[2023-03-17 08:39:27,181] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:39:27,181] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:39:27,181] [INFO] DQC Reference Directory: /var/lib/cwl/stg3492f166-d7ef-4a56-a321-2c228b3b0da6/dqc_reference
[2023-03-17 08:39:28,404] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:39:28,404] [INFO] Task started: Prodigal
[2023-03-17 08:39:28,404] [INFO] Running command: cat /var/lib/cwl/stg07a0ac50-c3f5-4f82-9031-2280c0935182/OceanDNA-a1826.fa | prodigal -d OceanDNA-a1826/cds.fna -a OceanDNA-a1826/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:39:33,345] [INFO] Task succeeded: Prodigal
[2023-03-17 08:39:33,345] [INFO] Task started: HMMsearch
[2023-03-17 08:39:33,345] [INFO] Running command: hmmsearch --tblout OceanDNA-a1826/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3492f166-d7ef-4a56-a321-2c228b3b0da6/dqc_reference/reference_markers.hmm OceanDNA-a1826/protein.faa > /dev/null
[2023-03-17 08:39:33,466] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:39:33,467] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg07a0ac50-c3f5-4f82-9031-2280c0935182/OceanDNA-a1826.fa]
[2023-03-17 08:39:33,480] [INFO] Query marker FASTA was written to OceanDNA-a1826/markers.fasta
[2023-03-17 08:39:33,481] [INFO] Task started: Blastn
[2023-03-17 08:39:33,481] [INFO] Running command: blastn -query OceanDNA-a1826/markers.fasta -db /var/lib/cwl/stg3492f166-d7ef-4a56-a321-2c228b3b0da6/dqc_reference/reference_markers.fasta -out OceanDNA-a1826/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:39:33,893] [INFO] Task succeeded: Blastn
[2023-03-17 08:39:33,894] [INFO] Selected 0 target genomes.
[2023-03-17 08:39:33,895] [INFO] Target genome list was writen to OceanDNA-a1826/target_genomes.txt
[2023-03-17 08:39:33,895] [ERROR] File is empty. [OceanDNA-a1826/target_genomes.txt]
[2023-03-17 08:39:33,895] [ERROR] Task failed. No target genome found.
[2023-03-17 08:39:33,895] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:39:33,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3492f166-d7ef-4a56-a321-2c228b3b0da6/dqc_reference/checkm_data
[2023-03-17 08:39:34,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:39:34,040] [INFO] Task started: CheckM
[2023-03-17 08:39:34,040] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1826/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1826/checkm_input OceanDNA-a1826/checkm_result
[2023-03-17 08:39:54,780] [INFO] Task succeeded: CheckM
[2023-03-17 08:39:54,780] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.29%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 08:39:54,783] [INFO] ===== Completeness check finished =====
[2023-03-17 08:39:54,783] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:39:54,783] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1826/markers.fasta)
[2023-03-17 08:39:54,783] [INFO] Task started: Blastn
[2023-03-17 08:39:54,784] [INFO] Running command: blastn -query OceanDNA-a1826/markers.fasta -db /var/lib/cwl/stg3492f166-d7ef-4a56-a321-2c228b3b0da6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1826/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:39:55,591] [INFO] Task succeeded: Blastn
[2023-03-17 08:39:55,593] [INFO] Selected 6 target genomes.
[2023-03-17 08:39:55,593] [INFO] Target genome list was writen to OceanDNA-a1826/target_genomes_gtdb.txt
[2023-03-17 08:39:55,873] [INFO] Task started: fastANI
[2023-03-17 08:39:55,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg07a0ac50-c3f5-4f82-9031-2280c0935182/OceanDNA-a1826.fa --refList OceanDNA-a1826/target_genomes_gtdb.txt --output OceanDNA-a1826/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:39:57,485] [INFO] Task succeeded: fastANI
[2023-03-17 08:39:57,488] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 08:39:57,488] [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_002699515.1	s__MGIIa-I sp002699515	78.5676	153	303	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696315.1	s__MGIIa-I sp002696315	78.4826	146	303	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	99.61	99.61	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-17 08:39:57,490] [INFO] GTDB search result was written to OceanDNA-a1826/result_gtdb.tsv
[2023-03-17 08:39:57,490] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:39:57,492] [INFO] DFAST_QC result json was written to OceanDNA-a1826/dqc_result.json
[2023-03-17 08:39:57,492] [INFO] DFAST_QC completed!
[2023-03-17 08:39:57,492] [INFO] Total running time: 0h0m30s