[2023-03-15 04:04:36,561] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:04:36,561] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:04:36,562] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f4a58cf-4ef9-4fc9-b36a-354cd50d058a/dqc_reference
[2023-03-15 04:04:39,814] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:04:39,815] [INFO] Task started: Prodigal
[2023-03-15 04:04:39,815] [INFO] Running command: cat /var/lib/cwl/stgf19af138-8016-4119-a114-fbeb17bd88ea/OceanDNA-a1844.fa | prodigal -d OceanDNA-a1844/cds.fna -a OceanDNA-a1844/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:04:48,685] [INFO] Task succeeded: Prodigal
[2023-03-15 04:04:48,686] [INFO] Task started: HMMsearch
[2023-03-15 04:04:48,686] [INFO] Running command: hmmsearch --tblout OceanDNA-a1844/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f4a58cf-4ef9-4fc9-b36a-354cd50d058a/dqc_reference/reference_markers.hmm OceanDNA-a1844/protein.faa > /dev/null
[2023-03-15 04:04:48,868] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:04:48,868] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgf19af138-8016-4119-a114-fbeb17bd88ea/OceanDNA-a1844.fa]
[2023-03-15 04:04:48,898] [INFO] Query marker FASTA was written to OceanDNA-a1844/markers.fasta
[2023-03-15 04:04:48,900] [INFO] Task started: Blastn
[2023-03-15 04:04:48,900] [INFO] Running command: blastn -query OceanDNA-a1844/markers.fasta -db /var/lib/cwl/stg8f4a58cf-4ef9-4fc9-b36a-354cd50d058a/dqc_reference/reference_markers.fasta -out OceanDNA-a1844/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:04:49,374] [INFO] Task succeeded: Blastn
[2023-03-15 04:04:49,379] [INFO] Selected 3 target genomes.
[2023-03-15 04:04:49,380] [INFO] Target genome list was writen to OceanDNA-a1844/target_genomes.txt
[2023-03-15 04:04:49,383] [INFO] Task started: fastANI
[2023-03-15 04:04:49,383] [INFO] Running command: fastANI --query /var/lib/cwl/stgf19af138-8016-4119-a114-fbeb17bd88ea/OceanDNA-a1844.fa --refList OceanDNA-a1844/target_genomes.txt --output OceanDNA-a1844/fastani_result.tsv --threads 1
[2023-03-15 04:04:50,543] [INFO] Task succeeded: fastANI
[2023-03-15 04:04:50,543] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f4a58cf-4ef9-4fc9-b36a-354cd50d058a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:04:50,543] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f4a58cf-4ef9-4fc9-b36a-354cd50d058a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:04:50,543] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:04:50,543] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 04:04:50,543] [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 04:04:50,546] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1844/tc_result.tsv
[2023-03-15 04:04:50,551] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:04:50,551] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:04:50,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f4a58cf-4ef9-4fc9-b36a-354cd50d058a/dqc_reference/checkm_data
[2023-03-15 04:04:50,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:04:50,592] [INFO] Task started: CheckM
[2023-03-15 04:04:50,592] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1844/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1844/checkm_input OceanDNA-a1844/checkm_result
[2023-03-15 04:05:19,845] [INFO] Task succeeded: CheckM
[2023-03-15 04:05:19,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.57%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:05:19,871] [INFO] ===== Completeness check finished =====
[2023-03-15 04:05:19,871] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:05:19,871] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1844/markers.fasta)
[2023-03-15 04:05:19,872] [INFO] Task started: Blastn
[2023-03-15 04:05:19,872] [INFO] Running command: blastn -query OceanDNA-a1844/markers.fasta -db /var/lib/cwl/stg8f4a58cf-4ef9-4fc9-b36a-354cd50d058a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1844/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:05:20,421] [INFO] Task succeeded: Blastn
[2023-03-15 04:05:20,426] [INFO] Selected 5 target genomes.
[2023-03-15 04:05:20,426] [INFO] Target genome list was writen to OceanDNA-a1844/target_genomes_gtdb.txt
[2023-03-15 04:05:20,444] [INFO] Task started: fastANI
[2023-03-15 04:05:20,444] [INFO] Running command: fastANI --query /var/lib/cwl/stgf19af138-8016-4119-a114-fbeb17bd88ea/OceanDNA-a1844.fa --refList OceanDNA-a1844/target_genomes_gtdb.txt --output OceanDNA-a1844/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:05:22,088] [INFO] Task succeeded: fastANI
[2023-03-15 04:05:22,091] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 04:05:22,092] [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_002720095.2	s__MGIIa-I sp002720095	99.7574	532	554	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	99.78	99.77	0.92	0.90	4	conclusive
GCA_002692465.1	s__MGIIa-I sp002692465	77.9882	184	554	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002498205.1	s__MGIIa-I sp002498205	77.9676	156	554	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699515.1	s__MGIIa-I sp002699515	77.8914	148	554	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 04:05:22,094] [INFO] GTDB search result was written to OceanDNA-a1844/result_gtdb.tsv
[2023-03-15 04:05:22,098] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:05:22,101] [INFO] DFAST_QC result json was written to OceanDNA-a1844/dqc_result.json
[2023-03-15 04:05:22,101] [INFO] DFAST_QC completed!
[2023-03-15 04:05:22,101] [INFO] Total running time: 0h0m46s