[2023-03-15 12:33:51,622] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:33:51,622] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:33:51,622] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d3dcaee-a840-4023-bcd8-32de1833f0d2/dqc_reference
[2023-03-15 12:33:52,749] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:33:52,749] [INFO] Task started: Prodigal
[2023-03-15 12:33:52,749] [INFO] Running command: cat /var/lib/cwl/stgdf48298c-3277-454f-84d5-e494ba023020/OceanDNA-b31523.fa | prodigal -d OceanDNA-b31523/cds.fna -a OceanDNA-b31523/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:34:02,898] [INFO] Task succeeded: Prodigal
[2023-03-15 12:34:02,899] [INFO] Task started: HMMsearch
[2023-03-15 12:34:02,899] [INFO] Running command: hmmsearch --tblout OceanDNA-b31523/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d3dcaee-a840-4023-bcd8-32de1833f0d2/dqc_reference/reference_markers.hmm OceanDNA-b31523/protein.faa > /dev/null
[2023-03-15 12:34:03,093] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:34:03,093] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdf48298c-3277-454f-84d5-e494ba023020/OceanDNA-b31523.fa]
[2023-03-15 12:34:03,116] [INFO] Query marker FASTA was written to OceanDNA-b31523/markers.fasta
[2023-03-15 12:34:03,116] [INFO] Task started: Blastn
[2023-03-15 12:34:03,116] [INFO] Running command: blastn -query OceanDNA-b31523/markers.fasta -db /var/lib/cwl/stg6d3dcaee-a840-4023-bcd8-32de1833f0d2/dqc_reference/reference_markers.fasta -out OceanDNA-b31523/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:03,679] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:03,682] [INFO] Selected 20 target genomes.
[2023-03-15 12:34:03,683] [INFO] Target genome list was writen to OceanDNA-b31523/target_genomes.txt
[2023-03-15 12:34:03,696] [INFO] Task started: fastANI
[2023-03-15 12:34:03,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf48298c-3277-454f-84d5-e494ba023020/OceanDNA-b31523.fa --refList OceanDNA-b31523/target_genomes.txt --output OceanDNA-b31523/fastani_result.tsv --threads 1
[2023-03-15 12:34:15,784] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:15,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d3dcaee-a840-4023-bcd8-32de1833f0d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:34:15,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d3dcaee-a840-4023-bcd8-32de1833f0d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:34:15,785] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:34:15,785] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 12:34:15,785] [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
--------------------------------------------------------------------------------
[2023-03-15 12:34:15,786] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31523/tc_result.tsv
[2023-03-15 12:34:15,786] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:34:15,786] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:34:15,786] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d3dcaee-a840-4023-bcd8-32de1833f0d2/dqc_reference/checkm_data
[2023-03-15 12:34:15,789] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:34:15,796] [INFO] Task started: CheckM
[2023-03-15 12:34:15,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31523/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31523/checkm_input OceanDNA-b31523/checkm_result
[2023-03-15 12:34:46,564] [INFO] Task succeeded: CheckM
[2023-03-15 12:34:46,564] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.10%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:34:46,602] [INFO] ===== Completeness check finished =====
[2023-03-15 12:34:46,602] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:34:46,602] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31523/markers.fasta)
[2023-03-15 12:34:46,604] [INFO] Task started: Blastn
[2023-03-15 12:34:46,604] [INFO] Running command: blastn -query OceanDNA-b31523/markers.fasta -db /var/lib/cwl/stg6d3dcaee-a840-4023-bcd8-32de1833f0d2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31523/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:47,426] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:47,429] [INFO] Selected 17 target genomes.
[2023-03-15 12:34:47,429] [INFO] Target genome list was writen to OceanDNA-b31523/target_genomes_gtdb.txt
[2023-03-15 12:34:47,547] [INFO] Task started: fastANI
[2023-03-15 12:34:47,547] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf48298c-3277-454f-84d5-e494ba023020/OceanDNA-b31523.fa --refList OceanDNA-b31523/target_genomes_gtdb.txt --output OceanDNA-b31523/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:34:58,038] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:58,041] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:34:58,041] [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_017640725.1	s__Kordiimonas sp017640725	77.7528	122	401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	100.00	100.00	0.99	0.98	3	-
GCA_011088215.1	s__Kordiimonas sp011088215	76.3496	51	401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:34:58,042] [INFO] GTDB search result was written to OceanDNA-b31523/result_gtdb.tsv
[2023-03-15 12:34:58,045] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:34:58,047] [INFO] DFAST_QC result json was written to OceanDNA-b31523/dqc_result.json
[2023-03-15 12:34:58,047] [INFO] DFAST_QC completed!
[2023-03-15 12:34:58,047] [INFO] Total running time: 0h1m6s