[2023-03-17 09:41:39,973] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:41:39,974] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:41:39,974] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8f8c082-72b0-4fd7-a331-2e6f23612ae9/dqc_reference
[2023-03-17 09:41:41,757] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:41:41,757] [INFO] Task started: Prodigal
[2023-03-17 09:41:41,757] [INFO] Running command: cat /var/lib/cwl/stg4adfe2fb-7e43-4b79-8233-b4943f7c1bf2/OceanDNA-a2820.fa | prodigal -d OceanDNA-a2820/cds.fna -a OceanDNA-a2820/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:41:49,985] [INFO] Task succeeded: Prodigal
[2023-03-17 09:41:49,985] [INFO] Task started: HMMsearch
[2023-03-17 09:41:49,985] [INFO] Running command: hmmsearch --tblout OceanDNA-a2820/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8f8c082-72b0-4fd7-a331-2e6f23612ae9/dqc_reference/reference_markers.hmm OceanDNA-a2820/protein.faa > /dev/null
[2023-03-17 09:41:50,156] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:41:50,156] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4adfe2fb-7e43-4b79-8233-b4943f7c1bf2/OceanDNA-a2820.fa]
[2023-03-17 09:41:50,183] [INFO] Query marker FASTA was written to OceanDNA-a2820/markers.fasta
[2023-03-17 09:41:50,184] [INFO] Task started: Blastn
[2023-03-17 09:41:50,184] [INFO] Running command: blastn -query OceanDNA-a2820/markers.fasta -db /var/lib/cwl/stgd8f8c082-72b0-4fd7-a331-2e6f23612ae9/dqc_reference/reference_markers.fasta -out OceanDNA-a2820/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:41:50,614] [INFO] Task succeeded: Blastn
[2023-03-17 09:41:50,621] [INFO] Selected 5 target genomes.
[2023-03-17 09:41:50,621] [INFO] Target genome list was writen to OceanDNA-a2820/target_genomes.txt
[2023-03-17 09:41:50,703] [INFO] Task started: fastANI
[2023-03-17 09:41:50,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg4adfe2fb-7e43-4b79-8233-b4943f7c1bf2/OceanDNA-a2820.fa --refList OceanDNA-a2820/target_genomes.txt --output OceanDNA-a2820/fastani_result.tsv --threads 1
[2023-03-17 09:41:52,413] [INFO] Task succeeded: fastANI
[2023-03-17 09:41:52,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8f8c082-72b0-4fd7-a331-2e6f23612ae9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:41:52,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8f8c082-72b0-4fd7-a331-2e6f23612ae9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:41:52,414] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:41:52,414] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:41:52,414] [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
--------------------------------------------------------------------------------
[2023-03-17 09:41:52,418] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2820/tc_result.tsv
[2023-03-17 09:41:52,422] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:41:52,422] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:41:52,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8f8c082-72b0-4fd7-a331-2e6f23612ae9/dqc_reference/checkm_data
[2023-03-17 09:41:52,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:41:52,722] [INFO] Task started: CheckM
[2023-03-17 09:41:52,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2820/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2820/checkm_input OceanDNA-a2820/checkm_result
[2023-03-17 09:42:20,963] [INFO] Task succeeded: CheckM
[2023-03-17 09:42:20,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:42:20,976] [INFO] ===== Completeness check finished =====
[2023-03-17 09:42:20,976] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:42:20,976] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2820/markers.fasta)
[2023-03-17 09:42:20,976] [INFO] Task started: Blastn
[2023-03-17 09:42:20,976] [INFO] Running command: blastn -query OceanDNA-a2820/markers.fasta -db /var/lib/cwl/stgd8f8c082-72b0-4fd7-a331-2e6f23612ae9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2820/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:42:21,405] [INFO] Task succeeded: Blastn
[2023-03-17 09:42:21,409] [INFO] Selected 7 target genomes.
[2023-03-17 09:42:21,409] [INFO] Target genome list was writen to OceanDNA-a2820/target_genomes_gtdb.txt
[2023-03-17 09:42:21,524] [INFO] Task started: fastANI
[2023-03-17 09:42:21,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg4adfe2fb-7e43-4b79-8233-b4943f7c1bf2/OceanDNA-a2820.fa --refList OceanDNA-a2820/target_genomes_gtdb.txt --output OceanDNA-a2820/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:42:24,033] [INFO] Task succeeded: fastANI
[2023-03-17 09:42:24,038] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:42:24,038] [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_018645535.1	s__MGIIa-L2 sp018645535	97.9289	307	459	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_009887135.1	s__MGIIa-L2 sp009887135	86.9495	382	459	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	98.87	98.45	0.83	0.81	3	-
GCA_016777125.1	s__MGIIa-L2 sp016777125	86.9147	425	459	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.94	99.94	0.96	0.96	2	-
GCA_003602665.1	s__MGIIa-L2 sp003602665	84.9732	367	459	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_018666575.1	s__MGIIa-L2 sp018666575	83.4068	348	459	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.20	99.20	0.82	0.82	2	-
GCA_002496635.1	s__MGIIa-L2 sp002496635	81.9185	301	459	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_002171315.2	s__MGIIa-L2 sp002171315	81.5497	308	459	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:42:24,041] [INFO] GTDB search result was written to OceanDNA-a2820/result_gtdb.tsv
[2023-03-17 09:42:24,044] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:42:24,048] [INFO] DFAST_QC result json was written to OceanDNA-a2820/dqc_result.json
[2023-03-17 09:42:24,048] [INFO] DFAST_QC completed!
[2023-03-17 09:42:24,048] [INFO] Total running time: 0h0m44s