[2023-03-16 04:54:07,036] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:54:07,036] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:54:07,036] [INFO] DQC Reference Directory: /var/lib/cwl/stgc579c5d9-77bc-4cbf-9904-e64bad626566/dqc_reference
[2023-03-16 04:54:08,318] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:54:08,318] [INFO] Task started: Prodigal
[2023-03-16 04:54:08,318] [INFO] Running command: cat /var/lib/cwl/stgec5c3294-dcac-4113-bc14-e2240a804f83/OceanDNA-a1605.fa | prodigal -d OceanDNA-a1605/cds.fna -a OceanDNA-a1605/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:54:12,068] [INFO] Task succeeded: Prodigal
[2023-03-16 04:54:12,069] [INFO] Task started: HMMsearch
[2023-03-16 04:54:12,069] [INFO] Running command: hmmsearch --tblout OceanDNA-a1605/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc579c5d9-77bc-4cbf-9904-e64bad626566/dqc_reference/reference_markers.hmm OceanDNA-a1605/protein.faa > /dev/null
[2023-03-16 04:54:12,253] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:54:12,253] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgec5c3294-dcac-4113-bc14-e2240a804f83/OceanDNA-a1605.fa]
[2023-03-16 04:54:12,262] [INFO] Query marker FASTA was written to OceanDNA-a1605/markers.fasta
[2023-03-16 04:54:12,262] [INFO] Task started: Blastn
[2023-03-16 04:54:12,262] [INFO] Running command: blastn -query OceanDNA-a1605/markers.fasta -db /var/lib/cwl/stgc579c5d9-77bc-4cbf-9904-e64bad626566/dqc_reference/reference_markers.fasta -out OceanDNA-a1605/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:12,710] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:12,711] [INFO] Selected 10 target genomes.
[2023-03-16 04:54:12,711] [INFO] Target genome list was writen to OceanDNA-a1605/target_genomes.txt
[2023-03-16 04:54:12,718] [INFO] Task started: fastANI
[2023-03-16 04:54:12,718] [INFO] Running command: fastANI --query /var/lib/cwl/stgec5c3294-dcac-4113-bc14-e2240a804f83/OceanDNA-a1605.fa --refList OceanDNA-a1605/target_genomes.txt --output OceanDNA-a1605/fastani_result.tsv --threads 1
[2023-03-16 04:54:17,375] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:17,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc579c5d9-77bc-4cbf-9904-e64bad626566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:54:17,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc579c5d9-77bc-4cbf-9904-e64bad626566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:54:17,376] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:54:17,376] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:54:17,376] [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
--------------------------------------------------------------------------------
[2023-03-16 04:54:17,376] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1605/tc_result.tsv
[2023-03-16 04:54:17,377] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:54:17,377] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:54:17,377] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc579c5d9-77bc-4cbf-9904-e64bad626566/dqc_reference/checkm_data
[2023-03-16 04:54:17,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:54:17,382] [INFO] Task started: CheckM
[2023-03-16 04:54:17,382] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1605/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1605/checkm_input OceanDNA-a1605/checkm_result
[2023-03-16 04:54:33,839] [INFO] Task succeeded: CheckM
[2023-03-16 04:54:33,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 1.91%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 04:54:33,846] [INFO] ===== Completeness check finished =====
[2023-03-16 04:54:33,846] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:54:33,846] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1605/markers.fasta)
[2023-03-16 04:54:33,847] [INFO] Task started: Blastn
[2023-03-16 04:54:33,847] [INFO] Running command: blastn -query OceanDNA-a1605/markers.fasta -db /var/lib/cwl/stgc579c5d9-77bc-4cbf-9904-e64bad626566/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1605/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:34,355] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:34,356] [INFO] Selected 10 target genomes.
[2023-03-16 04:54:34,356] [INFO] Target genome list was writen to OceanDNA-a1605/target_genomes_gtdb.txt
[2023-03-16 04:54:34,370] [INFO] Task started: fastANI
[2023-03-16 04:54:34,370] [INFO] Running command: fastANI --query /var/lib/cwl/stgec5c3294-dcac-4113-bc14-e2240a804f83/OceanDNA-a1605.fa --refList OceanDNA-a1605/target_genomes_gtdb.txt --output OceanDNA-a1605/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:54:36,659] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:36,665] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:54:36,665] [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_001875345.1	s__CG-Epi1 sp001875345	92.0692	185	216	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845825.1	s__CG-Epi1 sp016845825	90.3119	175	216	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001875365.1	s__CG-Epi1 sp001875365	84.3114	105	216	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724775.1	s__CG-Epi1 sp002724775	81.1715	151	216	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	96.65	95.92	0.84	0.84	3	-
GCA_002718915.1	s__CG-Epi1 sp002718915	80.353	121	216	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002497685.1	s__CG-Epi1 sp002497685	80.3386	100	216	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	99.79	99.79	0.70	0.70	2	-
GCA_902531985.1	s__CG-Epi1 sp902531985	78.1962	51	216	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:54:36,665] [INFO] GTDB search result was written to OceanDNA-a1605/result_gtdb.tsv
[2023-03-16 04:54:36,666] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:54:36,666] [INFO] DFAST_QC result json was written to OceanDNA-a1605/dqc_result.json
[2023-03-16 04:54:36,667] [INFO] DFAST_QC completed!
[2023-03-16 04:54:36,667] [INFO] Total running time: 0h0m30s