[2023-03-14 11:40:05,574] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:40:05,574] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:40:05,574] [INFO] DQC Reference Directory: /var/lib/cwl/stga8fc8930-621a-4a8b-b171-a8ce6be7ed71/dqc_reference
[2023-03-14 11:40:06,643] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:40:06,644] [INFO] Task started: Prodigal
[2023-03-14 11:40:06,644] [INFO] Running command: cat /var/lib/cwl/stg47d45996-1c5b-430a-90c4-aa7f06779930/OceanDNA-a4368.fa | prodigal -d OceanDNA-a4368/cds.fna -a OceanDNA-a4368/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:40:15,960] [INFO] Task succeeded: Prodigal
[2023-03-14 11:40:15,960] [INFO] Task started: HMMsearch
[2023-03-14 11:40:15,960] [INFO] Running command: hmmsearch --tblout OceanDNA-a4368/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8fc8930-621a-4a8b-b171-a8ce6be7ed71/dqc_reference/reference_markers.hmm OceanDNA-a4368/protein.faa > /dev/null
[2023-03-14 11:40:16,100] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:40:16,101] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg47d45996-1c5b-430a-90c4-aa7f06779930/OceanDNA-a4368.fa]
[2023-03-14 11:40:16,117] [INFO] Query marker FASTA was written to OceanDNA-a4368/markers.fasta
[2023-03-14 11:40:16,117] [INFO] Task started: Blastn
[2023-03-14 11:40:16,117] [INFO] Running command: blastn -query OceanDNA-a4368/markers.fasta -db /var/lib/cwl/stga8fc8930-621a-4a8b-b171-a8ce6be7ed71/dqc_reference/reference_markers.fasta -out OceanDNA-a4368/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:40:16,542] [INFO] Task succeeded: Blastn
[2023-03-14 11:40:16,548] [INFO] Selected 0 target genomes.
[2023-03-14 11:40:16,548] [INFO] Target genome list was writen to OceanDNA-a4368/target_genomes.txt
[2023-03-14 11:40:16,549] [ERROR] File is empty. [OceanDNA-a4368/target_genomes.txt]
[2023-03-14 11:40:16,549] [ERROR] Task failed. No target genome found.
[2023-03-14 11:40:16,549] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:40:16,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8fc8930-621a-4a8b-b171-a8ce6be7ed71/dqc_reference/checkm_data
[2023-03-14 11:40:16,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:40:16,556] [INFO] Task started: CheckM
[2023-03-14 11:40:16,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4368/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4368/checkm_input OceanDNA-a4368/checkm_result
[2023-03-14 11:40:45,000] [INFO] Task succeeded: CheckM
[2023-03-14 11:40:45,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.40%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:40:45,049] [INFO] ===== Completeness check finished =====
[2023-03-14 11:40:45,049] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:40:45,049] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4368/markers.fasta)
[2023-03-14 11:40:45,051] [INFO] Task started: Blastn
[2023-03-14 11:40:45,051] [INFO] Running command: blastn -query OceanDNA-a4368/markers.fasta -db /var/lib/cwl/stga8fc8930-621a-4a8b-b171-a8ce6be7ed71/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4368/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:40:45,467] [INFO] Task succeeded: Blastn
[2023-03-14 11:40:45,474] [INFO] Selected 11 target genomes.
[2023-03-14 11:40:45,474] [INFO] Target genome list was writen to OceanDNA-a4368/target_genomes_gtdb.txt
[2023-03-14 11:40:45,481] [INFO] Task started: fastANI
[2023-03-14 11:40:45,481] [INFO] Running command: fastANI --query /var/lib/cwl/stg47d45996-1c5b-430a-90c4-aa7f06779930/OceanDNA-a4368.fa --refList OceanDNA-a4368/target_genomes_gtdb.txt --output OceanDNA-a4368/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:40:48,154] [INFO] Task succeeded: fastANI
[2023-03-14 11:40:48,159] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:40:48,159] [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_002683155.1	s__MGIIb-O3 sp002683155	95.715	183	378	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002457155.1	s__MGIIb-O3 sp002457155	82.1275	258	378	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602515.1	s__MGIIb-O3 sp003602515	80.5796	273	378	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.42	99.42	0.80	0.80	2	-
GCA_014239955.1	s__MGIIb-O3 sp014239955	78.7844	202	378	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195615.1	s__MGIIb-O3 sp004195615	78.5353	219	378	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.94	99.91	0.95	0.93	3	-
GCA_902573015.1	s__MGIIb-O3 sp902573015	77.4883	92	378	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720055.1	s__MGIIb-O3 sp002720055	76.9661	53	378	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:40:48,162] [INFO] GTDB search result was written to OceanDNA-a4368/result_gtdb.tsv
[2023-03-14 11:40:48,164] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:40:48,167] [INFO] DFAST_QC result json was written to OceanDNA-a4368/dqc_result.json
[2023-03-14 11:40:48,167] [INFO] DFAST_QC completed!
[2023-03-14 11:40:48,167] [INFO] Total running time: 0h0m43s