[2023-03-18 08:31:56,343] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:31:56,344] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:31:56,344] [INFO] DQC Reference Directory: /var/lib/cwl/stg18472413-e490-46b5-8aa1-200f7efea684/dqc_reference
[2023-03-18 08:31:57,440] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:31:57,440] [INFO] Task started: Prodigal
[2023-03-18 08:31:57,440] [INFO] Running command: cat /var/lib/cwl/stg21701afa-a499-4ef0-b35a-ec74627d2021/OceanDNA-a862.fa | prodigal -d OceanDNA-a862/cds.fna -a OceanDNA-a862/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:32:01,543] [INFO] Task succeeded: Prodigal
[2023-03-18 08:32:01,543] [INFO] Task started: HMMsearch
[2023-03-18 08:32:01,544] [INFO] Running command: hmmsearch --tblout OceanDNA-a862/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18472413-e490-46b5-8aa1-200f7efea684/dqc_reference/reference_markers.hmm OceanDNA-a862/protein.faa > /dev/null
[2023-03-18 08:32:01,654] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:32:01,654] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg21701afa-a499-4ef0-b35a-ec74627d2021/OceanDNA-a862.fa]
[2023-03-18 08:32:01,661] [INFO] Query marker FASTA was written to OceanDNA-a862/markers.fasta
[2023-03-18 08:32:01,661] [INFO] Task started: Blastn
[2023-03-18 08:32:01,661] [INFO] Running command: blastn -query OceanDNA-a862/markers.fasta -db /var/lib/cwl/stg18472413-e490-46b5-8aa1-200f7efea684/dqc_reference/reference_markers.fasta -out OceanDNA-a862/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:32:02,084] [INFO] Task succeeded: Blastn
[2023-03-18 08:32:02,084] [INFO] Selected 0 target genomes.
[2023-03-18 08:32:02,084] [INFO] Target genome list was writen to OceanDNA-a862/target_genomes.txt
[2023-03-18 08:32:02,085] [ERROR] File is empty. [OceanDNA-a862/target_genomes.txt]
[2023-03-18 08:32:02,085] [ERROR] Task failed. No target genome found.
[2023-03-18 08:32:02,085] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:32:02,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18472413-e490-46b5-8aa1-200f7efea684/dqc_reference/checkm_data
[2023-03-18 08:32:02,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:32:02,142] [INFO] Task started: CheckM
[2023-03-18 08:32:02,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a862/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a862/checkm_input OceanDNA-a862/checkm_result
[2023-03-18 08:32:19,703] [INFO] Task succeeded: CheckM
[2023-03-18 08:32:19,704] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:32:19,705] [INFO] ===== Completeness check finished =====
[2023-03-18 08:32:19,705] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:32:19,705] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a862/markers.fasta)
[2023-03-18 08:32:19,706] [INFO] Task started: Blastn
[2023-03-18 08:32:19,706] [INFO] Running command: blastn -query OceanDNA-a862/markers.fasta -db /var/lib/cwl/stg18472413-e490-46b5-8aa1-200f7efea684/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a862/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:32:20,185] [INFO] Task succeeded: Blastn
[2023-03-18 08:32:20,186] [INFO] Selected 4 target genomes.
[2023-03-18 08:32:20,186] [INFO] Target genome list was writen to OceanDNA-a862/target_genomes_gtdb.txt
[2023-03-18 08:32:20,246] [INFO] Task started: fastANI
[2023-03-18 08:32:20,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg21701afa-a499-4ef0-b35a-ec74627d2021/OceanDNA-a862.fa --refList OceanDNA-a862/target_genomes_gtdb.txt --output OceanDNA-a862/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:32:20,953] [INFO] Task succeeded: fastANI
[2023-03-18 08:32:20,956] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:32:20,956] [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_002713205.1	s__UBA57 sp002713205	91.3449	218	266	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	77.6787	74	266	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__UBA57;g__UBA57	95.0	98.92	96.91	0.92	0.82	6	-
GCA_002495905.1	s__UBA57 sp002495905	76.5388	77	266	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__UBA57;g__UBA57	95.0	98.98	98.92	0.81	0.77	4	-
--------------------------------------------------------------------------------
[2023-03-18 08:32:20,956] [INFO] GTDB search result was written to OceanDNA-a862/result_gtdb.tsv
[2023-03-18 08:32:20,956] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:32:20,957] [INFO] DFAST_QC result json was written to OceanDNA-a862/dqc_result.json
[2023-03-18 08:32:20,957] [INFO] DFAST_QC completed!
[2023-03-18 08:32:20,957] [INFO] Total running time: 0h0m25s