[2023-03-19 01:38:53,928] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:38:53,931] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:38:53,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f17b906-90c4-42b1-8002-c3fea9383ba1/dqc_reference
[2023-03-19 01:38:55,009] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:38:55,009] [INFO] Task started: Prodigal
[2023-03-19 01:38:55,009] [INFO] Running command: cat /var/lib/cwl/stg3b28ce5b-5388-4820-8126-3ed58d7172f9/OceanDNA-b19679.fa | prodigal -d OceanDNA-b19679/cds.fna -a OceanDNA-b19679/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:39:01,712] [INFO] Task succeeded: Prodigal
[2023-03-19 01:39:01,712] [INFO] Task started: HMMsearch
[2023-03-19 01:39:01,712] [INFO] Running command: hmmsearch --tblout OceanDNA-b19679/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f17b906-90c4-42b1-8002-c3fea9383ba1/dqc_reference/reference_markers.hmm OceanDNA-b19679/protein.faa > /dev/null
[2023-03-19 01:39:01,849] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:39:01,850] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3b28ce5b-5388-4820-8126-3ed58d7172f9/OceanDNA-b19679.fa]
[2023-03-19 01:39:01,886] [INFO] Query marker FASTA was written to OceanDNA-b19679/markers.fasta
[2023-03-19 01:39:01,887] [INFO] Task started: Blastn
[2023-03-19 01:39:01,887] [INFO] Running command: blastn -query OceanDNA-b19679/markers.fasta -db /var/lib/cwl/stg0f17b906-90c4-42b1-8002-c3fea9383ba1/dqc_reference/reference_markers.fasta -out OceanDNA-b19679/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:39:02,341] [INFO] Task succeeded: Blastn
[2023-03-19 01:39:02,350] [INFO] Selected 11 target genomes.
[2023-03-19 01:39:02,350] [INFO] Target genome list was writen to OceanDNA-b19679/target_genomes.txt
[2023-03-19 01:39:02,358] [INFO] Task started: fastANI
[2023-03-19 01:39:02,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b28ce5b-5388-4820-8126-3ed58d7172f9/OceanDNA-b19679.fa --refList OceanDNA-b19679/target_genomes.txt --output OceanDNA-b19679/fastani_result.tsv --threads 1
[2023-03-19 01:39:05,953] [INFO] Task succeeded: fastANI
[2023-03-19 01:39:05,953] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f17b906-90c4-42b1-8002-c3fea9383ba1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:39:05,953] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f17b906-90c4-42b1-8002-c3fea9383ba1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:39:05,953] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:39:05,953] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:39:05,954] [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 01:39:05,957] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19679/tc_result.tsv
[2023-03-19 01:39:05,962] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:39:05,962] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:39:05,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f17b906-90c4-42b1-8002-c3fea9383ba1/dqc_reference/checkm_data
[2023-03-19 01:39:05,965] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:39:05,969] [INFO] Task started: CheckM
[2023-03-19 01:39:05,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19679/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19679/checkm_input OceanDNA-b19679/checkm_result
[2023-03-19 01:39:28,683] [INFO] Task succeeded: CheckM
[2023-03-19 01:39:28,684] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.62%
Contamintation: 2.26%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-19 01:39:28,759] [INFO] ===== Completeness check finished =====
[2023-03-19 01:39:28,759] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:39:28,759] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19679/markers.fasta)
[2023-03-19 01:39:28,759] [INFO] Task started: Blastn
[2023-03-19 01:39:28,759] [INFO] Running command: blastn -query OceanDNA-b19679/markers.fasta -db /var/lib/cwl/stg0f17b906-90c4-42b1-8002-c3fea9383ba1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19679/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:39:29,283] [INFO] Task succeeded: Blastn
[2023-03-19 01:39:29,287] [INFO] Selected 12 target genomes.
[2023-03-19 01:39:29,287] [INFO] Target genome list was writen to OceanDNA-b19679/target_genomes_gtdb.txt
[2023-03-19 01:39:29,326] [INFO] Task started: fastANI
[2023-03-19 01:39:29,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b28ce5b-5388-4820-8126-3ed58d7172f9/OceanDNA-b19679.fa --refList OceanDNA-b19679/target_genomes_gtdb.txt --output OceanDNA-b19679/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:39:32,671] [INFO] Task succeeded: fastANI
[2023-03-19 01:39:32,674] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:39:32,674] [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_902562835.1	s__CACEUX01 sp902562835	80.0338	223	426	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__CACEUX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167345.2	s__CACEUX01 sp002167345	79.9388	301	426	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__CACEUX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:39:32,678] [INFO] GTDB search result was written to OceanDNA-b19679/result_gtdb.tsv
[2023-03-19 01:39:32,687] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:39:32,692] [INFO] DFAST_QC result json was written to OceanDNA-b19679/dqc_result.json
[2023-03-19 01:39:32,692] [INFO] DFAST_QC completed!
[2023-03-19 01:39:32,692] [INFO] Total running time: 0h0m39s