[2023-03-18 08:36:16,001] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:36:16,001] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:36:16,001] [INFO] DQC Reference Directory: /var/lib/cwl/stga3069561-e227-4b8b-bde8-31135c4303d7/dqc_reference
[2023-03-18 08:36:17,826] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:36:17,826] [INFO] Task started: Prodigal
[2023-03-18 08:36:17,826] [INFO] Running command: cat /var/lib/cwl/stg199419c8-2a48-41ef-969a-59e28f1ca624/OceanDNA-a640.fa | prodigal -d OceanDNA-a640/cds.fna -a OceanDNA-a640/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:36:22,157] [INFO] Task succeeded: Prodigal
[2023-03-18 08:36:22,157] [INFO] Task started: HMMsearch
[2023-03-18 08:36:22,157] [INFO] Running command: hmmsearch --tblout OceanDNA-a640/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3069561-e227-4b8b-bde8-31135c4303d7/dqc_reference/reference_markers.hmm OceanDNA-a640/protein.faa > /dev/null
[2023-03-18 08:36:22,286] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:36:22,287] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg199419c8-2a48-41ef-969a-59e28f1ca624/OceanDNA-a640.fa]
[2023-03-18 08:36:22,295] [INFO] Query marker FASTA was written to OceanDNA-a640/markers.fasta
[2023-03-18 08:36:22,295] [INFO] Task started: Blastn
[2023-03-18 08:36:22,295] [INFO] Running command: blastn -query OceanDNA-a640/markers.fasta -db /var/lib/cwl/stga3069561-e227-4b8b-bde8-31135c4303d7/dqc_reference/reference_markers.fasta -out OceanDNA-a640/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:36:22,725] [INFO] Task succeeded: Blastn
[2023-03-18 08:36:22,726] [INFO] Selected 0 target genomes.
[2023-03-18 08:36:22,726] [INFO] Target genome list was writen to OceanDNA-a640/target_genomes.txt
[2023-03-18 08:36:22,726] [ERROR] File is empty. [OceanDNA-a640/target_genomes.txt]
[2023-03-18 08:36:22,726] [ERROR] Task failed. No target genome found.
[2023-03-18 08:36:22,726] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:36:22,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3069561-e227-4b8b-bde8-31135c4303d7/dqc_reference/checkm_data
[2023-03-18 08:36:22,779] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:36:22,781] [INFO] Task started: CheckM
[2023-03-18 08:36:22,781] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a640/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a640/checkm_input OceanDNA-a640/checkm_result
[2023-03-18 08:36:41,695] [INFO] Task succeeded: CheckM
[2023-03-18 08:36:41,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:36:41,697] [INFO] ===== Completeness check finished =====
[2023-03-18 08:36:41,697] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:36:41,697] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a640/markers.fasta)
[2023-03-18 08:36:41,697] [INFO] Task started: Blastn
[2023-03-18 08:36:41,697] [INFO] Running command: blastn -query OceanDNA-a640/markers.fasta -db /var/lib/cwl/stga3069561-e227-4b8b-bde8-31135c4303d7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a640/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:36:42,063] [INFO] Task succeeded: Blastn
[2023-03-18 08:36:42,064] [INFO] Selected 5 target genomes.
[2023-03-18 08:36:42,064] [INFO] Target genome list was writen to OceanDNA-a640/target_genomes_gtdb.txt
[2023-03-18 08:36:42,067] [INFO] Task started: fastANI
[2023-03-18 08:36:42,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg199419c8-2a48-41ef-969a-59e28f1ca624/OceanDNA-a640.fa --refList OceanDNA-a640/target_genomes_gtdb.txt --output OceanDNA-a640/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:36:43,070] [INFO] Task succeeded: fastANI
[2023-03-18 08:36:43,074] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:36:43,074] [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_014384445.1	s__Nitrosopumilus sp014384445	98.0099	111	153	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905612295.1	s__Nitrosopumilus sp905612295	93.8322	110	153	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001437625.1	s__Nitrosopumilus sp001437625	92.3502	139	153	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.62	95.42	0.85	0.75	5	-
GCA_018657375.1	s__Nitrosopumilus sp018657375	91.6943	99	153	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.79	98.40	0.79	0.75	5	-
GCA_018674605.1	s__Nitrosopumilus sp018674605	85.6301	88	153	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.83	98.50	0.79	0.69	12	-
--------------------------------------------------------------------------------
[2023-03-18 08:36:43,074] [INFO] GTDB search result was written to OceanDNA-a640/result_gtdb.tsv
[2023-03-18 08:36:43,074] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:36:43,075] [INFO] DFAST_QC result json was written to OceanDNA-a640/dqc_result.json
[2023-03-18 08:36:43,075] [INFO] DFAST_QC completed!
[2023-03-18 08:36:43,075] [INFO] Total running time: 0h0m27s