[2023-03-16 18:07:32,305] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:07:32,306] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:07:32,306] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa720016-c96f-4f46-8a57-ec8f2ae8532e/dqc_reference
[2023-03-16 18:07:34,963] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:07:34,964] [INFO] Task started: Prodigal
[2023-03-16 18:07:34,965] [INFO] Running command: cat /var/lib/cwl/stg11d1851d-f515-47d8-8c5d-06addf411e50/OceanDNA-b20522.fa | prodigal -d OceanDNA-b20522/cds.fna -a OceanDNA-b20522/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:07:42,544] [INFO] Task succeeded: Prodigal
[2023-03-16 18:07:42,544] [INFO] Task started: HMMsearch
[2023-03-16 18:07:42,544] [INFO] Running command: hmmsearch --tblout OceanDNA-b20522/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa720016-c96f-4f46-8a57-ec8f2ae8532e/dqc_reference/reference_markers.hmm OceanDNA-b20522/protein.faa > /dev/null
[2023-03-16 18:07:42,764] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:07:42,765] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg11d1851d-f515-47d8-8c5d-06addf411e50/OceanDNA-b20522.fa]
[2023-03-16 18:07:42,776] [INFO] Query marker FASTA was written to OceanDNA-b20522/markers.fasta
[2023-03-16 18:07:42,777] [INFO] Task started: Blastn
[2023-03-16 18:07:42,778] [INFO] Running command: blastn -query OceanDNA-b20522/markers.fasta -db /var/lib/cwl/stgaa720016-c96f-4f46-8a57-ec8f2ae8532e/dqc_reference/reference_markers.fasta -out OceanDNA-b20522/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:07:43,341] [INFO] Task succeeded: Blastn
[2023-03-16 18:07:43,341] [INFO] Selected 5 target genomes.
[2023-03-16 18:07:43,342] [INFO] Target genome list was writen to OceanDNA-b20522/target_genomes.txt
[2023-03-16 18:07:43,347] [INFO] Task started: fastANI
[2023-03-16 18:07:43,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg11d1851d-f515-47d8-8c5d-06addf411e50/OceanDNA-b20522.fa --refList OceanDNA-b20522/target_genomes.txt --output OceanDNA-b20522/fastani_result.tsv --threads 1
[2023-03-16 18:07:46,173] [INFO] Task succeeded: fastANI
[2023-03-16 18:07:46,174] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa720016-c96f-4f46-8a57-ec8f2ae8532e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:07:46,174] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa720016-c96f-4f46-8a57-ec8f2ae8532e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:07:46,174] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:07:46,174] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 18:07:46,174] [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 18:07:46,174] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20522/tc_result.tsv
[2023-03-16 18:07:46,174] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:07:46,175] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:07:46,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa720016-c96f-4f46-8a57-ec8f2ae8532e/dqc_reference/checkm_data
[2023-03-16 18:07:46,177] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:07:46,180] [INFO] Task started: CheckM
[2023-03-16 18:07:46,180] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20522/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20522/checkm_input OceanDNA-b20522/checkm_result
[2023-03-16 18:08:04,799] [INFO] Task succeeded: CheckM
[2023-03-16 18:08:04,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.10%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 18:08:04,801] [INFO] ===== Completeness check finished =====
[2023-03-16 18:08:04,802] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:08:04,802] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20522/markers.fasta)
[2023-03-16 18:08:04,802] [INFO] Task started: Blastn
[2023-03-16 18:08:04,802] [INFO] Running command: blastn -query OceanDNA-b20522/markers.fasta -db /var/lib/cwl/stgaa720016-c96f-4f46-8a57-ec8f2ae8532e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20522/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:08:05,403] [INFO] Task succeeded: Blastn
[2023-03-16 18:08:05,403] [INFO] Selected 10 target genomes.
[2023-03-16 18:08:05,403] [INFO] Target genome list was writen to OceanDNA-b20522/target_genomes_gtdb.txt
[2023-03-16 18:08:05,412] [INFO] Task started: fastANI
[2023-03-16 18:08:05,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg11d1851d-f515-47d8-8c5d-06addf411e50/OceanDNA-b20522.fa --refList OceanDNA-b20522/target_genomes_gtdb.txt --output OceanDNA-b20522/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:08:07,796] [INFO] Task succeeded: fastANI
[2023-03-16 18:08:07,800] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:08:07,801] [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_002705605.1	s__GCA-002707645 sp002705605	84.5145	287	329	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707645.1	s__GCA-002707645 sp002707645	80.5851	231	329	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704685.1	s__GCA-002707645 sp002704685	79.6195	233	329	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002693365.1	s__GCA-002707645 sp002693365	79.511	185	329	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	98.01	98.01	0.73	0.73	2	-
GCA_002717625.1	s__GCA-2717625 sp002717625	76.1351	61	329	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-2717625	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:08:07,801] [INFO] GTDB search result was written to OceanDNA-b20522/result_gtdb.tsv
[2023-03-16 18:08:07,801] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:08:07,802] [INFO] DFAST_QC result json was written to OceanDNA-b20522/dqc_result.json
[2023-03-16 18:08:07,802] [INFO] DFAST_QC completed!
[2023-03-16 18:08:07,802] [INFO] Total running time: 0h0m35s