:05,531] [INFO] Task succeeded: fastANI
[2023-06-05 05:16:05,541] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 05:16:05,541] [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_902630945.1	s__Pelagibacter sp902630945	89.4168	85	164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902571375.1	s__Pelagibacter sp902571375	82.3526	119	164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902601235.1	s__Pelagibacter sp902601235	81.2063	79	164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014654455.1	s__Pelagibacter sp014654455	81.1299	123	164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902568875.1	s__Pelagibacter sp902568875	80.806	97	164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 05:16:05,544] [INFO] GTDB search result was written to GCA_902624705.1_AH-287-J02_genomic.fna/result_gtdb.tsv
[2023-06-05 05:16:05,544] [INFO] ===== GTDB Search completed =====
[2023-06-05 05:16:05,547] [INFO] DFAST_QC result json was written to GCA_902624705.1_AH-287-J02_genomic.fna/dqc_result.json
[2023-06-05 05:16:05,548] [INFO] DFAST_QC completed!
[2023-06-05 05:16:05,548] [INFO] Total running time: 0h0m19s