[2023-03-17 11:52:51,140] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:52:51,146] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:52:51,146] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c5d69c4-7129-4106-bc88-d53a19b13d9b/dqc_reference
[2023-03-17 11:52:52,827] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:52:52,828] [INFO] Task started: Prodigal
[2023-03-17 11:52:52,828] [INFO] Running command: cat /var/lib/cwl/stg719d0795-04c0-4904-9422-c2e21c0f7823/OceanDNA-b32942.fa | prodigal -d OceanDNA-b32942/cds.fna -a OceanDNA-b32942/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:53:03,277] [INFO] Task succeeded: Prodigal
[2023-03-17 11:53:03,277] [INFO] Task started: HMMsearch
[2023-03-17 11:53:03,277] [INFO] Running command: hmmsearch --tblout OceanDNA-b32942/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c5d69c4-7129-4106-bc88-d53a19b13d9b/dqc_reference/reference_markers.hmm OceanDNA-b32942/protein.faa > /dev/null
[2023-03-17 11:53:03,456] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:53:03,457] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg719d0795-04c0-4904-9422-c2e21c0f7823/OceanDNA-b32942.fa]
[2023-03-17 11:53:03,542] [INFO] Query marker FASTA was written to OceanDNA-b32942/markers.fasta
[2023-03-17 11:53:03,542] [INFO] Task started: Blastn
[2023-03-17 11:53:03,542] [INFO] Running command: blastn -query OceanDNA-b32942/markers.fasta -db /var/lib/cwl/stg1c5d69c4-7129-4106-bc88-d53a19b13d9b/dqc_reference/reference_markers.fasta -out OceanDNA-b32942/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:53:04,087] [INFO] Task succeeded: Blastn
[2023-03-17 11:53:04,114] [INFO] Selected 25 target genomes.
[2023-03-17 11:53:04,114] [INFO] Target genome list was writen to OceanDNA-b32942/target_genomes.txt
[2023-03-17 11:53:04,125] [INFO] Task started: fastANI
[2023-03-17 11:53:04,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg719d0795-04c0-4904-9422-c2e21c0f7823/OceanDNA-b32942.fa --refList OceanDNA-b32942/target_genomes.txt --output OceanDNA-b32942/fastani_result.tsv --threads 1
[2023-03-17 11:53:19,764] [INFO] Task succeeded: fastANI
[2023-03-17 11:53:19,764] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c5d69c4-7129-4106-bc88-d53a19b13d9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:53:19,764] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c5d69c4-7129-4106-bc88-d53a19b13d9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:53:19,764] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:53:19,765] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:53:19,765] [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
--------------------------------------------------------------------------------
[2023-03-17 11:53:19,771] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32942/tc_result.tsv
[2023-03-17 11:53:19,783] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:53:19,783] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:53:19,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c5d69c4-7129-4106-bc88-d53a19b13d9b/dqc_reference/checkm_data
[2023-03-17 11:53:19,787] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:53:19,895] [INFO] Task started: CheckM
[2023-03-17 11:53:19,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32942/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32942/checkm_input OceanDNA-b32942/checkm_result
[2023-03-17 11:53:50,656] [INFO] Task succeeded: CheckM
[2023-03-17 11:53:50,657] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.40%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 11:53:50,912] [INFO] ===== Completeness check finished =====
[2023-03-17 11:53:50,912] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:53:50,912] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32942/markers.fasta)
[2023-03-17 11:53:50,913] [INFO] Task started: Blastn
[2023-03-17 11:53:50,913] [INFO] Running command: blastn -query OceanDNA-b32942/markers.fasta -db /var/lib/cwl/stg1c5d69c4-7129-4106-bc88-d53a19b13d9b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32942/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:53:51,706] [INFO] Task succeeded: Blastn
[2023-03-17 11:53:51,733] [INFO] Selected 25 target genomes.
[2023-03-17 11:53:51,733] [INFO] Target genome list was writen to OceanDNA-b32942/target_genomes_gtdb.txt
[2023-03-17 11:53:51,757] [INFO] Task started: fastANI
[2023-03-17 11:53:51,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg719d0795-04c0-4904-9422-c2e21c0f7823/OceanDNA-b32942.fa --refList OceanDNA-b32942/target_genomes_gtdb.txt --output OceanDNA-b32942/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:54:08,005] [INFO] Task succeeded: fastANI
[2023-03-17 11:54:08,007] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:54:08,008] [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_002937555.1	s__PTKB01 sp002937555	79.7303	245	545	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666805.1	s__PTKB01 sp018666805	77.6572	245	545	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	99.32	99.22	0.89	0.88	8	-
--------------------------------------------------------------------------------
[2023-03-17 11:54:08,017] [INFO] GTDB search result was written to OceanDNA-b32942/result_gtdb.tsv
[2023-03-17 11:54:08,035] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:54:08,046] [INFO] DFAST_QC result json was written to OceanDNA-b32942/dqc_result.json
[2023-03-17 11:54:08,046] [INFO] DFAST_QC completed!
[2023-03-17 11:54:08,047] [INFO] Total running time: 0h1m17s