[2023-03-18 00:15:08,339] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:15:08,339] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:15:08,339] [INFO] DQC Reference Directory: /var/lib/cwl/stg913cd338-844e-4b4b-950a-47dc17c577dc/dqc_reference
[2023-03-18 00:15:09,426] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:15:09,427] [INFO] Task started: Prodigal
[2023-03-18 00:15:09,427] [INFO] Running command: cat /var/lib/cwl/stg6f97c91a-90cd-4b7d-b376-a68867a9659c/OceanDNA-a483.fa | prodigal -d OceanDNA-a483/cds.fna -a OceanDNA-a483/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:15:14,536] [INFO] Task succeeded: Prodigal
[2023-03-18 00:15:14,536] [INFO] Task started: HMMsearch
[2023-03-18 00:15:14,536] [INFO] Running command: hmmsearch --tblout OceanDNA-a483/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg913cd338-844e-4b4b-950a-47dc17c577dc/dqc_reference/reference_markers.hmm OceanDNA-a483/protein.faa > /dev/null
[2023-03-18 00:15:14,650] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:15:14,651] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg6f97c91a-90cd-4b7d-b376-a68867a9659c/OceanDNA-a483.fa]
[2023-03-18 00:15:14,658] [INFO] Query marker FASTA was written to OceanDNA-a483/markers.fasta
[2023-03-18 00:15:14,659] [INFO] Task started: Blastn
[2023-03-18 00:15:14,659] [INFO] Running command: blastn -query OceanDNA-a483/markers.fasta -db /var/lib/cwl/stg913cd338-844e-4b4b-950a-47dc17c577dc/dqc_reference/reference_markers.fasta -out OceanDNA-a483/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:15:15,071] [INFO] Task succeeded: Blastn
[2023-03-18 00:15:15,073] [INFO] Selected 0 target genomes.
[2023-03-18 00:15:15,073] [INFO] Target genome list was writen to OceanDNA-a483/target_genomes.txt
[2023-03-18 00:15:15,073] [ERROR] File is empty. [OceanDNA-a483/target_genomes.txt]
[2023-03-18 00:15:15,073] [ERROR] Task failed. No target genome found.
[2023-03-18 00:15:15,073] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:15:15,074] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg913cd338-844e-4b4b-950a-47dc17c577dc/dqc_reference/checkm_data
[2023-03-18 00:15:15,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:15:15,084] [INFO] Task started: CheckM
[2023-03-18 00:15:15,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a483/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a483/checkm_input OceanDNA-a483/checkm_result
[2023-03-18 00:15:32,501] [INFO] Task succeeded: CheckM
[2023-03-18 00:15:32,502] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:15:32,504] [INFO] ===== Completeness check finished =====
[2023-03-18 00:15:32,504] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:15:32,505] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a483/markers.fasta)
[2023-03-18 00:15:32,506] [INFO] Task started: Blastn
[2023-03-18 00:15:32,506] [INFO] Running command: blastn -query OceanDNA-a483/markers.fasta -db /var/lib/cwl/stg913cd338-844e-4b4b-950a-47dc17c577dc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a483/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:15:33,020] [INFO] Task succeeded: Blastn
[2023-03-18 00:15:33,020] [INFO] Selected 5 target genomes.
[2023-03-18 00:15:33,021] [INFO] Target genome list was writen to OceanDNA-a483/target_genomes_gtdb.txt
[2023-03-18 00:15:33,028] [INFO] Task started: fastANI
[2023-03-18 00:15:33,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f97c91a-90cd-4b7d-b376-a68867a9659c/OceanDNA-a483.fa --refList OceanDNA-a483/target_genomes_gtdb.txt --output OceanDNA-a483/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:15:34,023] [INFO] Task succeeded: fastANI
[2023-03-18 00:15:34,027] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:15:34,028] [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_902578515.1	s__Nitrosopelagicus sp902578515	96.3635	131	237	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	96.49	96.49	0.54	0.54	2	conclusive
GCA_902590655.1	s__Nitrosopelagicus sp902590655	94.5778	173	237	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013390745.1	s__Nitrosopelagicus sp013390745	83.7991	207	237	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013390375.1	s__Nitrosopelagicus sp000484935	82.8727	214	237	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	97.75	96.12	0.83	0.80	4	-
GCA_013390765.1	s__Nitrosopelagicus sp013390765	81.6772	121	237	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:15:34,033] [INFO] GTDB search result was written to OceanDNA-a483/result_gtdb.tsv
[2023-03-18 00:15:34,034] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:15:34,035] [INFO] DFAST_QC result json was written to OceanDNA-a483/dqc_result.json
[2023-03-18 00:15:34,035] [INFO] DFAST_QC completed!
[2023-03-18 00:15:34,036] [INFO] Total running time: 0h0m26s