[2023-03-17 05:54:59,363] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:54:59,363] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:54:59,363] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1b8c600-877a-4102-a807-2e4fa6b76622/dqc_reference
[2023-03-17 05:55:01,034] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:55:01,035] [INFO] Task started: Prodigal
[2023-03-17 05:55:01,035] [INFO] Running command: cat /var/lib/cwl/stge87ebe3d-d5f3-4f81-aba9-02b36e62a201/OceanDNA-b14480.fa | prodigal -d OceanDNA-b14480/cds.fna -a OceanDNA-b14480/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:55:05,671] [INFO] Task succeeded: Prodigal
[2023-03-17 05:55:05,671] [INFO] Task started: HMMsearch
[2023-03-17 05:55:05,671] [INFO] Running command: hmmsearch --tblout OceanDNA-b14480/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1b8c600-877a-4102-a807-2e4fa6b76622/dqc_reference/reference_markers.hmm OceanDNA-b14480/protein.faa > /dev/null
[2023-03-17 05:55:05,814] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:55:05,814] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge87ebe3d-d5f3-4f81-aba9-02b36e62a201/OceanDNA-b14480.fa]
[2023-03-17 05:55:05,887] [INFO] Query marker FASTA was written to OceanDNA-b14480/markers.fasta
[2023-03-17 05:55:05,887] [INFO] Task started: Blastn
[2023-03-17 05:55:05,887] [INFO] Running command: blastn -query OceanDNA-b14480/markers.fasta -db /var/lib/cwl/stgf1b8c600-877a-4102-a807-2e4fa6b76622/dqc_reference/reference_markers.fasta -out OceanDNA-b14480/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:55:07,219] [INFO] Task succeeded: Blastn
[2023-03-17 05:55:07,219] [INFO] Selected 8 target genomes.
[2023-03-17 05:55:07,219] [INFO] Target genome list was writen to OceanDNA-b14480/target_genomes.txt
[2023-03-17 05:55:07,224] [INFO] Task started: fastANI
[2023-03-17 05:55:07,224] [INFO] Running command: fastANI --query /var/lib/cwl/stge87ebe3d-d5f3-4f81-aba9-02b36e62a201/OceanDNA-b14480.fa --refList OceanDNA-b14480/target_genomes.txt --output OceanDNA-b14480/fastani_result.tsv --threads 1
[2023-03-17 05:55:10,957] [INFO] Task succeeded: fastANI
[2023-03-17 05:55:10,957] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1b8c600-877a-4102-a807-2e4fa6b76622/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:55:10,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1b8c600-877a-4102-a807-2e4fa6b76622/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:55:10,957] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:55:10,957] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:55:10,957] [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 05:55:10,958] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14480/tc_result.tsv
[2023-03-17 05:55:10,958] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:55:10,958] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:55:10,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1b8c600-877a-4102-a807-2e4fa6b76622/dqc_reference/checkm_data
[2023-03-17 05:55:10,961] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:55:10,964] [INFO] Task started: CheckM
[2023-03-17 05:55:10,964] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14480/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14480/checkm_input OceanDNA-b14480/checkm_result
[2023-03-17 05:55:31,371] [INFO] Task succeeded: CheckM
[2023-03-17 05:55:31,371] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.71%
Contamintation: 6.05%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-17 05:55:31,396] [INFO] ===== Completeness check finished =====
[2023-03-17 05:55:31,396] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:55:31,397] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14480/markers.fasta)
[2023-03-17 05:55:31,397] [INFO] Task started: Blastn
[2023-03-17 05:55:31,397] [INFO] Running command: blastn -query OceanDNA-b14480/markers.fasta -db /var/lib/cwl/stgf1b8c600-877a-4102-a807-2e4fa6b76622/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14480/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:55:32,071] [INFO] Task succeeded: Blastn
[2023-03-17 05:55:32,078] [INFO] Selected 9 target genomes.
[2023-03-17 05:55:32,078] [INFO] Target genome list was writen to OceanDNA-b14480/target_genomes_gtdb.txt
[2023-03-17 05:55:32,086] [INFO] Task started: fastANI
[2023-03-17 05:55:32,086] [INFO] Running command: fastANI --query /var/lib/cwl/stge87ebe3d-d5f3-4f81-aba9-02b36e62a201/OceanDNA-b14480.fa --refList OceanDNA-b14480/target_genomes_gtdb.txt --output OceanDNA-b14480/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:55:35,130] [INFO] Task succeeded: fastANI
[2023-03-17 05:55:35,134] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:55:35,134] [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_002687335.1	s__GCA-002725925 sp002687335	98.1878	133	205	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002725925	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_008373165.1	s__GCA-002725925 sp009392785	90.6113	180	205	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002725925	95.0	98.70	97.00	0.83	0.72	6	-
GCA_009392215.1	s__GCA-002725925 sp009392215	87.8686	172	205	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002725925	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725925.1	s__GCA-002725925 sp002725925	83.8228	145	205	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002725925	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:55:35,136] [INFO] GTDB search result was written to OceanDNA-b14480/result_gtdb.tsv
[2023-03-17 05:55:35,136] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:55:35,137] [INFO] DFAST_QC result json was written to OceanDNA-b14480/dqc_result.json
[2023-03-17 05:55:35,137] [INFO] DFAST_QC completed!
[2023-03-17 05:55:35,137] [INFO] Total running time: 0h0m36s