[2023-03-15 06:28:21,408] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:28:21,408] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:28:21,408] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ef1be6c-00ec-4ac0-a333-614e342c8884/dqc_reference
[2023-03-15 06:28:22,489] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:28:22,489] [INFO] Task started: Prodigal
[2023-03-15 06:28:22,489] [INFO] Running command: cat /var/lib/cwl/stga9bb083f-0935-49ae-ac01-ae6e4cd68e1e/OceanDNA-a2713.fa | prodigal -d OceanDNA-a2713/cds.fna -a OceanDNA-a2713/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:28:32,638] [INFO] Task succeeded: Prodigal
[2023-03-15 06:28:32,638] [INFO] Task started: HMMsearch
[2023-03-15 06:28:32,638] [INFO] Running command: hmmsearch --tblout OceanDNA-a2713/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ef1be6c-00ec-4ac0-a333-614e342c8884/dqc_reference/reference_markers.hmm OceanDNA-a2713/protein.faa > /dev/null
[2023-03-15 06:28:32,816] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:28:32,817] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga9bb083f-0935-49ae-ac01-ae6e4cd68e1e/OceanDNA-a2713.fa]
[2023-03-15 06:28:32,829] [INFO] Query marker FASTA was written to OceanDNA-a2713/markers.fasta
[2023-03-15 06:28:32,830] [INFO] Task started: Blastn
[2023-03-15 06:28:32,830] [INFO] Running command: blastn -query OceanDNA-a2713/markers.fasta -db /var/lib/cwl/stg9ef1be6c-00ec-4ac0-a333-614e342c8884/dqc_reference/reference_markers.fasta -out OceanDNA-a2713/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:28:33,254] [INFO] Task succeeded: Blastn
[2023-03-15 06:28:33,255] [INFO] Selected 5 target genomes.
[2023-03-15 06:28:33,255] [INFO] Target genome list was writen to OceanDNA-a2713/target_genomes.txt
[2023-03-15 06:28:33,258] [INFO] Task started: fastANI
[2023-03-15 06:28:33,258] [INFO] Running command: fastANI --query /var/lib/cwl/stga9bb083f-0935-49ae-ac01-ae6e4cd68e1e/OceanDNA-a2713.fa --refList OceanDNA-a2713/target_genomes.txt --output OceanDNA-a2713/fastani_result.tsv --threads 1
[2023-03-15 06:28:37,209] [INFO] Task succeeded: fastANI
[2023-03-15 06:28:37,210] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ef1be6c-00ec-4ac0-a333-614e342c8884/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:28:37,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ef1be6c-00ec-4ac0-a333-614e342c8884/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:28:37,210] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:28:37,210] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 06:28:37,210] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-15 06:28:37,211] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2713/tc_result.tsv
[2023-03-15 06:28:37,211] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:28:37,211] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:28:37,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ef1be6c-00ec-4ac0-a333-614e342c8884/dqc_reference/checkm_data
[2023-03-15 06:28:37,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:28:37,218] [INFO] Task started: CheckM
[2023-03-15 06:28:37,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2713/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2713/checkm_input OceanDNA-a2713/checkm_result
[2023-03-15 06:29:08,054] [INFO] Task succeeded: CheckM
[2023-03-15 06:29:08,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 06:29:08,061] [INFO] ===== Completeness check finished =====
[2023-03-15 06:29:08,062] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:29:08,062] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2713/markers.fasta)
[2023-03-15 06:29:08,063] [INFO] Task started: Blastn
[2023-03-15 06:29:08,063] [INFO] Running command: blastn -query OceanDNA-a2713/markers.fasta -db /var/lib/cwl/stg9ef1be6c-00ec-4ac0-a333-614e342c8884/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2713/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:29:08,486] [INFO] Task succeeded: Blastn
[2023-03-15 06:29:08,487] [INFO] Selected 9 target genomes.
[2023-03-15 06:29:08,487] [INFO] Target genome list was writen to OceanDNA-a2713/target_genomes_gtdb.txt
[2023-03-15 06:29:08,492] [INFO] Task started: fastANI
[2023-03-15 06:29:08,492] [INFO] Running command: fastANI --query /var/lib/cwl/stga9bb083f-0935-49ae-ac01-ae6e4cd68e1e/OceanDNA-a2713.fa --refList OceanDNA-a2713/target_genomes_gtdb.txt --output OceanDNA-a2713/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:29:11,555] [INFO] Task succeeded: fastANI
[2023-03-15 06:29:11,560] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:29:11,560] [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_002698145.1	s__MGIIa-L2 sp002698145	93.8277	492	520	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	98.10	97.13	0.94	0.83	7	-
GCA_002502215.1	s__MGIIa-L2 sp002502215	92.7217	438	520	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	98.03	97.17	0.84	0.82	4	-
GCA_002499195.1	s__MGIIa-L2 sp002499195	79.555	290	520	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.80	99.66	0.93	0.91	5	-
GCA_002706065.1	s__MGIIa-L2 sp002706065	78.9277	272	520	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623995.1	s__MGIIa-L2 sp018623995	78.6218	203	520	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018645535.1	s__MGIIa-L2 sp018645535	77.0567	85	520	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602665.1	s__MGIIa-L2 sp003602665	76.9275	106	520	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 06:29:11,560] [INFO] GTDB search result was written to OceanDNA-a2713/result_gtdb.tsv
[2023-03-15 06:29:11,561] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:29:11,561] [INFO] DFAST_QC result json was written to OceanDNA-a2713/dqc_result.json
[2023-03-15 06:29:11,561] [INFO] DFAST_QC completed!
[2023-03-15 06:29:11,561] [INFO] Total running time: 0h0m50s