[2023-03-16 23:05:03,861] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:05:03,861] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:05:03,861] [INFO] DQC Reference Directory: /var/lib/cwl/stg6017a2b7-d7c5-4741-83e4-f8519ddaf3c3/dqc_reference
[2023-03-16 23:05:05,095] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:05:05,096] [INFO] Task started: Prodigal
[2023-03-16 23:05:05,096] [INFO] Running command: cat /var/lib/cwl/stgda4c613f-d7ac-424c-8910-6ff176752bc4/OceanDNA-b21006.fa | prodigal -d OceanDNA-b21006/cds.fna -a OceanDNA-b21006/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:05:16,985] [INFO] Task succeeded: Prodigal
[2023-03-16 23:05:16,985] [INFO] Task started: HMMsearch
[2023-03-16 23:05:16,985] [INFO] Running command: hmmsearch --tblout OceanDNA-b21006/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6017a2b7-d7c5-4741-83e4-f8519ddaf3c3/dqc_reference/reference_markers.hmm OceanDNA-b21006/protein.faa > /dev/null
[2023-03-16 23:05:17,161] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:05:17,162] [INFO] Found 6/6 markers.
[2023-03-16 23:05:17,179] [INFO] Query marker FASTA was written to OceanDNA-b21006/markers.fasta
[2023-03-16 23:05:17,179] [INFO] Task started: Blastn
[2023-03-16 23:05:17,179] [INFO] Running command: blastn -query OceanDNA-b21006/markers.fasta -db /var/lib/cwl/stg6017a2b7-d7c5-4741-83e4-f8519ddaf3c3/dqc_reference/reference_markers.fasta -out OceanDNA-b21006/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:17,755] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:17,756] [INFO] Selected 21 target genomes.
[2023-03-16 23:05:17,756] [INFO] Target genome list was writen to OceanDNA-b21006/target_genomes.txt
[2023-03-16 23:05:17,767] [INFO] Task started: fastANI
[2023-03-16 23:05:17,767] [INFO] Running command: fastANI --query /var/lib/cwl/stgda4c613f-d7ac-424c-8910-6ff176752bc4/OceanDNA-b21006.fa --refList OceanDNA-b21006/target_genomes.txt --output OceanDNA-b21006/fastani_result.tsv --threads 1
[2023-03-16 23:05:35,601] [INFO] Task succeeded: fastANI
[2023-03-16 23:05:35,601] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6017a2b7-d7c5-4741-83e4-f8519ddaf3c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:05:35,601] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6017a2b7-d7c5-4741-83e4-f8519ddaf3c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:05:35,601] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:05:35,601] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 23:05:35,602] [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 23:05:35,602] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21006/tc_result.tsv
[2023-03-16 23:05:35,602] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:05:35,602] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:05:35,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6017a2b7-d7c5-4741-83e4-f8519ddaf3c3/dqc_reference/checkm_data
[2023-03-16 23:05:35,604] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:05:35,609] [INFO] Task started: CheckM
[2023-03-16 23:05:35,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21006/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21006/checkm_input OceanDNA-b21006/checkm_result
[2023-03-16 23:06:08,813] [INFO] Task succeeded: CheckM
[2023-03-16 23:06:08,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 3.01%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-16 23:06:08,816] [INFO] ===== Completeness check finished =====
[2023-03-16 23:06:08,816] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:06:08,816] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21006/markers.fasta)
[2023-03-16 23:06:08,816] [INFO] Task started: Blastn
[2023-03-16 23:06:08,816] [INFO] Running command: blastn -query OceanDNA-b21006/markers.fasta -db /var/lib/cwl/stg6017a2b7-d7c5-4741-83e4-f8519ddaf3c3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21006/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:06:09,639] [INFO] Task succeeded: Blastn
[2023-03-16 23:06:09,639] [INFO] Selected 22 target genomes.
[2023-03-16 23:06:09,640] [INFO] Target genome list was writen to OceanDNA-b21006/target_genomes_gtdb.txt
[2023-03-16 23:06:10,255] [INFO] Task started: fastANI
[2023-03-16 23:06:10,256] [INFO] Running command: fastANI --query /var/lib/cwl/stgda4c613f-d7ac-424c-8910-6ff176752bc4/OceanDNA-b21006.fa --refList OceanDNA-b21006/target_genomes_gtdb.txt --output OceanDNA-b21006/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:06:25,261] [INFO] Task succeeded: fastANI
[2023-03-16 23:06:25,264] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:06:25,264] [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_016875225.1	s__VGRW01 sp016875225	76.3216	107	639	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__VGRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576805.1	s__PR03 sp003576805	75.4069	76	639	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707895.1	s__UBA2376 sp016707895	74.9108	56	639	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	99.64	99.63	0.96	0.96	3	-
GCA_016794525.1	s__UBA2376 sp016794525	74.8421	62	639	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:06:25,264] [INFO] GTDB search result was written to OceanDNA-b21006/result_gtdb.tsv
[2023-03-16 23:06:25,264] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:06:25,265] [INFO] DFAST_QC result json was written to OceanDNA-b21006/dqc_result.json
[2023-03-16 23:06:25,265] [INFO] DFAST_QC completed!
[2023-03-16 23:06:25,265] [INFO] Total running time: 0h1m21s