[2023-03-17 11:25:37,170] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:25:37,175] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:25:37,175] [INFO] DQC Reference Directory: /var/lib/cwl/stg31ec588a-54d0-4a86-8994-e58f60fc2e76/dqc_reference
[2023-03-17 11:25:38,283] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:25:38,284] [INFO] Task started: Prodigal
[2023-03-17 11:25:38,284] [INFO] Running command: cat /var/lib/cwl/stg8362a030-1d88-4c95-8e7c-ad5d62e07ad5/OceanDNA-a2096.fa | prodigal -d OceanDNA-a2096/cds.fna -a OceanDNA-a2096/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:25:48,691] [INFO] Task succeeded: Prodigal
[2023-03-17 11:25:48,692] [INFO] Task started: HMMsearch
[2023-03-17 11:25:48,692] [INFO] Running command: hmmsearch --tblout OceanDNA-a2096/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31ec588a-54d0-4a86-8994-e58f60fc2e76/dqc_reference/reference_markers.hmm OceanDNA-a2096/protein.faa > /dev/null
[2023-03-17 11:25:48,860] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:25:48,860] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8362a030-1d88-4c95-8e7c-ad5d62e07ad5/OceanDNA-a2096.fa]
[2023-03-17 11:25:48,891] [INFO] Query marker FASTA was written to OceanDNA-a2096/markers.fasta
[2023-03-17 11:25:48,892] [INFO] Task started: Blastn
[2023-03-17 11:25:48,892] [INFO] Running command: blastn -query OceanDNA-a2096/markers.fasta -db /var/lib/cwl/stg31ec588a-54d0-4a86-8994-e58f60fc2e76/dqc_reference/reference_markers.fasta -out OceanDNA-a2096/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:25:49,328] [INFO] Task succeeded: Blastn
[2023-03-17 11:25:49,336] [INFO] Selected 5 target genomes.
[2023-03-17 11:25:49,336] [INFO] Target genome list was writen to OceanDNA-a2096/target_genomes.txt
[2023-03-17 11:25:49,339] [INFO] Task started: fastANI
[2023-03-17 11:25:49,339] [INFO] Running command: fastANI --query /var/lib/cwl/stg8362a030-1d88-4c95-8e7c-ad5d62e07ad5/OceanDNA-a2096.fa --refList OceanDNA-a2096/target_genomes.txt --output OceanDNA-a2096/fastani_result.tsv --threads 1
[2023-03-17 11:25:52,379] [INFO] Task succeeded: fastANI
[2023-03-17 11:25:52,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31ec588a-54d0-4a86-8994-e58f60fc2e76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:25:52,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31ec588a-54d0-4a86-8994-e58f60fc2e76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:25:52,379] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:25:52,379] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:25:52,379] [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 11:25:52,382] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2096/tc_result.tsv
[2023-03-17 11:25:52,390] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:25:52,390] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:25:52,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31ec588a-54d0-4a86-8994-e58f60fc2e76/dqc_reference/checkm_data
[2023-03-17 11:25:52,392] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:25:52,417] [INFO] Task started: CheckM
[2023-03-17 11:25:52,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2096/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2096/checkm_input OceanDNA-a2096/checkm_result
[2023-03-17 11:26:23,564] [INFO] Task succeeded: CheckM
[2023-03-17 11:26:23,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:26:23,742] [INFO] ===== Completeness check finished =====
[2023-03-17 11:26:23,742] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:26:23,742] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2096/markers.fasta)
[2023-03-17 11:26:23,743] [INFO] Task started: Blastn
[2023-03-17 11:26:23,743] [INFO] Running command: blastn -query OceanDNA-a2096/markers.fasta -db /var/lib/cwl/stg31ec588a-54d0-4a86-8994-e58f60fc2e76/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2096/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:26:24,171] [INFO] Task succeeded: Blastn
[2023-03-17 11:26:24,187] [INFO] Selected 9 target genomes.
[2023-03-17 11:26:24,187] [INFO] Target genome list was writen to OceanDNA-a2096/target_genomes_gtdb.txt
[2023-03-17 11:26:24,197] [INFO] Task started: fastANI
[2023-03-17 11:26:24,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg8362a030-1d88-4c95-8e7c-ad5d62e07ad5/OceanDNA-a2096.fa --refList OceanDNA-a2096/target_genomes_gtdb.txt --output OceanDNA-a2096/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:26:26,664] [INFO] Task succeeded: fastANI
[2023-03-17 11:26:26,667] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:26:26,667] [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_002719395.1	s__MGIIa-K2 sp002719395	99.4471	480	577	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K2	95.0	97.60	96.03	0.75	0.68	6	conclusive
GCA_002699425.1	s__MGIIa-K2 sp002699425	85.5392	483	577	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:26:26,672] [INFO] GTDB search result was written to OceanDNA-a2096/result_gtdb.tsv
[2023-03-17 11:26:26,677] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:26:26,683] [INFO] DFAST_QC result json was written to OceanDNA-a2096/dqc_result.json
[2023-03-17 11:26:26,683] [INFO] DFAST_QC completed!
[2023-03-17 11:26:26,683] [INFO] Total running time: 0h0m50s