[2023-03-15 17:50:52,689] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:50:52,689] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:50:52,689] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b15b22e-ce3d-450c-ba57-3c93a6dbe616/dqc_reference
[2023-03-15 17:50:53,785] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:50:53,785] [INFO] Task started: Prodigal
[2023-03-15 17:50:53,785] [INFO] Running command: cat /var/lib/cwl/stgcaf6d9ba-40ad-4856-9330-ada01e177300/OceanDNA-a1861.fa | prodigal -d OceanDNA-a1861/cds.fna -a OceanDNA-a1861/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:51:00,359] [INFO] Task succeeded: Prodigal
[2023-03-15 17:51:00,359] [INFO] Task started: HMMsearch
[2023-03-15 17:51:00,359] [INFO] Running command: hmmsearch --tblout OceanDNA-a1861/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b15b22e-ce3d-450c-ba57-3c93a6dbe616/dqc_reference/reference_markers.hmm OceanDNA-a1861/protein.faa > /dev/null
[2023-03-15 17:51:00,487] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:51:00,488] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgcaf6d9ba-40ad-4856-9330-ada01e177300/OceanDNA-a1861.fa]
[2023-03-15 17:51:00,499] [INFO] Query marker FASTA was written to OceanDNA-a1861/markers.fasta
[2023-03-15 17:51:00,501] [INFO] Task started: Blastn
[2023-03-15 17:51:00,501] [INFO] Running command: blastn -query OceanDNA-a1861/markers.fasta -db /var/lib/cwl/stg8b15b22e-ce3d-450c-ba57-3c93a6dbe616/dqc_reference/reference_markers.fasta -out OceanDNA-a1861/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:51:00,934] [INFO] Task succeeded: Blastn
[2023-03-15 17:51:00,935] [INFO] Selected 1 target genomes.
[2023-03-15 17:51:00,935] [INFO] Target genome list was writen to OceanDNA-a1861/target_genomes.txt
[2023-03-15 17:51:00,936] [INFO] Task started: fastANI
[2023-03-15 17:51:00,936] [INFO] Running command: fastANI --query /var/lib/cwl/stgcaf6d9ba-40ad-4856-9330-ada01e177300/OceanDNA-a1861.fa --refList OceanDNA-a1861/target_genomes.txt --output OceanDNA-a1861/fastani_result.tsv --threads 1
[2023-03-15 17:51:01,199] [INFO] Task succeeded: fastANI
[2023-03-15 17:51:01,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b15b22e-ce3d-450c-ba57-3c93a6dbe616/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:51:01,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b15b22e-ce3d-450c-ba57-3c93a6dbe616/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:51:01,200] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:51:01,200] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:51:01,200] [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 17:51:01,200] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1861/tc_result.tsv
[2023-03-15 17:51:01,201] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:51:01,201] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:51:01,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b15b22e-ce3d-450c-ba57-3c93a6dbe616/dqc_reference/checkm_data
[2023-03-15 17:51:01,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:51:01,259] [INFO] Task started: CheckM
[2023-03-15 17:51:01,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1861/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1861/checkm_input OceanDNA-a1861/checkm_result
[2023-03-15 17:51:23,237] [INFO] Task succeeded: CheckM
[2023-03-15 17:51:23,237] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.55%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:51:23,239] [INFO] ===== Completeness check finished =====
[2023-03-15 17:51:23,239] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:51:23,240] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1861/markers.fasta)
[2023-03-15 17:51:23,241] [INFO] Task started: Blastn
[2023-03-15 17:51:23,241] [INFO] Running command: blastn -query OceanDNA-a1861/markers.fasta -db /var/lib/cwl/stg8b15b22e-ce3d-450c-ba57-3c93a6dbe616/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1861/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:51:23,709] [INFO] Task succeeded: Blastn
[2023-03-15 17:51:23,710] [INFO] Selected 10 target genomes.
[2023-03-15 17:51:23,710] [INFO] Target genome list was writen to OceanDNA-a1861/target_genomes_gtdb.txt
[2023-03-15 17:51:23,716] [INFO] Task started: fastANI
[2023-03-15 17:51:23,716] [INFO] Running command: fastANI --query /var/lib/cwl/stgcaf6d9ba-40ad-4856-9330-ada01e177300/OceanDNA-a1861.fa --refList OceanDNA-a1861/target_genomes_gtdb.txt --output OceanDNA-a1861/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:51:26,549] [INFO] Task succeeded: fastANI
[2023-03-15 17:51:26,553] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:51:26,553] [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_002506705.1	s__MGIIa-K1 sp002506705	83.271	203	376	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525095.1	s__MGIIa-K1 sp011525095	82.7455	255	376	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694245.1	s__MGIIa-K1 sp002694245	77.8792	76	376	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727695.1	s__MGIIa-K1 sp002727695	77.5616	121	376	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902563095.1	s__MGIIa-K1 sp902563095	77.0829	101	376	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.06	97.94	0.61	0.59	4	-
GCA_002689345.1	s__MGIIa-K1 sp002689345	76.5019	70	376	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:51:26,554] [INFO] GTDB search result was written to OceanDNA-a1861/result_gtdb.tsv
[2023-03-15 17:51:26,554] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:51:26,555] [INFO] DFAST_QC result json was written to OceanDNA-a1861/dqc_result.json
[2023-03-15 17:51:26,555] [INFO] DFAST_QC completed!
[2023-03-15 17:51:26,555] [INFO] Total running time: 0h0m34s