[2023-03-18 23:18:18,391] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:18:18,391] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:18:18,391] [INFO] DQC Reference Directory: /var/lib/cwl/stg174ae35b-4117-45f8-877a-0978430c6997/dqc_reference
[2023-03-18 23:18:19,493] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:18:19,493] [INFO] Task started: Prodigal
[2023-03-18 23:18:19,493] [INFO] Running command: cat /var/lib/cwl/stge64a0cc6-ff2b-46e6-ac3c-b615e9f0a5ac/OceanDNA-a3135.fa | prodigal -d OceanDNA-a3135/cds.fna -a OceanDNA-a3135/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:18:29,970] [INFO] Task succeeded: Prodigal
[2023-03-18 23:18:29,971] [INFO] Task started: HMMsearch
[2023-03-18 23:18:29,971] [INFO] Running command: hmmsearch --tblout OceanDNA-a3135/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg174ae35b-4117-45f8-877a-0978430c6997/dqc_reference/reference_markers.hmm OceanDNA-a3135/protein.faa > /dev/null
[2023-03-18 23:18:30,109] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:18:30,110] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge64a0cc6-ff2b-46e6-ac3c-b615e9f0a5ac/OceanDNA-a3135.fa]
[2023-03-18 23:18:30,123] [INFO] Query marker FASTA was written to OceanDNA-a3135/markers.fasta
[2023-03-18 23:18:30,124] [INFO] Task started: Blastn
[2023-03-18 23:18:30,124] [INFO] Running command: blastn -query OceanDNA-a3135/markers.fasta -db /var/lib/cwl/stg174ae35b-4117-45f8-877a-0978430c6997/dqc_reference/reference_markers.fasta -out OceanDNA-a3135/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:18:30,609] [INFO] Task succeeded: Blastn
[2023-03-18 23:18:30,610] [INFO] Selected 0 target genomes.
[2023-03-18 23:18:30,610] [INFO] Target genome list was writen to OceanDNA-a3135/target_genomes.txt
[2023-03-18 23:18:30,610] [ERROR] File is empty. [OceanDNA-a3135/target_genomes.txt]
[2023-03-18 23:18:30,611] [ERROR] Task failed. No target genome found.
[2023-03-18 23:18:30,611] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:18:30,611] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg174ae35b-4117-45f8-877a-0978430c6997/dqc_reference/checkm_data
[2023-03-18 23:18:30,614] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:18:30,617] [INFO] Task started: CheckM
[2023-03-18 23:18:30,617] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3135/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3135/checkm_input OceanDNA-a3135/checkm_result
[2023-03-18 23:19:04,040] [INFO] Task succeeded: CheckM
[2023-03-18 23:19:04,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.85%
Contamintation: 2.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:19:04,043] [INFO] ===== Completeness check finished =====
[2023-03-18 23:19:04,043] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:19:04,043] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3135/markers.fasta)
[2023-03-18 23:19:04,044] [INFO] Task started: Blastn
[2023-03-18 23:19:04,044] [INFO] Running command: blastn -query OceanDNA-a3135/markers.fasta -db /var/lib/cwl/stg174ae35b-4117-45f8-877a-0978430c6997/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3135/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:19:04,901] [INFO] Task succeeded: Blastn
[2023-03-18 23:19:04,902] [INFO] Selected 7 target genomes.
[2023-03-18 23:19:04,902] [INFO] Target genome list was writen to OceanDNA-a3135/target_genomes_gtdb.txt
[2023-03-18 23:19:04,992] [INFO] Task started: fastANI
[2023-03-18 23:19:04,992] [INFO] Running command: fastANI --query /var/lib/cwl/stge64a0cc6-ff2b-46e6-ac3c-b615e9f0a5ac/OceanDNA-a3135.fa --refList OceanDNA-a3135/target_genomes_gtdb.txt --output OceanDNA-a3135/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:19:07,152] [INFO] Task succeeded: fastANI
[2023-03-18 23:19:07,157] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:19:07,157] [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_002725275.1	s__Poseidonia sp002725275	99.4754	422	517	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.76	96.60	0.76	0.75	3	conclusive
GCA_002694525.1	s__Poseidonia sp002694525	79.4168	247	517	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002495645.1	s__Poseidonia sp002495645	79.1665	274	517	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.68	99.68	0.84	0.84	2	-
GCA_002722695.1	s__Poseidonia sp002722695	79.0161	221	517	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.22	99.22	0.79	0.79	3	-
GCA_002689105.1	s__Poseidonia sp002689105	78.8677	224	517	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.72	96.72	0.80	0.80	2	-
GCA_002714305.1	s__Poseidonia sp002714305	78.8323	228	517	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	98.69	98.28	0.79	0.76	8	-
GCA_011524855.1	s__Poseidonia sp011524855	78.0311	166	517	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:19:07,157] [INFO] GTDB search result was written to OceanDNA-a3135/result_gtdb.tsv
[2023-03-18 23:19:07,158] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:19:07,158] [INFO] DFAST_QC result json was written to OceanDNA-a3135/dqc_result.json
[2023-03-18 23:19:07,159] [INFO] DFAST_QC completed!
[2023-03-18 23:19:07,159] [INFO] Total running time: 0h0m49s