[2023-03-15 07:11:33,440] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:11:33,441] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:11:33,441] [INFO] DQC Reference Directory: /var/lib/cwl/stga1e496fe-1f52-48eb-b77c-5b85c68736fd/dqc_reference
[2023-03-15 07:11:34,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:11:34,534] [INFO] Task started: Prodigal
[2023-03-15 07:11:34,534] [INFO] Running command: cat /var/lib/cwl/stg47c28e18-3d72-4c06-b1f1-fa8ac140a65a/OceanDNA-a1690.fa | prodigal -d OceanDNA-a1690/cds.fna -a OceanDNA-a1690/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:11:39,853] [INFO] Task succeeded: Prodigal
[2023-03-15 07:11:39,853] [INFO] Task started: HMMsearch
[2023-03-15 07:11:39,853] [INFO] Running command: hmmsearch --tblout OceanDNA-a1690/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1e496fe-1f52-48eb-b77c-5b85c68736fd/dqc_reference/reference_markers.hmm OceanDNA-a1690/protein.faa > /dev/null
[2023-03-15 07:11:39,995] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:11:39,995] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg47c28e18-3d72-4c06-b1f1-fa8ac140a65a/OceanDNA-a1690.fa]
[2023-03-15 07:11:40,004] [INFO] Query marker FASTA was written to OceanDNA-a1690/markers.fasta
[2023-03-15 07:11:40,004] [INFO] Task started: Blastn
[2023-03-15 07:11:40,004] [INFO] Running command: blastn -query OceanDNA-a1690/markers.fasta -db /var/lib/cwl/stga1e496fe-1f52-48eb-b77c-5b85c68736fd/dqc_reference/reference_markers.fasta -out OceanDNA-a1690/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:11:40,420] [INFO] Task succeeded: Blastn
[2023-03-15 07:11:40,420] [INFO] Selected 0 target genomes.
[2023-03-15 07:11:40,421] [INFO] Target genome list was writen to OceanDNA-a1690/target_genomes.txt
[2023-03-15 07:11:40,421] [ERROR] File is empty. [OceanDNA-a1690/target_genomes.txt]
[2023-03-15 07:11:40,421] [ERROR] Task failed. No target genome found.
[2023-03-15 07:11:40,421] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:11:40,421] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1e496fe-1f52-48eb-b77c-5b85c68736fd/dqc_reference/checkm_data
[2023-03-15 07:11:40,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:11:40,473] [INFO] Task started: CheckM
[2023-03-15 07:11:40,474] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1690/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1690/checkm_input OceanDNA-a1690/checkm_result
[2023-03-15 07:12:01,823] [INFO] Task succeeded: CheckM
[2023-03-15 07:12:01,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 07:12:01,911] [INFO] ===== Completeness check finished =====
[2023-03-15 07:12:01,911] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:12:01,912] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1690/markers.fasta)
[2023-03-15 07:12:01,912] [INFO] Task started: Blastn
[2023-03-15 07:12:01,913] [INFO] Running command: blastn -query OceanDNA-a1690/markers.fasta -db /var/lib/cwl/stga1e496fe-1f52-48eb-b77c-5b85c68736fd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1690/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:12:02,510] [INFO] Task succeeded: Blastn
[2023-03-15 07:12:02,512] [INFO] Selected 9 target genomes.
[2023-03-15 07:12:02,512] [INFO] Target genome list was writen to OceanDNA-a1690/target_genomes_gtdb.txt
[2023-03-15 07:12:02,523] [INFO] Task started: fastANI
[2023-03-15 07:12:02,523] [INFO] Running command: fastANI --query /var/lib/cwl/stg47c28e18-3d72-4c06-b1f1-fa8ac140a65a/OceanDNA-a1690.fa --refList OceanDNA-a1690/target_genomes_gtdb.txt --output OceanDNA-a1690/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:12:05,444] [INFO] Task succeeded: fastANI
[2023-03-15 07:12:05,447] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:12:05,447] [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_002506485.1	s__CG-Epi1 sp002506485	99.5028	263	311	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	99.64	99.58	0.87	0.83	4	conclusive
GCA_015658585.1	s__CG-Epi1 sp015658585	91.7264	152	311	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240255.1	s__CG-Epi1 sp014240255	77.2923	59	311	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240055.1	s__CG-Epi1 sp014240055	76.8649	52	311	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:12:05,449] [INFO] GTDB search result was written to OceanDNA-a1690/result_gtdb.tsv
[2023-03-15 07:12:05,450] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:12:05,451] [INFO] DFAST_QC result json was written to OceanDNA-a1690/dqc_result.json
[2023-03-15 07:12:05,451] [INFO] DFAST_QC completed!
[2023-03-15 07:12:05,451] [INFO] Total running time: 0h0m32s