[2023-03-18 06:37:17,741] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:37:17,742] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:37:17,742] [INFO] DQC Reference Directory: /var/lib/cwl/stg3178aafe-3128-4732-8000-be1279e0ea50/dqc_reference
[2023-03-18 06:37:18,835] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:37:18,836] [INFO] Task started: Prodigal
[2023-03-18 06:37:18,836] [INFO] Running command: cat /var/lib/cwl/stgc1eba097-7999-4cf7-9c87-9b9f58f3fb9c/OceanDNA-a2191.fa | prodigal -d OceanDNA-a2191/cds.fna -a OceanDNA-a2191/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:37:23,051] [INFO] Task succeeded: Prodigal
[2023-03-18 06:37:23,052] [INFO] Task started: HMMsearch
[2023-03-18 06:37:23,052] [INFO] Running command: hmmsearch --tblout OceanDNA-a2191/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3178aafe-3128-4732-8000-be1279e0ea50/dqc_reference/reference_markers.hmm OceanDNA-a2191/protein.faa > /dev/null
[2023-03-18 06:37:23,192] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:37:23,193] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgc1eba097-7999-4cf7-9c87-9b9f58f3fb9c/OceanDNA-a2191.fa]
[2023-03-18 06:37:23,203] [INFO] Query marker FASTA was written to OceanDNA-a2191/markers.fasta
[2023-03-18 06:37:23,204] [INFO] Task started: Blastn
[2023-03-18 06:37:23,204] [INFO] Running command: blastn -query OceanDNA-a2191/markers.fasta -db /var/lib/cwl/stg3178aafe-3128-4732-8000-be1279e0ea50/dqc_reference/reference_markers.fasta -out OceanDNA-a2191/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:37:23,638] [INFO] Task succeeded: Blastn
[2023-03-18 06:37:23,639] [INFO] Selected 0 target genomes.
[2023-03-18 06:37:23,639] [INFO] Target genome list was writen to OceanDNA-a2191/target_genomes.txt
[2023-03-18 06:37:23,639] [ERROR] File is empty. [OceanDNA-a2191/target_genomes.txt]
[2023-03-18 06:37:23,639] [ERROR] Task failed. No target genome found.
[2023-03-18 06:37:23,639] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:37:23,639] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3178aafe-3128-4732-8000-be1279e0ea50/dqc_reference/checkm_data
[2023-03-18 06:37:23,642] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:37:23,645] [INFO] Task started: CheckM
[2023-03-18 06:37:23,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2191/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2191/checkm_input OceanDNA-a2191/checkm_result
[2023-03-18 06:37:40,692] [INFO] Task succeeded: CheckM
[2023-03-18 06:37:40,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.36%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:37:40,695] [INFO] ===== Completeness check finished =====
[2023-03-18 06:37:40,695] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:37:40,695] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2191/markers.fasta)
[2023-03-18 06:37:40,695] [INFO] Task started: Blastn
[2023-03-18 06:37:40,695] [INFO] Running command: blastn -query OceanDNA-a2191/markers.fasta -db /var/lib/cwl/stg3178aafe-3128-4732-8000-be1279e0ea50/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2191/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:37:41,175] [INFO] Task succeeded: Blastn
[2023-03-18 06:37:41,176] [INFO] Selected 5 target genomes.
[2023-03-18 06:37:41,176] [INFO] Target genome list was writen to OceanDNA-a2191/target_genomes_gtdb.txt
[2023-03-18 06:37:41,227] [INFO] Task started: fastANI
[2023-03-18 06:37:41,228] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1eba097-7999-4cf7-9c87-9b9f58f3fb9c/OceanDNA-a2191.fa --refList OceanDNA-a2191/target_genomes_gtdb.txt --output OceanDNA-a2191/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:37:42,485] [INFO] Task succeeded: fastANI
[2023-03-18 06:37:42,487] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 06:37:42,488] [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_011526375.1	s__MGIIa-L1 sp011526375	80.723	135	160	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013329295.1	s__MGIIa-L1 sp9596u	79.4282	80	160	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.51	99.26	0.88	0.84	4	-
--------------------------------------------------------------------------------
[2023-03-18 06:37:42,488] [INFO] GTDB search result was written to OceanDNA-a2191/result_gtdb.tsv
[2023-03-18 06:37:42,488] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:37:42,488] [INFO] DFAST_QC result json was written to OceanDNA-a2191/dqc_result.json
[2023-03-18 06:37:42,488] [INFO] DFAST_QC completed!
[2023-03-18 06:37:42,488] [INFO] Total running time: 0h0m25s