[2023-03-15 11:20:29,258] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:20:29,259] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:20:29,259] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8015ed6-1b5b-4cb2-b675-85ab931a0402/dqc_reference
[2023-03-15 11:20:30,358] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:20:30,358] [INFO] Task started: Prodigal
[2023-03-15 11:20:30,358] [INFO] Running command: cat /var/lib/cwl/stg7ddc8b91-a090-4b0f-a3e4-832c07e36fe2/OceanDNA-a1584.fa | prodigal -d OceanDNA-a1584/cds.fna -a OceanDNA-a1584/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:20:34,786] [INFO] Task succeeded: Prodigal
[2023-03-15 11:20:34,786] [INFO] Task started: HMMsearch
[2023-03-15 11:20:34,786] [INFO] Running command: hmmsearch --tblout OceanDNA-a1584/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8015ed6-1b5b-4cb2-b675-85ab931a0402/dqc_reference/reference_markers.hmm OceanDNA-a1584/protein.faa > /dev/null
[2023-03-15 11:20:34,950] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:20:34,951] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg7ddc8b91-a090-4b0f-a3e4-832c07e36fe2/OceanDNA-a1584.fa]
[2023-03-15 11:20:34,992] [INFO] Query marker FASTA was written to OceanDNA-a1584/markers.fasta
[2023-03-15 11:20:34,999] [INFO] Task started: Blastn
[2023-03-15 11:20:35,000] [INFO] Running command: blastn -query OceanDNA-a1584/markers.fasta -db /var/lib/cwl/stgb8015ed6-1b5b-4cb2-b675-85ab931a0402/dqc_reference/reference_markers.fasta -out OceanDNA-a1584/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:20:35,682] [INFO] Task succeeded: Blastn
[2023-03-15 11:20:35,690] [INFO] Selected 5 target genomes.
[2023-03-15 11:20:35,690] [INFO] Target genome list was writen to OceanDNA-a1584/target_genomes.txt
[2023-03-15 11:20:35,696] [INFO] Task started: fastANI
[2023-03-15 11:20:35,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ddc8b91-a090-4b0f-a3e4-832c07e36fe2/OceanDNA-a1584.fa --refList OceanDNA-a1584/target_genomes.txt --output OceanDNA-a1584/fastani_result.tsv --threads 1
[2023-03-15 11:20:37,544] [INFO] Task succeeded: fastANI
[2023-03-15 11:20:37,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8015ed6-1b5b-4cb2-b675-85ab931a0402/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:20:37,544] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8015ed6-1b5b-4cb2-b675-85ab931a0402/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:20:37,544] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:20:37,544] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:20:37,544] [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 11:20:37,546] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1584/tc_result.tsv
[2023-03-15 11:20:37,549] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:20:37,549] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:20:37,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8015ed6-1b5b-4cb2-b675-85ab931a0402/dqc_reference/checkm_data
[2023-03-15 11:20:37,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:20:37,555] [INFO] Task started: CheckM
[2023-03-15 11:20:37,555] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1584/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1584/checkm_input OceanDNA-a1584/checkm_result
[2023-03-15 11:20:55,760] [INFO] Task succeeded: CheckM
[2023-03-15 11:20:55,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:20:55,798] [INFO] ===== Completeness check finished =====
[2023-03-15 11:20:55,798] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:20:55,799] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1584/markers.fasta)
[2023-03-15 11:20:55,799] [INFO] Task started: Blastn
[2023-03-15 11:20:55,799] [INFO] Running command: blastn -query OceanDNA-a1584/markers.fasta -db /var/lib/cwl/stgb8015ed6-1b5b-4cb2-b675-85ab931a0402/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1584/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:20:56,471] [INFO] Task succeeded: Blastn
[2023-03-15 11:20:56,475] [INFO] Selected 6 target genomes.
[2023-03-15 11:20:56,475] [INFO] Target genome list was writen to OceanDNA-a1584/target_genomes_gtdb.txt
[2023-03-15 11:20:56,482] [INFO] Task started: fastANI
[2023-03-15 11:20:56,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ddc8b91-a090-4b0f-a3e4-832c07e36fe2/OceanDNA-a1584.fa --refList OceanDNA-a1584/target_genomes_gtdb.txt --output OceanDNA-a1584/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:20:57,902] [INFO] Task succeeded: fastANI
[2023-03-15 11:20:57,906] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:20:57,906] [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_014240055.1	s__CG-Epi1 sp014240055	91.2903	219	274	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_014240255.1	s__CG-Epi1 sp014240255	83.6899	213	274	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_002718915.1	s__CG-Epi1 sp002718915	77.8809	68	274	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	77.4516	71	274	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_016845825.1	s__CG-Epi1 sp016845825	77.3882	83	274	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	-
--------------------------------------------------------------------------------
[2023-03-15 11:20:57,908] [INFO] GTDB search result was written to OceanDNA-a1584/result_gtdb.tsv
[2023-03-15 11:20:57,909] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:20:57,911] [INFO] DFAST_QC result json was written to OceanDNA-a1584/dqc_result.json
[2023-03-15 11:20:57,911] [INFO] DFAST_QC completed!
[2023-03-15 11:20:57,911] [INFO] Total running time: 0h0m29s