[2023-03-17 11:57:19,287] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:57:19,287] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:57:19,288] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c8db377-3cf5-4937-bd30-0630579e99b2/dqc_reference
[2023-03-17 11:57:20,887] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:57:20,888] [INFO] Task started: Prodigal
[2023-03-17 11:57:20,888] [INFO] Running command: cat /var/lib/cwl/stg109c2b54-a735-46db-aa37-077cc69b4446/OceanDNA-a4119.fa | prodigal -d OceanDNA-a4119/cds.fna -a OceanDNA-a4119/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:57:27,131] [INFO] Task succeeded: Prodigal
[2023-03-17 11:57:27,131] [INFO] Task started: HMMsearch
[2023-03-17 11:57:27,131] [INFO] Running command: hmmsearch --tblout OceanDNA-a4119/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c8db377-3cf5-4937-bd30-0630579e99b2/dqc_reference/reference_markers.hmm OceanDNA-a4119/protein.faa > /dev/null
[2023-03-17 11:57:27,251] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:57:27,252] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg109c2b54-a735-46db-aa37-077cc69b4446/OceanDNA-a4119.fa]
[2023-03-17 11:57:27,258] [INFO] Query marker FASTA was written to OceanDNA-a4119/markers.fasta
[2023-03-17 11:57:27,258] [INFO] Task started: Blastn
[2023-03-17 11:57:27,258] [INFO] Running command: blastn -query OceanDNA-a4119/markers.fasta -db /var/lib/cwl/stg7c8db377-3cf5-4937-bd30-0630579e99b2/dqc_reference/reference_markers.fasta -out OceanDNA-a4119/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:57:29,496] [INFO] Task succeeded: Blastn
[2023-03-17 11:57:29,496] [INFO] Selected 2 target genomes.
[2023-03-17 11:57:29,497] [INFO] Target genome list was writen to OceanDNA-a4119/target_genomes.txt
[2023-03-17 11:57:29,498] [INFO] Task started: fastANI
[2023-03-17 11:57:29,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg109c2b54-a735-46db-aa37-077cc69b4446/OceanDNA-a4119.fa --refList OceanDNA-a4119/target_genomes.txt --output OceanDNA-a4119/fastani_result.tsv --threads 1
[2023-03-17 11:57:30,026] [INFO] Task succeeded: fastANI
[2023-03-17 11:57:30,026] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c8db377-3cf5-4937-bd30-0630579e99b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:57:30,026] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c8db377-3cf5-4937-bd30-0630579e99b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:57:30,027] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:57:30,027] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:57:30,027] [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 11:57:30,027] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4119/tc_result.tsv
[2023-03-17 11:57:30,027] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:57:30,027] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:57:30,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c8db377-3cf5-4937-bd30-0630579e99b2/dqc_reference/checkm_data
[2023-03-17 11:57:30,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:57:30,079] [INFO] Task started: CheckM
[2023-03-17 11:57:30,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4119/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4119/checkm_input OceanDNA-a4119/checkm_result
[2023-03-17 11:57:51,936] [INFO] Task succeeded: CheckM
[2023-03-17 11:57:51,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:57:51,938] [INFO] ===== Completeness check finished =====
[2023-03-17 11:57:51,938] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:57:51,938] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4119/markers.fasta)
[2023-03-17 11:57:51,940] [INFO] Task started: Blastn
[2023-03-17 11:57:51,940] [INFO] Running command: blastn -query OceanDNA-a4119/markers.fasta -db /var/lib/cwl/stg7c8db377-3cf5-4937-bd30-0630579e99b2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4119/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:57:52,634] [INFO] Task succeeded: Blastn
[2023-03-17 11:57:52,634] [INFO] Selected 7 target genomes.
[2023-03-17 11:57:52,634] [INFO] Target genome list was writen to OceanDNA-a4119/target_genomes_gtdb.txt
[2023-03-17 11:57:52,670] [INFO] Task started: fastANI
[2023-03-17 11:57:52,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg109c2b54-a735-46db-aa37-077cc69b4446/OceanDNA-a4119.fa --refList OceanDNA-a4119/target_genomes_gtdb.txt --output OceanDNA-a4119/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:57:54,265] [INFO] Task succeeded: fastANI
[2023-03-17 11:57:54,268] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:57:54,268] [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_002172185.1	s__MGIIb-O3 sp002172185	99.9703	167	276	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_002720055.1	s__MGIIb-O3 sp002720055	88.4988	249	276	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713185.1	s__MGIIb-O3 sp002713185	85.7561	229	276	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:57:54,268] [INFO] GTDB search result was written to OceanDNA-a4119/result_gtdb.tsv
[2023-03-17 11:57:54,268] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:57:54,269] [INFO] DFAST_QC result json was written to OceanDNA-a4119/dqc_result.json
[2023-03-17 11:57:54,269] [INFO] DFAST_QC completed!
[2023-03-17 11:57:54,269] [INFO] Total running time: 0h0m35s