[2023-03-19 03:10:00,727] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:10:00,727] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:10:00,727] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a856503-f153-4a2b-a5a8-c08adb356eab/dqc_reference
[2023-03-19 03:10:01,840] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:10:01,840] [INFO] Task started: Prodigal
[2023-03-19 03:10:01,841] [INFO] Running command: cat /var/lib/cwl/stg645973d5-f803-4924-b80e-96ae31750b39/OceanDNA-a1493.fa | prodigal -d OceanDNA-a1493/cds.fna -a OceanDNA-a1493/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:10:06,669] [INFO] Task succeeded: Prodigal
[2023-03-19 03:10:06,669] [INFO] Task started: HMMsearch
[2023-03-19 03:10:06,669] [INFO] Running command: hmmsearch --tblout OceanDNA-a1493/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a856503-f153-4a2b-a5a8-c08adb356eab/dqc_reference/reference_markers.hmm OceanDNA-a1493/protein.faa > /dev/null
[2023-03-19 03:10:06,814] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:10:06,815] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg645973d5-f803-4924-b80e-96ae31750b39/OceanDNA-a1493.fa]
[2023-03-19 03:10:06,827] [INFO] Query marker FASTA was written to OceanDNA-a1493/markers.fasta
[2023-03-19 03:10:06,828] [INFO] Task started: Blastn
[2023-03-19 03:10:06,828] [INFO] Running command: blastn -query OceanDNA-a1493/markers.fasta -db /var/lib/cwl/stg5a856503-f153-4a2b-a5a8-c08adb356eab/dqc_reference/reference_markers.fasta -out OceanDNA-a1493/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:10:07,256] [INFO] Task succeeded: Blastn
[2023-03-19 03:10:07,256] [INFO] Selected 5 target genomes.
[2023-03-19 03:10:07,257] [INFO] Target genome list was writen to OceanDNA-a1493/target_genomes.txt
[2023-03-19 03:10:07,260] [INFO] Task started: fastANI
[2023-03-19 03:10:07,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg645973d5-f803-4924-b80e-96ae31750b39/OceanDNA-a1493.fa --refList OceanDNA-a1493/target_genomes.txt --output OceanDNA-a1493/fastani_result.tsv --threads 1
[2023-03-19 03:10:09,437] [INFO] Task succeeded: fastANI
[2023-03-19 03:10:09,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a856503-f153-4a2b-a5a8-c08adb356eab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:10:09,437] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a856503-f153-4a2b-a5a8-c08adb356eab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:10:09,438] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:10:09,438] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:10:09,438] [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
--------------------------------------------------------------------------------
[2023-03-19 03:10:09,438] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1493/tc_result.tsv
[2023-03-19 03:10:09,438] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:10:09,438] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:10:09,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a856503-f153-4a2b-a5a8-c08adb356eab/dqc_reference/checkm_data
[2023-03-19 03:10:09,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:10:09,514] [INFO] Task started: CheckM
[2023-03-19 03:10:09,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1493/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1493/checkm_input OceanDNA-a1493/checkm_result
[2023-03-19 03:10:27,828] [INFO] Task succeeded: CheckM
[2023-03-19 03:10:27,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.88%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:10:27,831] [INFO] ===== Completeness check finished =====
[2023-03-19 03:10:27,831] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:10:27,831] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1493/markers.fasta)
[2023-03-19 03:10:27,831] [INFO] Task started: Blastn
[2023-03-19 03:10:27,831] [INFO] Running command: blastn -query OceanDNA-a1493/markers.fasta -db /var/lib/cwl/stg5a856503-f153-4a2b-a5a8-c08adb356eab/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1493/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:10:28,282] [INFO] Task succeeded: Blastn
[2023-03-19 03:10:28,283] [INFO] Selected 9 target genomes.
[2023-03-19 03:10:28,283] [INFO] Target genome list was writen to OceanDNA-a1493/target_genomes_gtdb.txt
[2023-03-19 03:10:28,326] [INFO] Task started: fastANI
[2023-03-19 03:10:28,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg645973d5-f803-4924-b80e-96ae31750b39/OceanDNA-a1493.fa --refList OceanDNA-a1493/target_genomes_gtdb.txt --output OceanDNA-a1493/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:10:29,977] [INFO] Task succeeded: fastANI
[2023-03-19 03:10:29,980] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:10:29,980] [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_018668595.1	s__JABJCP01 sp018668595	99.9322	250	261	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Woesearchaeales;f__UBA11576;g__JABJCP01	95.0	99.97	99.96	0.92	0.92	3	conclusive
--------------------------------------------------------------------------------
[2023-03-19 03:10:29,980] [INFO] GTDB search result was written to OceanDNA-a1493/result_gtdb.tsv
[2023-03-19 03:10:29,980] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:10:29,980] [INFO] DFAST_QC result json was written to OceanDNA-a1493/dqc_result.json
[2023-03-19 03:10:29,980] [INFO] DFAST_QC completed!
[2023-03-19 03:10:29,981] [INFO] Total running time: 0h0m29s