[2023-03-16 10:57:32,972] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:57:32,972] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:57:32,972] [INFO] DQC Reference Directory: /var/lib/cwl/stge2b6ed89-9b0f-4075-b7dc-03eb7d758c1a/dqc_reference
[2023-03-16 10:57:34,142] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:57:34,143] [INFO] Task started: Prodigal
[2023-03-16 10:57:34,143] [INFO] Running command: cat /var/lib/cwl/stgdbc9be64-c0d3-430f-b81e-7498e77c366d/OceanDNA-a1041.fa | prodigal -d OceanDNA-a1041/cds.fna -a OceanDNA-a1041/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:57:36,552] [INFO] Task succeeded: Prodigal
[2023-03-16 10:57:36,553] [INFO] Task started: HMMsearch
[2023-03-16 10:57:36,553] [INFO] Running command: hmmsearch --tblout OceanDNA-a1041/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2b6ed89-9b0f-4075-b7dc-03eb7d758c1a/dqc_reference/reference_markers.hmm OceanDNA-a1041/protein.faa > /dev/null
[2023-03-16 10:57:36,741] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:57:36,741] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgdbc9be64-c0d3-430f-b81e-7498e77c366d/OceanDNA-a1041.fa]
[2023-03-16 10:57:36,745] [INFO] Query marker FASTA was written to OceanDNA-a1041/markers.fasta
[2023-03-16 10:57:36,747] [INFO] Task started: Blastn
[2023-03-16 10:57:36,747] [INFO] Running command: blastn -query OceanDNA-a1041/markers.fasta -db /var/lib/cwl/stge2b6ed89-9b0f-4075-b7dc-03eb7d758c1a/dqc_reference/reference_markers.fasta -out OceanDNA-a1041/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:57:37,706] [INFO] Task succeeded: Blastn
[2023-03-16 10:57:37,708] [INFO] Selected 0 target genomes.
[2023-03-16 10:57:37,708] [INFO] Target genome list was writen to OceanDNA-a1041/target_genomes.txt
[2023-03-16 10:57:37,708] [ERROR] File is empty. [OceanDNA-a1041/target_genomes.txt]
[2023-03-16 10:57:37,708] [ERROR] Task failed. No target genome found.
[2023-03-16 10:57:37,708] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:57:37,708] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2b6ed89-9b0f-4075-b7dc-03eb7d758c1a/dqc_reference/checkm_data
[2023-03-16 10:57:37,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:57:37,759] [INFO] Task started: CheckM
[2023-03-16 10:57:37,759] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1041/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1041/checkm_input OceanDNA-a1041/checkm_result
[2023-03-16 10:58:04,311] [INFO] Task succeeded: CheckM
[2023-03-16 10:58:04,312] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.21%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:58:04,314] [INFO] ===== Completeness check finished =====
[2023-03-16 10:58:04,314] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:58:04,314] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1041/markers.fasta)
[2023-03-16 10:58:04,315] [INFO] Task started: Blastn
[2023-03-16 10:58:04,315] [INFO] Running command: blastn -query OceanDNA-a1041/markers.fasta -db /var/lib/cwl/stge2b6ed89-9b0f-4075-b7dc-03eb7d758c1a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1041/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:58:04,970] [INFO] Task succeeded: Blastn
[2023-03-16 10:58:04,972] [INFO] Selected 5 target genomes.
[2023-03-16 10:58:04,972] [INFO] Target genome list was writen to OceanDNA-a1041/target_genomes_gtdb.txt
[2023-03-16 10:58:04,997] [INFO] Task started: fastANI
[2023-03-16 10:58:04,998] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbc9be64-c0d3-430f-b81e-7498e77c366d/OceanDNA-a1041.fa --refList OceanDNA-a1041/target_genomes_gtdb.txt --output OceanDNA-a1041/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:58:05,988] [INFO] Task succeeded: fastANI
[2023-03-16 10:58:05,990] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:58:05,990] [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_018693315.1	s__JAGVXH01 sp018693315	88.452	58	70	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Pacearchaeales;f__GW2011-AR1;g__JAGVXH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:58:05,991] [INFO] GTDB search result was written to OceanDNA-a1041/result_gtdb.tsv
[2023-03-16 10:58:05,991] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:58:05,992] [INFO] DFAST_QC result json was written to OceanDNA-a1041/dqc_result.json
[2023-03-16 10:58:05,992] [INFO] DFAST_QC completed!
[2023-03-16 10:58:05,992] [INFO] Total running time: 0h0m33s