[2023-03-17 04:48:53,966] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:48:53,966] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:48:53,966] [INFO] DQC Reference Directory: /var/lib/cwl/stg9490eabc-8716-4d69-a245-e83e3bfff6a8/dqc_reference
[2023-03-17 04:48:55,155] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:48:55,156] [INFO] Task started: Prodigal
[2023-03-17 04:48:55,156] [INFO] Running command: cat /var/lib/cwl/stge3dec58f-cab2-4ffa-8591-0ae4fe7863d2/OceanDNA-b34259.fa | prodigal -d OceanDNA-b34259/cds.fna -a OceanDNA-b34259/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:48:59,452] [INFO] Task succeeded: Prodigal
[2023-03-17 04:48:59,452] [INFO] Task started: HMMsearch
[2023-03-17 04:48:59,452] [INFO] Running command: hmmsearch --tblout OceanDNA-b34259/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9490eabc-8716-4d69-a245-e83e3bfff6a8/dqc_reference/reference_markers.hmm OceanDNA-b34259/protein.faa > /dev/null
[2023-03-17 04:48:59,611] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:48:59,612] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge3dec58f-cab2-4ffa-8591-0ae4fe7863d2/OceanDNA-b34259.fa]
[2023-03-17 04:48:59,622] [INFO] Query marker FASTA was written to OceanDNA-b34259/markers.fasta
[2023-03-17 04:48:59,622] [INFO] Task started: Blastn
[2023-03-17 04:48:59,622] [INFO] Running command: blastn -query OceanDNA-b34259/markers.fasta -db /var/lib/cwl/stg9490eabc-8716-4d69-a245-e83e3bfff6a8/dqc_reference/reference_markers.fasta -out OceanDNA-b34259/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:00,144] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:00,144] [INFO] Selected 20 target genomes.
[2023-03-17 04:49:00,145] [INFO] Target genome list was writen to OceanDNA-b34259/target_genomes.txt
[2023-03-17 04:49:00,155] [INFO] Task started: fastANI
[2023-03-17 04:49:00,155] [INFO] Running command: fastANI --query /var/lib/cwl/stge3dec58f-cab2-4ffa-8591-0ae4fe7863d2/OceanDNA-b34259.fa --refList OceanDNA-b34259/target_genomes.txt --output OceanDNA-b34259/fastani_result.tsv --threads 1
[2023-03-17 04:49:09,044] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:09,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9490eabc-8716-4d69-a245-e83e3bfff6a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:49:09,045] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9490eabc-8716-4d69-a245-e83e3bfff6a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:49:09,045] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:49:09,045] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 04:49:09,045] [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
--------------------------------------------------------------------------------
[2023-03-17 04:49:09,045] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34259/tc_result.tsv
[2023-03-17 04:49:09,045] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:49:09,045] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:49:09,045] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9490eabc-8716-4d69-a245-e83e3bfff6a8/dqc_reference/checkm_data
[2023-03-17 04:49:09,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:49:09,050] [INFO] Task started: CheckM
[2023-03-17 04:49:09,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34259/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34259/checkm_input OceanDNA-b34259/checkm_result
[2023-03-17 04:49:26,081] [INFO] Task succeeded: CheckM
[2023-03-17 04:49:26,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:49:26,083] [INFO] ===== Completeness check finished =====
[2023-03-17 04:49:26,083] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:49:26,084] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34259/markers.fasta)
[2023-03-17 04:49:26,084] [INFO] Task started: Blastn
[2023-03-17 04:49:26,084] [INFO] Running command: blastn -query OceanDNA-b34259/markers.fasta -db /var/lib/cwl/stg9490eabc-8716-4d69-a245-e83e3bfff6a8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34259/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:26,841] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:26,842] [INFO] Selected 19 target genomes.
[2023-03-17 04:49:26,842] [INFO] Target genome list was writen to OceanDNA-b34259/target_genomes_gtdb.txt
[2023-03-17 04:49:27,277] [INFO] Task started: fastANI
[2023-03-17 04:49:27,277] [INFO] Running command: fastANI --query /var/lib/cwl/stge3dec58f-cab2-4ffa-8591-0ae4fe7863d2/OceanDNA-b34259.fa --refList OceanDNA-b34259/target_genomes_gtdb.txt --output OceanDNA-b34259/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:49:35,395] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:35,398] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:49:35,398] [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_005877695.1	s__Aquirickettsiella sp005877695	86.007	210	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Diplorickettsiales;f__Diplorickettsiaceae;g__Aquirickettsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001881495.1	s__Aquirickettsiella isopodorum	80.8414	180	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Diplorickettsiales;f__Diplorickettsiaceae;g__Aquirickettsiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002290645.2	s__Aquirickettsiella gammari	77.9952	107	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Diplorickettsiales;f__Diplorickettsiaceae;g__Aquirickettsiella	95.0	98.52	98.48	0.89	0.87	3	-
GCF_000168295.1	s__Aquirickettsiella grylli	77.9308	102	237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Diplorickettsiales;f__Diplorickettsiaceae;g__Aquirickettsiella	95.0	98.61	98.61	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 04:49:35,398] [INFO] GTDB search result was written to OceanDNA-b34259/result_gtdb.tsv
[2023-03-17 04:49:35,398] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:49:35,399] [INFO] DFAST_QC result json was written to OceanDNA-b34259/dqc_result.json
[2023-03-17 04:49:35,399] [INFO] DFAST_QC completed!
[2023-03-17 04:49:35,399] [INFO] Total running time: 0h0m41s