[2023-03-15 07:52:40,220] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:52:40,220] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:52:40,220] [INFO] DQC Reference Directory: /var/lib/cwl/stg186ce53d-a201-4d1b-806a-19d9a783531d/dqc_reference
[2023-03-15 07:52:41,381] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:52:41,381] [INFO] Task started: Prodigal
[2023-03-15 07:52:41,381] [INFO] Running command: cat /var/lib/cwl/stg201f5373-b3df-4b0e-a6a1-30e80473ae8e/OceanDNA-a952.fa | prodigal -d OceanDNA-a952/cds.fna -a OceanDNA-a952/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:52:45,292] [INFO] Task succeeded: Prodigal
[2023-03-15 07:52:45,292] [INFO] Task started: HMMsearch
[2023-03-15 07:52:45,292] [INFO] Running command: hmmsearch --tblout OceanDNA-a952/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg186ce53d-a201-4d1b-806a-19d9a783531d/dqc_reference/reference_markers.hmm OceanDNA-a952/protein.faa > /dev/null
[2023-03-15 07:52:45,434] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:52:45,434] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg201f5373-b3df-4b0e-a6a1-30e80473ae8e/OceanDNA-a952.fa]
[2023-03-15 07:52:45,441] [INFO] Query marker FASTA was written to OceanDNA-a952/markers.fasta
[2023-03-15 07:52:45,441] [INFO] Task started: Blastn
[2023-03-15 07:52:45,441] [INFO] Running command: blastn -query OceanDNA-a952/markers.fasta -db /var/lib/cwl/stg186ce53d-a201-4d1b-806a-19d9a783531d/dqc_reference/reference_markers.fasta -out OceanDNA-a952/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:52:45,877] [INFO] Task succeeded: Blastn
[2023-03-15 07:52:45,877] [INFO] Selected 2 target genomes.
[2023-03-15 07:52:45,878] [INFO] Target genome list was writen to OceanDNA-a952/target_genomes.txt
[2023-03-15 07:52:45,879] [INFO] Task started: fastANI
[2023-03-15 07:52:45,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg201f5373-b3df-4b0e-a6a1-30e80473ae8e/OceanDNA-a952.fa --refList OceanDNA-a952/target_genomes.txt --output OceanDNA-a952/fastani_result.tsv --threads 1
[2023-03-15 07:52:46,537] [INFO] Task succeeded: fastANI
[2023-03-15 07:52:46,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg186ce53d-a201-4d1b-806a-19d9a783531d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:52:46,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg186ce53d-a201-4d1b-806a-19d9a783531d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:52:46,537] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:52:46,537] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:52:46,538] [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
--------------------------------------------------------------------------------
[2023-03-15 07:52:46,538] [INFO] DFAST Taxonomy check result was written to OceanDNA-a952/tc_result.tsv
[2023-03-15 07:52:46,538] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:52:46,538] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:52:46,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg186ce53d-a201-4d1b-806a-19d9a783531d/dqc_reference/checkm_data
[2023-03-15 07:52:46,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:52:47,026] [INFO] Task started: CheckM
[2023-03-15 07:52:47,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a952/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a952/checkm_input OceanDNA-a952/checkm_result
[2023-03-15 07:53:03,735] [INFO] Task succeeded: CheckM
[2023-03-15 07:53:03,735] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:53:03,737] [INFO] ===== Completeness check finished =====
[2023-03-15 07:53:03,737] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:53:03,737] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a952/markers.fasta)
[2023-03-15 07:53:03,737] [INFO] Task started: Blastn
[2023-03-15 07:53:03,737] [INFO] Running command: blastn -query OceanDNA-a952/markers.fasta -db /var/lib/cwl/stg186ce53d-a201-4d1b-806a-19d9a783531d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a952/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:53:04,451] [INFO] Task succeeded: Blastn
[2023-03-15 07:53:04,452] [INFO] Selected 8 target genomes.
[2023-03-15 07:53:04,452] [INFO] Target genome list was writen to OceanDNA-a952/target_genomes_gtdb.txt
[2023-03-15 07:53:04,463] [INFO] Task started: fastANI
[2023-03-15 07:53:04,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg201f5373-b3df-4b0e-a6a1-30e80473ae8e/OceanDNA-a952.fa --refList OceanDNA-a952/target_genomes_gtdb.txt --output OceanDNA-a952/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:53:06,253] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:06,257] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:53:06,257] [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_002495905.1	s__UBA57 sp002495905	99.0847	211	256	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__UBA57;g__UBA57	95.0	98.98	98.92	0.81	0.77	4	conclusive
GCA_013378385.1	s__UBA57 sp013378385	81.8508	190	256	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__UBA57;g__UBA57	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013306035.1	s__UBA57 sp002494565	81.292	190	256	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__UBA57;g__UBA57	95.0	98.92	96.91	0.92	0.82	6	-
GCA_002713205.1	s__UBA57 sp002713205	77.2343	70	256	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__UBA57;g__UBA57	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:53:06,258] [INFO] GTDB search result was written to OceanDNA-a952/result_gtdb.tsv
[2023-03-15 07:53:06,258] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:53:06,258] [INFO] DFAST_QC result json was written to OceanDNA-a952/dqc_result.json
[2023-03-15 07:53:06,258] [INFO] DFAST_QC completed!
[2023-03-15 07:53:06,259] [INFO] Total running time: 0h0m26s