[2023-03-17 01:01:12,724] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:01:12,724] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:01:12,724] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdfcad3b-34f3-40f3-984f-7ec4cdbc0ce7/dqc_reference
[2023-03-17 01:01:14,611] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:01:14,611] [INFO] Task started: Prodigal
[2023-03-17 01:01:14,611] [INFO] Running command: cat /var/lib/cwl/stgfa0f341d-2cfa-4da1-aa6c-649b133f1a31/OceanDNA-a2870.fa | prodigal -d OceanDNA-a2870/cds.fna -a OceanDNA-a2870/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:01:25,022] [INFO] Task succeeded: Prodigal
[2023-03-17 01:01:25,022] [INFO] Task started: HMMsearch
[2023-03-17 01:01:25,022] [INFO] Running command: hmmsearch --tblout OceanDNA-a2870/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdfcad3b-34f3-40f3-984f-7ec4cdbc0ce7/dqc_reference/reference_markers.hmm OceanDNA-a2870/protein.faa > /dev/null
[2023-03-17 01:01:25,181] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:01:25,182] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgfa0f341d-2cfa-4da1-aa6c-649b133f1a31/OceanDNA-a2870.fa]
[2023-03-17 01:01:25,194] [INFO] Query marker FASTA was written to OceanDNA-a2870/markers.fasta
[2023-03-17 01:01:25,194] [INFO] Task started: Blastn
[2023-03-17 01:01:25,194] [INFO] Running command: blastn -query OceanDNA-a2870/markers.fasta -db /var/lib/cwl/stgbdfcad3b-34f3-40f3-984f-7ec4cdbc0ce7/dqc_reference/reference_markers.fasta -out OceanDNA-a2870/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:01:25,615] [INFO] Task succeeded: Blastn
[2023-03-17 01:01:25,616] [INFO] Selected 5 target genomes.
[2023-03-17 01:01:25,616] [INFO] Target genome list was writen to OceanDNA-a2870/target_genomes.txt
[2023-03-17 01:01:25,619] [INFO] Task started: fastANI
[2023-03-17 01:01:25,619] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa0f341d-2cfa-4da1-aa6c-649b133f1a31/OceanDNA-a2870.fa --refList OceanDNA-a2870/target_genomes.txt --output OceanDNA-a2870/fastani_result.tsv --threads 1
[2023-03-17 01:01:27,208] [INFO] Task succeeded: fastANI
[2023-03-17 01:01:27,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdfcad3b-34f3-40f3-984f-7ec4cdbc0ce7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:01:27,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdfcad3b-34f3-40f3-984f-7ec4cdbc0ce7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:01:27,209] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:01:27,209] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 01:01:27,209] [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 01:01:27,209] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2870/tc_result.tsv
[2023-03-17 01:01:27,209] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:01:27,209] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:01:27,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdfcad3b-34f3-40f3-984f-7ec4cdbc0ce7/dqc_reference/checkm_data
[2023-03-17 01:01:27,212] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:01:27,217] [INFO] Task started: CheckM
[2023-03-17 01:01:27,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2870/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2870/checkm_input OceanDNA-a2870/checkm_result
[2023-03-17 01:01:58,740] [INFO] Task succeeded: CheckM
[2023-03-17 01:01:58,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 01:01:58,743] [INFO] ===== Completeness check finished =====
[2023-03-17 01:01:58,743] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:01:58,743] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2870/markers.fasta)
[2023-03-17 01:01:58,743] [INFO] Task started: Blastn
[2023-03-17 01:01:58,743] [INFO] Running command: blastn -query OceanDNA-a2870/markers.fasta -db /var/lib/cwl/stgbdfcad3b-34f3-40f3-984f-7ec4cdbc0ce7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2870/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:01:59,146] [INFO] Task succeeded: Blastn
[2023-03-17 01:01:59,147] [INFO] Selected 9 target genomes.
[2023-03-17 01:01:59,147] [INFO] Target genome list was writen to OceanDNA-a2870/target_genomes_gtdb.txt
[2023-03-17 01:01:59,418] [INFO] Task started: fastANI
[2023-03-17 01:01:59,418] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa0f341d-2cfa-4da1-aa6c-649b133f1a31/OceanDNA-a2870.fa --refList OceanDNA-a2870/target_genomes_gtdb.txt --output OceanDNA-a2870/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:02:02,292] [INFO] Task succeeded: fastANI
[2023-03-17 01:02:02,298] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 01:02:02,298] [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_013330015.1	s__MGIIa-L2 sp8574u	97.6891	281	520	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	100.00	100.00	0.98	0.98	2	conclusive
GCA_018623995.1	s__MGIIa-L2 sp018623995	89.8358	364	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_012270265.1	s__MGIIa-L2 sp012270265	89.3257	318	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_002692685.1	s__MGIIa-L2 sp002692685	89.2123	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_002722615.1	s__MGIIa-L2 sp002722615	79.1854	234	520	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_002706065.1	s__MGIIa-L2 sp002706065	79.0501	243	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_013911465.1	s__MGIIa-L2 sp013911465	78.8531	194	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_002499195.1	s__MGIIa-L2 sp002499195	78.7847	272	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_018666575.1	s__MGIIa-L2 sp018666575	76.8772	111	520	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.20	99.20	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-03-17 01:02:02,299] [INFO] GTDB search result was written to OceanDNA-a2870/result_gtdb.tsv
[2023-03-17 01:02:02,299] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:02:02,300] [INFO] DFAST_QC result json was written to OceanDNA-a2870/dqc_result.json
[2023-03-17 01:02:02,300] [INFO] DFAST_QC completed!
[2023-03-17 01:02:02,300] [INFO] Total running time: 0h0m50s