[2023-03-19 04:46:19,985] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:46:19,985] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:46:19,985] [INFO] DQC Reference Directory: /var/lib/cwl/stgdae7c187-c06a-452c-ba27-72a86136cd99/dqc_reference
[2023-03-19 04:46:21,052] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:46:21,052] [INFO] Task started: Prodigal
[2023-03-19 04:46:21,052] [INFO] Running command: cat /var/lib/cwl/stg18a62b6d-0939-4de8-a425-ea51fac4df0c/OceanDNA-b4346.fa | prodigal -d OceanDNA-b4346/cds.fna -a OceanDNA-b4346/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:46:24,963] [INFO] Task succeeded: Prodigal
[2023-03-19 04:46:24,964] [INFO] Task started: HMMsearch
[2023-03-19 04:46:24,964] [INFO] Running command: hmmsearch --tblout OceanDNA-b4346/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdae7c187-c06a-452c-ba27-72a86136cd99/dqc_reference/reference_markers.hmm OceanDNA-b4346/protein.faa > /dev/null
[2023-03-19 04:46:25,110] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:46:25,111] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg18a62b6d-0939-4de8-a425-ea51fac4df0c/OceanDNA-b4346.fa]
[2023-03-19 04:46:25,120] [INFO] Query marker FASTA was written to OceanDNA-b4346/markers.fasta
[2023-03-19 04:46:25,122] [INFO] Task started: Blastn
[2023-03-19 04:46:25,122] [INFO] Running command: blastn -query OceanDNA-b4346/markers.fasta -db /var/lib/cwl/stgdae7c187-c06a-452c-ba27-72a86136cd99/dqc_reference/reference_markers.fasta -out OceanDNA-b4346/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:46:25,672] [INFO] Task succeeded: Blastn
[2023-03-19 04:46:25,673] [INFO] Selected 17 target genomes.
[2023-03-19 04:46:25,673] [INFO] Target genome list was writen to OceanDNA-b4346/target_genomes.txt
[2023-03-19 04:46:25,685] [INFO] Task started: fastANI
[2023-03-19 04:46:25,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg18a62b6d-0939-4de8-a425-ea51fac4df0c/OceanDNA-b4346.fa --refList OceanDNA-b4346/target_genomes.txt --output OceanDNA-b4346/fastani_result.tsv --threads 1
[2023-03-19 04:46:33,144] [INFO] Task succeeded: fastANI
[2023-03-19 04:46:33,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdae7c187-c06a-452c-ba27-72a86136cd99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:46:33,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdae7c187-c06a-452c-ba27-72a86136cd99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:46:33,145] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:46:33,145] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:46:33,145] [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
--------------------------------------------------------------------------------
[2023-03-19 04:46:33,145] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4346/tc_result.tsv
[2023-03-19 04:46:33,145] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:46:33,145] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:46:33,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdae7c187-c06a-452c-ba27-72a86136cd99/dqc_reference/checkm_data
[2023-03-19 04:46:33,148] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:46:33,203] [INFO] Task started: CheckM
[2023-03-19 04:46:33,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4346/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4346/checkm_input OceanDNA-b4346/checkm_result
[2023-03-19 04:46:49,174] [INFO] Task succeeded: CheckM
[2023-03-19 04:46:49,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.61%
Contamintation: 1.56%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-19 04:46:49,177] [INFO] ===== Completeness check finished =====
[2023-03-19 04:46:49,177] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:46:49,177] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4346/markers.fasta)
[2023-03-19 04:46:49,178] [INFO] Task started: Blastn
[2023-03-19 04:46:49,178] [INFO] Running command: blastn -query OceanDNA-b4346/markers.fasta -db /var/lib/cwl/stgdae7c187-c06a-452c-ba27-72a86136cd99/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4346/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:46:49,576] [INFO] Task succeeded: Blastn
[2023-03-19 04:46:49,577] [INFO] Selected 19 target genomes.
[2023-03-19 04:46:49,577] [INFO] Target genome list was writen to OceanDNA-b4346/target_genomes_gtdb.txt
[2023-03-19 04:46:49,599] [INFO] Task started: fastANI
[2023-03-19 04:46:49,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg18a62b6d-0939-4de8-a425-ea51fac4df0c/OceanDNA-b4346.fa --refList OceanDNA-b4346/target_genomes_gtdb.txt --output OceanDNA-b4346/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:46:55,898] [INFO] Task succeeded: fastANI
[2023-03-19 04:46:55,900] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:46:55,900] [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_902626505.1	s__MED-G16 sp902626505	84.2856	99	120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:46:55,900] [INFO] GTDB search result was written to OceanDNA-b4346/result_gtdb.tsv
[2023-03-19 04:46:55,900] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:46:55,901] [INFO] DFAST_QC result json was written to OceanDNA-b4346/dqc_result.json
[2023-03-19 04:46:55,901] [INFO] DFAST_QC completed!
[2023-03-19 04:46:55,901] [INFO] Total running time: 0h0m36s