[2023-03-19 05:19:33,770] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,770] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,770] [INFO] DQC Reference Directory: /var/lib/cwl/stgec718b0c-0a7d-4472-b9a0-818655489462/dqc_reference
[2023-03-19 05:19:35,400] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:35,400] [INFO] Task started: Prodigal
[2023-03-19 05:19:35,401] [INFO] Running command: cat /var/lib/cwl/stg2ce992ef-2bce-4c63-b328-2fb9b3eb8dd2/OceanDNA-a2848.fa | prodigal -d OceanDNA-a2848/cds.fna -a OceanDNA-a2848/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:19:44,213] [INFO] Task succeeded: Prodigal
[2023-03-19 05:19:44,213] [INFO] Task started: HMMsearch
[2023-03-19 05:19:44,213] [INFO] Running command: hmmsearch --tblout OceanDNA-a2848/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec718b0c-0a7d-4472-b9a0-818655489462/dqc_reference/reference_markers.hmm OceanDNA-a2848/protein.faa > /dev/null
[2023-03-19 05:19:44,387] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:19:44,388] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2ce992ef-2bce-4c63-b328-2fb9b3eb8dd2/OceanDNA-a2848.fa]
[2023-03-19 05:19:44,400] [INFO] Query marker FASTA was written to OceanDNA-a2848/markers.fasta
[2023-03-19 05:19:44,400] [INFO] Task started: Blastn
[2023-03-19 05:19:44,400] [INFO] Running command: blastn -query OceanDNA-a2848/markers.fasta -db /var/lib/cwl/stgec718b0c-0a7d-4472-b9a0-818655489462/dqc_reference/reference_markers.fasta -out OceanDNA-a2848/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:44,860] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:44,861] [INFO] Selected 5 target genomes.
[2023-03-19 05:19:44,861] [INFO] Target genome list was writen to OceanDNA-a2848/target_genomes.txt
[2023-03-19 05:19:44,865] [INFO] Task started: fastANI
[2023-03-19 05:19:44,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ce992ef-2bce-4c63-b328-2fb9b3eb8dd2/OceanDNA-a2848.fa --refList OceanDNA-a2848/target_genomes.txt --output OceanDNA-a2848/fastani_result.tsv --threads 1
[2023-03-19 05:19:47,307] [INFO] Task succeeded: fastANI
[2023-03-19 05:19:47,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec718b0c-0a7d-4472-b9a0-818655489462/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:19:47,308] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec718b0c-0a7d-4472-b9a0-818655489462/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:19:47,308] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:19:47,308] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 05:19:47,308] [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
--------------------------------------------------------------------------------
[2023-03-19 05:19:47,308] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2848/tc_result.tsv
[2023-03-19 05:19:47,308] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:19:47,308] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:19:47,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec718b0c-0a7d-4472-b9a0-818655489462/dqc_reference/checkm_data
[2023-03-19 05:19:47,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:19:47,314] [INFO] Task started: CheckM
[2023-03-19 05:19:47,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2848/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2848/checkm_input OceanDNA-a2848/checkm_result
[2023-03-19 05:20:15,301] [INFO] Task succeeded: CheckM
[2023-03-19 05:20:15,301] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:20:15,303] [INFO] ===== Completeness check finished =====
[2023-03-19 05:20:15,303] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:20:15,303] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2848/markers.fasta)
[2023-03-19 05:20:15,303] [INFO] Task started: Blastn
[2023-03-19 05:20:15,303] [INFO] Running command: blastn -query OceanDNA-a2848/markers.fasta -db /var/lib/cwl/stgec718b0c-0a7d-4472-b9a0-818655489462/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2848/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:20:15,718] [INFO] Task succeeded: Blastn
[2023-03-19 05:20:15,719] [INFO] Selected 7 target genomes.
[2023-03-19 05:20:15,719] [INFO] Target genome list was writen to OceanDNA-a2848/target_genomes_gtdb.txt
[2023-03-19 05:20:15,730] [INFO] Task started: fastANI
[2023-03-19 05:20:15,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ce992ef-2bce-4c63-b328-2fb9b3eb8dd2/OceanDNA-a2848.fa --refList OceanDNA-a2848/target_genomes_gtdb.txt --output OceanDNA-a2848/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:20:17,756] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:17,759] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:20:17,759] [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_002706065.1	s__MGIIa-L2 sp002706065	99.6785	413	445	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002499195.1	s__MGIIa-L2 sp002499195	79.1246	287	445	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_013330015.1	s__MGIIa-L2 sp8574u	78.8766	134	445	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	100.00	100.00	0.98	0.98	2	-
GCA_002698145.1	s__MGIIa-L2 sp002698145	78.5623	222	445	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	98.10	97.13	0.94	0.83	7	-
--------------------------------------------------------------------------------
[2023-03-19 05:20:17,760] [INFO] GTDB search result was written to OceanDNA-a2848/result_gtdb.tsv
[2023-03-19 05:20:17,760] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:20:17,760] [INFO] DFAST_QC result json was written to OceanDNA-a2848/dqc_result.json
[2023-03-19 05:20:17,761] [INFO] DFAST_QC completed!
[2023-03-19 05:20:17,761] [INFO] Total running time: 0h0m44s