[2023-03-16 00:43:24,411] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:43:24,413] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:43:24,413] [INFO] DQC Reference Directory: /var/lib/cwl/stg414cc0b0-8b19-48fa-bdaf-60c16dbd0b21/dqc_reference
[2023-03-16 00:43:25,536] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:43:25,536] [INFO] Task started: Prodigal
[2023-03-16 00:43:25,536] [INFO] Running command: cat /var/lib/cwl/stgb3a87863-72fa-460d-8017-d272da0e2405/OceanDNA-a4832.fa | prodigal -d OceanDNA-a4832/cds.fna -a OceanDNA-a4832/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:43:33,028] [INFO] Task succeeded: Prodigal
[2023-03-16 00:43:33,028] [INFO] Task started: HMMsearch
[2023-03-16 00:43:33,028] [INFO] Running command: hmmsearch --tblout OceanDNA-a4832/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg414cc0b0-8b19-48fa-bdaf-60c16dbd0b21/dqc_reference/reference_markers.hmm OceanDNA-a4832/protein.faa > /dev/null
[2023-03-16 00:43:33,197] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:43:33,198] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb3a87863-72fa-460d-8017-d272da0e2405/OceanDNA-a4832.fa]
[2023-03-16 00:43:33,226] [INFO] Query marker FASTA was written to OceanDNA-a4832/markers.fasta
[2023-03-16 00:43:33,228] [INFO] Task started: Blastn
[2023-03-16 00:43:33,228] [INFO] Running command: blastn -query OceanDNA-a4832/markers.fasta -db /var/lib/cwl/stg414cc0b0-8b19-48fa-bdaf-60c16dbd0b21/dqc_reference/reference_markers.fasta -out OceanDNA-a4832/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:43:33,656] [INFO] Task succeeded: Blastn
[2023-03-16 00:43:33,665] [INFO] Selected 3 target genomes.
[2023-03-16 00:43:33,665] [INFO] Target genome list was writen to OceanDNA-a4832/target_genomes.txt
[2023-03-16 00:43:33,667] [INFO] Task started: fastANI
[2023-03-16 00:43:33,667] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3a87863-72fa-460d-8017-d272da0e2405/OceanDNA-a4832.fa --refList OceanDNA-a4832/target_genomes.txt --output OceanDNA-a4832/fastani_result.tsv --threads 1
[2023-03-16 00:43:35,364] [INFO] Task succeeded: fastANI
[2023-03-16 00:43:35,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg414cc0b0-8b19-48fa-bdaf-60c16dbd0b21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:43:35,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg414cc0b0-8b19-48fa-bdaf-60c16dbd0b21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:43:35,365] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:43:35,365] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:43:35,365] [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
--------------------------------------------------------------------------------
[2023-03-16 00:43:35,368] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4832/tc_result.tsv
[2023-03-16 00:43:35,374] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:43:35,374] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:43:35,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg414cc0b0-8b19-48fa-bdaf-60c16dbd0b21/dqc_reference/checkm_data
[2023-03-16 00:43:35,377] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:43:35,475] [INFO] Task started: CheckM
[2023-03-16 00:43:35,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4832/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4832/checkm_input OceanDNA-a4832/checkm_result
[2023-03-16 00:43:59,502] [INFO] Task succeeded: CheckM
[2023-03-16 00:43:59,503] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:43:59,555] [INFO] ===== Completeness check finished =====
[2023-03-16 00:43:59,555] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:43:59,555] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4832/markers.fasta)
[2023-03-16 00:43:59,556] [INFO] Task started: Blastn
[2023-03-16 00:43:59,556] [INFO] Running command: blastn -query OceanDNA-a4832/markers.fasta -db /var/lib/cwl/stg414cc0b0-8b19-48fa-bdaf-60c16dbd0b21/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4832/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:44:00,001] [INFO] Task succeeded: Blastn
[2023-03-16 00:44:00,016] [INFO] Selected 8 target genomes.
[2023-03-16 00:44:00,016] [INFO] Target genome list was writen to OceanDNA-a4832/target_genomes_gtdb.txt
[2023-03-16 00:44:00,034] [INFO] Task started: fastANI
[2023-03-16 00:44:00,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3a87863-72fa-460d-8017-d272da0e2405/OceanDNA-a4832.fa --refList OceanDNA-a4832/target_genomes_gtdb.txt --output OceanDNA-a4832/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:44:02,058] [INFO] Task succeeded: fastANI
[2023-03-16 00:44:02,060] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:44:02,060] [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_002725475.1	s__MGIIb-Q1 sp002725475	80.8387	272	440	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685895.1	s__MGIIb-Q1 sp002685895	78.1227	199	440	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	99.01	99.01	0.75	0.75	3	-
--------------------------------------------------------------------------------
[2023-03-16 00:44:02,068] [INFO] GTDB search result was written to OceanDNA-a4832/result_gtdb.tsv
[2023-03-16 00:44:02,078] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:44:02,083] [INFO] DFAST_QC result json was written to OceanDNA-a4832/dqc_result.json
[2023-03-16 00:44:02,083] [INFO] DFAST_QC completed!
[2023-03-16 00:44:02,083] [INFO] Total running time: 0h0m38s