[2023-03-15 21:16:33,623] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:16:33,623] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:16:33,623] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f6316fe-d47a-448d-bb48-f98b23c2e9bb/dqc_reference
[2023-03-15 21:16:35,472] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:16:35,472] [INFO] Task started: Prodigal
[2023-03-15 21:16:35,472] [INFO] Running command: cat /var/lib/cwl/stg1a1db004-9d23-4010-8bd3-ae91d5125698/OceanDNA-a3133.fa | prodigal -d OceanDNA-a3133/cds.fna -a OceanDNA-a3133/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:16:46,324] [INFO] Task succeeded: Prodigal
[2023-03-15 21:16:46,325] [INFO] Task started: HMMsearch
[2023-03-15 21:16:46,325] [INFO] Running command: hmmsearch --tblout OceanDNA-a3133/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f6316fe-d47a-448d-bb48-f98b23c2e9bb/dqc_reference/reference_markers.hmm OceanDNA-a3133/protein.faa > /dev/null
[2023-03-15 21:16:46,484] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:16:46,485] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg1a1db004-9d23-4010-8bd3-ae91d5125698/OceanDNA-a3133.fa]
[2023-03-15 21:16:46,497] [INFO] Query marker FASTA was written to OceanDNA-a3133/markers.fasta
[2023-03-15 21:16:46,498] [INFO] Task started: Blastn
[2023-03-15 21:16:46,498] [INFO] Running command: blastn -query OceanDNA-a3133/markers.fasta -db /var/lib/cwl/stg6f6316fe-d47a-448d-bb48-f98b23c2e9bb/dqc_reference/reference_markers.fasta -out OceanDNA-a3133/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:16:46,973] [INFO] Task succeeded: Blastn
[2023-03-15 21:16:46,974] [INFO] Selected 3 target genomes.
[2023-03-15 21:16:46,974] [INFO] Target genome list was writen to OceanDNA-a3133/target_genomes.txt
[2023-03-15 21:16:46,977] [INFO] Task started: fastANI
[2023-03-15 21:16:46,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a1db004-9d23-4010-8bd3-ae91d5125698/OceanDNA-a3133.fa --refList OceanDNA-a3133/target_genomes.txt --output OceanDNA-a3133/fastani_result.tsv --threads 1
[2023-03-15 21:16:48,696] [INFO] Task succeeded: fastANI
[2023-03-15 21:16:48,696] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f6316fe-d47a-448d-bb48-f98b23c2e9bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:16:48,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f6316fe-d47a-448d-bb48-f98b23c2e9bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:16:48,696] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:16:48,697] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:16:48,697] [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 21:16:48,697] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3133/tc_result.tsv
[2023-03-15 21:16:48,697] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:16:48,697] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:16:48,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f6316fe-d47a-448d-bb48-f98b23c2e9bb/dqc_reference/checkm_data
[2023-03-15 21:16:48,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:16:48,702] [INFO] Task started: CheckM
[2023-03-15 21:16:48,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3133/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3133/checkm_input OceanDNA-a3133/checkm_result
[2023-03-15 21:17:22,215] [INFO] Task succeeded: CheckM
[2023-03-15 21:17:22,215] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.79%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 21:17:22,217] [INFO] ===== Completeness check finished =====
[2023-03-15 21:17:22,217] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:17:22,218] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3133/markers.fasta)
[2023-03-15 21:17:22,219] [INFO] Task started: Blastn
[2023-03-15 21:17:22,219] [INFO] Running command: blastn -query OceanDNA-a3133/markers.fasta -db /var/lib/cwl/stg6f6316fe-d47a-448d-bb48-f98b23c2e9bb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3133/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:17:22,846] [INFO] Task succeeded: Blastn
[2023-03-15 21:17:22,847] [INFO] Selected 7 target genomes.
[2023-03-15 21:17:22,847] [INFO] Target genome list was writen to OceanDNA-a3133/target_genomes_gtdb.txt
[2023-03-15 21:17:22,951] [INFO] Task started: fastANI
[2023-03-15 21:17:22,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a1db004-9d23-4010-8bd3-ae91d5125698/OceanDNA-a3133.fa --refList OceanDNA-a3133/target_genomes_gtdb.txt --output OceanDNA-a3133/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:17:25,352] [INFO] Task succeeded: fastANI
[2023-03-15 21:17:25,357] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:17:25,357] [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_002722695.1	s__Poseidonia sp002722695	99.4326	422	532	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.22	99.22	0.79	0.79	3	conclusive
GCA_002694525.1	s__Poseidonia sp002694525	81.4054	338	532	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725275.1	s__Poseidonia sp002725275	78.9593	242	532	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.76	96.60	0.76	0.75	3	-
GCA_002502295.1	s__Poseidonia sp002502295	78.0562	203	532	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002495645.1	s__Poseidonia sp002495645	78.0056	230	532	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.68	99.68	0.84	0.84	2	-
GCA_016779705.1	s__Poseidonia sp016779705	77.4846	140	532	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524855.1	s__Poseidonia sp011524855	77.365	122	532	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:17:25,357] [INFO] GTDB search result was written to OceanDNA-a3133/result_gtdb.tsv
[2023-03-15 21:17:25,358] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:17:25,358] [INFO] DFAST_QC result json was written to OceanDNA-a3133/dqc_result.json
[2023-03-15 21:17:25,358] [INFO] DFAST_QC completed!
[2023-03-15 21:17:25,358] [INFO] Total running time: 0h0m52s