[2023-03-16 09:43:37,170] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:43:37,170] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:43:37,170] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbe413df-3c1a-4116-8a5e-295bd2f4bd87/dqc_reference
[2023-03-16 09:43:39,242] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:43:39,242] [INFO] Task started: Prodigal
[2023-03-16 09:43:39,242] [INFO] Running command: cat /var/lib/cwl/stg1afaaa05-f00a-44cf-8c1c-d5b8baa5dbe1/OceanDNA-a5129.fa | prodigal -d OceanDNA-a5129/cds.fna -a OceanDNA-a5129/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:43:46,617] [INFO] Task succeeded: Prodigal
[2023-03-16 09:43:46,617] [INFO] Task started: HMMsearch
[2023-03-16 09:43:46,617] [INFO] Running command: hmmsearch --tblout OceanDNA-a5129/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbe413df-3c1a-4116-8a5e-295bd2f4bd87/dqc_reference/reference_markers.hmm OceanDNA-a5129/protein.faa > /dev/null
[2023-03-16 09:43:46,771] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:43:46,771] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1afaaa05-f00a-44cf-8c1c-d5b8baa5dbe1/OceanDNA-a5129.fa]
[2023-03-16 09:43:46,780] [INFO] Query marker FASTA was written to OceanDNA-a5129/markers.fasta
[2023-03-16 09:43:46,781] [INFO] Task started: Blastn
[2023-03-16 09:43:46,781] [INFO] Running command: blastn -query OceanDNA-a5129/markers.fasta -db /var/lib/cwl/stgdbe413df-3c1a-4116-8a5e-295bd2f4bd87/dqc_reference/reference_markers.fasta -out OceanDNA-a5129/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:43:47,237] [INFO] Task succeeded: Blastn
[2023-03-16 09:43:47,238] [INFO] Selected 0 target genomes.
[2023-03-16 09:43:47,238] [INFO] Target genome list was writen to OceanDNA-a5129/target_genomes.txt
[2023-03-16 09:43:47,238] [ERROR] File is empty. [OceanDNA-a5129/target_genomes.txt]
[2023-03-16 09:43:47,238] [ERROR] Task failed. No target genome found.
[2023-03-16 09:43:47,238] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:43:47,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbe413df-3c1a-4116-8a5e-295bd2f4bd87/dqc_reference/checkm_data
[2023-03-16 09:43:47,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:43:47,591] [INFO] Task started: CheckM
[2023-03-16 09:43:47,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a5129/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a5129/checkm_input OceanDNA-a5129/checkm_result
[2023-03-16 09:44:14,192] [INFO] Task succeeded: CheckM
[2023-03-16 09:44:14,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.32%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:44:14,194] [INFO] ===== Completeness check finished =====
[2023-03-16 09:44:14,194] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:44:14,194] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a5129/markers.fasta)
[2023-03-16 09:44:14,194] [INFO] Task started: Blastn
[2023-03-16 09:44:14,194] [INFO] Running command: blastn -query OceanDNA-a5129/markers.fasta -db /var/lib/cwl/stgdbe413df-3c1a-4116-8a5e-295bd2f4bd87/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a5129/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:44:14,926] [INFO] Task succeeded: Blastn
[2023-03-16 09:44:14,927] [INFO] Selected 8 target genomes.
[2023-03-16 09:44:14,927] [INFO] Target genome list was writen to OceanDNA-a5129/target_genomes_gtdb.txt
[2023-03-16 09:44:14,933] [INFO] Task started: fastANI
[2023-03-16 09:44:14,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg1afaaa05-f00a-44cf-8c1c-d5b8baa5dbe1/OceanDNA-a5129.fa --refList OceanDNA-a5129/target_genomes_gtdb.txt --output OceanDNA-a5129/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:44:17,003] [INFO] Task succeeded: fastANI
[2023-03-16 09:44:17,008] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:44:17,008] [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_002698225.1	s__Thalassarchaeum sp002698225	99.3908	337	416	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.66	99.66	0.83	0.83	2	conclusive
GCA_002714745.1	s__Thalassarchaeum sp002714745	81.1132	241	416	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	97.82	95.69	0.77	0.69	7	-
GCA_002727275.1	s__Thalassarchaeum sp002727275	79.5728	221	416	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002503055.1	s__Thalassarchaeum sp002503055	79.1104	196	416	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.71	99.22	0.93	0.84	5	-
GCA_002501885.1	s__Thalassarchaeum sp002501885	78.6824	182	416	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	98.85	97.05	0.83	0.68	9	-
GCA_014240285.1	s__Thalassarchaeum sp014240285	77.7014	114	416	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195715.1	s__Thalassarchaeum sp004195715	77.5367	114	416	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.87	99.86	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2023-03-16 09:44:17,009] [INFO] GTDB search result was written to OceanDNA-a5129/result_gtdb.tsv
[2023-03-16 09:44:17,009] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:44:17,009] [INFO] DFAST_QC result json was written to OceanDNA-a5129/dqc_result.json
[2023-03-16 09:44:17,010] [INFO] DFAST_QC completed!
[2023-03-16 09:44:17,010] [INFO] Total running time: 0h0m40s