[2023-03-16 17:08:13,824] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:08:13,824] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:08:13,825] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a43d715-0b8f-47c5-945f-0cd808498ce2/dqc_reference
[2023-03-16 17:08:15,907] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:08:15,908] [INFO] Task started: Prodigal
[2023-03-16 17:08:15,909] [INFO] Running command: cat /var/lib/cwl/stg3e8088a8-08df-4153-ad13-c71538824f68/OceanDNA-b13850.fa | prodigal -d OceanDNA-b13850/cds.fna -a OceanDNA-b13850/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:08:20,624] [INFO] Task succeeded: Prodigal
[2023-03-16 17:08:20,624] [INFO] Task started: HMMsearch
[2023-03-16 17:08:20,624] [INFO] Running command: hmmsearch --tblout OceanDNA-b13850/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a43d715-0b8f-47c5-945f-0cd808498ce2/dqc_reference/reference_markers.hmm OceanDNA-b13850/protein.faa > /dev/null
[2023-03-16 17:08:20,843] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:08:20,843] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3e8088a8-08df-4153-ad13-c71538824f68/OceanDNA-b13850.fa]
[2023-03-16 17:08:20,852] [INFO] Query marker FASTA was written to OceanDNA-b13850/markers.fasta
[2023-03-16 17:08:20,855] [INFO] Task started: Blastn
[2023-03-16 17:08:20,856] [INFO] Running command: blastn -query OceanDNA-b13850/markers.fasta -db /var/lib/cwl/stg2a43d715-0b8f-47c5-945f-0cd808498ce2/dqc_reference/reference_markers.fasta -out OceanDNA-b13850/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:08:21,819] [INFO] Task succeeded: Blastn
[2023-03-16 17:08:21,820] [INFO] Selected 15 target genomes.
[2023-03-16 17:08:21,821] [INFO] Target genome list was writen to OceanDNA-b13850/target_genomes.txt
[2023-03-16 17:08:21,897] [INFO] Task started: fastANI
[2023-03-16 17:08:21,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e8088a8-08df-4153-ad13-c71538824f68/OceanDNA-b13850.fa --refList OceanDNA-b13850/target_genomes.txt --output OceanDNA-b13850/fastani_result.tsv --threads 1
[2023-03-16 17:08:30,276] [INFO] Task succeeded: fastANI
[2023-03-16 17:08:30,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a43d715-0b8f-47c5-945f-0cd808498ce2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:08:30,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a43d715-0b8f-47c5-945f-0cd808498ce2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:08:30,277] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:08:30,277] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:08:30,277] [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 17:08:30,351] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13850/tc_result.tsv
[2023-03-16 17:08:30,352] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:08:30,352] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:08:30,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a43d715-0b8f-47c5-945f-0cd808498ce2/dqc_reference/checkm_data
[2023-03-16 17:08:30,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:08:30,367] [INFO] Task started: CheckM
[2023-03-16 17:08:30,367] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13850/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13850/checkm_input OceanDNA-b13850/checkm_result
[2023-03-16 17:08:44,901] [INFO] Task succeeded: CheckM
[2023-03-16 17:08:44,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.78%
Contamintation: 1.28%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-16 17:08:44,905] [INFO] ===== Completeness check finished =====
[2023-03-16 17:08:44,905] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:08:44,905] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13850/markers.fasta)
[2023-03-16 17:08:44,907] [INFO] Task started: Blastn
[2023-03-16 17:08:44,907] [INFO] Running command: blastn -query OceanDNA-b13850/markers.fasta -db /var/lib/cwl/stg2a43d715-0b8f-47c5-945f-0cd808498ce2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13850/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:08:45,647] [INFO] Task succeeded: Blastn
[2023-03-16 17:08:45,649] [INFO] Selected 13 target genomes.
[2023-03-16 17:08:45,649] [INFO] Target genome list was writen to OceanDNA-b13850/target_genomes_gtdb.txt
[2023-03-16 17:08:45,678] [INFO] Task started: fastANI
[2023-03-16 17:08:45,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e8088a8-08df-4153-ad13-c71538824f68/OceanDNA-b13850.fa --refList OceanDNA-b13850/target_genomes_gtdb.txt --output OceanDNA-b13850/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:08:49,119] [INFO] Task succeeded: fastANI
[2023-03-16 17:08:49,121] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:08:49,122] [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_002722455.1	s__GCA-2722455 sp002722455	89.1919	96	104	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__GCA-2722455;g__GCA-2722455	95.0	99.91	99.91	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2023-03-16 17:08:49,122] [INFO] GTDB search result was written to OceanDNA-b13850/result_gtdb.tsv
[2023-03-16 17:08:49,123] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:08:49,124] [INFO] DFAST_QC result json was written to OceanDNA-b13850/dqc_result.json
[2023-03-16 17:08:49,124] [INFO] DFAST_QC completed!
[2023-03-16 17:08:49,125] [INFO] Total running time: 0h0m35s