[2023-03-15 21:48:06,749] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:06,749] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:06,749] [INFO] DQC Reference Directory: /var/lib/cwl/stge6f93424-188b-4cec-ae5e-c2e0a9fe7755/dqc_reference
[2023-03-15 21:48:07,835] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:07,836] [INFO] Task started: Prodigal
[2023-03-15 21:48:07,836] [INFO] Running command: cat /var/lib/cwl/stg62009273-cde4-49e2-ae88-178398819633/OceanDNA-a2737.fa | prodigal -d OceanDNA-a2737/cds.fna -a OceanDNA-a2737/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:15,778] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:15,778] [INFO] Task started: HMMsearch
[2023-03-15 21:48:15,778] [INFO] Running command: hmmsearch --tblout OceanDNA-a2737/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6f93424-188b-4cec-ae5e-c2e0a9fe7755/dqc_reference/reference_markers.hmm OceanDNA-a2737/protein.faa > /dev/null
[2023-03-15 21:48:15,938] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:15,939] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg62009273-cde4-49e2-ae88-178398819633/OceanDNA-a2737.fa]
[2023-03-15 21:48:15,949] [INFO] Query marker FASTA was written to OceanDNA-a2737/markers.fasta
[2023-03-15 21:48:15,950] [INFO] Task started: Blastn
[2023-03-15 21:48:15,950] [INFO] Running command: blastn -query OceanDNA-a2737/markers.fasta -db /var/lib/cwl/stge6f93424-188b-4cec-ae5e-c2e0a9fe7755/dqc_reference/reference_markers.fasta -out OceanDNA-a2737/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:16,386] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:16,387] [INFO] Selected 5 target genomes.
[2023-03-15 21:48:16,387] [INFO] Target genome list was writen to OceanDNA-a2737/target_genomes.txt
[2023-03-15 21:48:16,390] [INFO] Task started: fastANI
[2023-03-15 21:48:16,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg62009273-cde4-49e2-ae88-178398819633/OceanDNA-a2737.fa --refList OceanDNA-a2737/target_genomes.txt --output OceanDNA-a2737/fastani_result.tsv --threads 1
[2023-03-15 21:48:20,040] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:20,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6f93424-188b-4cec-ae5e-c2e0a9fe7755/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:48:20,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6f93424-188b-4cec-ae5e-c2e0a9fe7755/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:48:20,041] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:48:20,041] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:48:20,041] [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 21:48:20,041] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2737/tc_result.tsv
[2023-03-15 21:48:20,042] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:48:20,042] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:48:20,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6f93424-188b-4cec-ae5e-c2e0a9fe7755/dqc_reference/checkm_data
[2023-03-15 21:48:20,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:48:20,057] [INFO] Task started: CheckM
[2023-03-15 21:48:20,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2737/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2737/checkm_input OceanDNA-a2737/checkm_result
[2023-03-15 21:48:46,161] [INFO] Task succeeded: CheckM
[2023-03-15 21:48:46,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:48:46,177] [INFO] ===== Completeness check finished =====
[2023-03-15 21:48:46,177] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:48:46,177] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2737/markers.fasta)
[2023-03-15 21:48:46,178] [INFO] Task started: Blastn
[2023-03-15 21:48:46,178] [INFO] Running command: blastn -query OceanDNA-a2737/markers.fasta -db /var/lib/cwl/stge6f93424-188b-4cec-ae5e-c2e0a9fe7755/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2737/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:46,606] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:46,610] [INFO] Selected 8 target genomes.
[2023-03-15 21:48:46,610] [INFO] Target genome list was writen to OceanDNA-a2737/target_genomes_gtdb.txt
[2023-03-15 21:48:46,622] [INFO] Task started: fastANI
[2023-03-15 21:48:46,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg62009273-cde4-49e2-ae88-178398819633/OceanDNA-a2737.fa --refList OceanDNA-a2737/target_genomes_gtdb.txt --output OceanDNA-a2737/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:48:49,076] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:49,082] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:48:49,082] [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_018623995.1	s__MGIIa-L2 sp018623995	90.7674	300	405	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_012270265.1	s__MGIIa-L2 sp012270265	90.7545	285	405	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_002692685.1	s__MGIIa-L2 sp002692685	89.3146	218	405	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_013330015.1	s__MGIIa-L2 sp8574u	88.5054	233	405	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_002719815.1	s__MGIIa-L2 sp002719815	79.5031	191	405	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_002706065.1	s__MGIIa-L2 sp002706065	78.9109	197	405	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_002722615.1	s__MGIIa-L2 sp002722615	78.6861	184	405	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	97.14	95.81	0.83	0.81	4	-
GCA_018666575.1	s__MGIIa-L2 sp018666575	77.0654	87	405	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.20	99.20	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-03-15 21:48:49,084] [INFO] GTDB search result was written to OceanDNA-a2737/result_gtdb.tsv
[2023-03-15 21:48:49,084] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:48:49,085] [INFO] DFAST_QC result json was written to OceanDNA-a2737/dqc_result.json
[2023-03-15 21:48:49,086] [INFO] DFAST_QC completed!
[2023-03-15 21:48:49,086] [INFO] Total running time: 0h0m42s