[2023-03-19 01:38:53,974] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:38:53,974] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:38:53,974] [INFO] DQC Reference Directory: /var/lib/cwl/stg1050d26c-ad12-4331-bdae-34603ee89a53/dqc_reference
[2023-03-19 01:38:55,096] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:38:55,096] [INFO] Task started: Prodigal
[2023-03-19 01:38:55,096] [INFO] Running command: cat /var/lib/cwl/stgff620024-ae52-4406-8992-f4a833501a90/OceanDNA-b42991.fa | prodigal -d OceanDNA-b42991/cds.fna -a OceanDNA-b42991/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:38:58,048] [INFO] Task succeeded: Prodigal
[2023-03-19 01:38:58,048] [INFO] Task started: HMMsearch
[2023-03-19 01:38:58,048] [INFO] Running command: hmmsearch --tblout OceanDNA-b42991/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1050d26c-ad12-4331-bdae-34603ee89a53/dqc_reference/reference_markers.hmm OceanDNA-b42991/protein.faa > /dev/null
[2023-03-19 01:38:58,186] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:38:58,187] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgff620024-ae52-4406-8992-f4a833501a90/OceanDNA-b42991.fa]
[2023-03-19 01:38:58,198] [INFO] Query marker FASTA was written to OceanDNA-b42991/markers.fasta
[2023-03-19 01:38:58,200] [INFO] Task started: Blastn
[2023-03-19 01:38:58,200] [INFO] Running command: blastn -query OceanDNA-b42991/markers.fasta -db /var/lib/cwl/stg1050d26c-ad12-4331-bdae-34603ee89a53/dqc_reference/reference_markers.fasta -out OceanDNA-b42991/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:38:58,684] [INFO] Task succeeded: Blastn
[2023-03-19 01:38:58,686] [INFO] Selected 16 target genomes.
[2023-03-19 01:38:58,686] [INFO] Target genome list was writen to OceanDNA-b42991/target_genomes.txt
[2023-03-19 01:38:58,698] [INFO] Task started: fastANI
[2023-03-19 01:38:58,698] [INFO] Running command: fastANI --query /var/lib/cwl/stgff620024-ae52-4406-8992-f4a833501a90/OceanDNA-b42991.fa --refList OceanDNA-b42991/target_genomes.txt --output OceanDNA-b42991/fastani_result.tsv --threads 1
[2023-03-19 01:39:06,551] [INFO] Task succeeded: fastANI
[2023-03-19 01:39:06,551] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1050d26c-ad12-4331-bdae-34603ee89a53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:39:06,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1050d26c-ad12-4331-bdae-34603ee89a53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:39:06,554] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:39:06,554] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:39:06,554] [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
Candidatus Pseudothioglobus singularis	strain=PS1	GCA_001281385.1	1427364	1427364	type	True	79.1299	68	103	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:39:06,555] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42991/tc_result.tsv
[2023-03-19 01:39:06,556] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:39:06,556] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:39:06,556] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1050d26c-ad12-4331-bdae-34603ee89a53/dqc_reference/checkm_data
[2023-03-19 01:39:06,557] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:39:06,560] [INFO] Task started: CheckM
[2023-03-19 01:39:06,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42991/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42991/checkm_input OceanDNA-b42991/checkm_result
[2023-03-19 01:39:21,241] [INFO] Task succeeded: CheckM
[2023-03-19 01:39:21,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.97%
Contamintation: 8.85%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-19 01:39:21,330] [INFO] ===== Completeness check finished =====
[2023-03-19 01:39:21,330] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:39:21,331] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42991/markers.fasta)
[2023-03-19 01:39:21,332] [INFO] Task started: Blastn
[2023-03-19 01:39:21,332] [INFO] Running command: blastn -query OceanDNA-b42991/markers.fasta -db /var/lib/cwl/stg1050d26c-ad12-4331-bdae-34603ee89a53/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42991/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:39:21,905] [INFO] Task succeeded: Blastn
[2023-03-19 01:39:21,907] [INFO] Selected 7 target genomes.
[2023-03-19 01:39:21,907] [INFO] Target genome list was writen to OceanDNA-b42991/target_genomes_gtdb.txt
[2023-03-19 01:39:21,916] [INFO] Task started: fastANI
[2023-03-19 01:39:21,916] [INFO] Running command: fastANI --query /var/lib/cwl/stgff620024-ae52-4406-8992-f4a833501a90/OceanDNA-b42991.fa --refList OceanDNA-b42991/target_genomes_gtdb.txt --output OceanDNA-b42991/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:39:23,439] [INFO] Task succeeded: fastANI
[2023-03-19 01:39:23,443] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:39:23,443] [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_001628405.1	s__Pseudothioglobus sp001628405	84.9819	88	103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	97.86	96.69	0.86	0.83	3	-
GCA_902556205.1	s__Pseudothioglobus sp002169705	83.6053	86	103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.58	95.16	0.83	0.80	5	-
GCA_902509905.1	s__Pseudothioglobus sp902509905	82.8102	79	103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	95.83	95.81	0.73	0.73	3	-
GCA_902512305.1	s__Pseudothioglobus sp902512305	81.9903	83	103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.03	95.27	0.77	0.74	5	-
GCF_001281385.1	s__Pseudothioglobus singularis	79.1299	68	103	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__PS1;f__Thioglobaceae;g__Pseudothioglobus	95.0	96.68	95.87	0.84	0.66	7	-
--------------------------------------------------------------------------------
[2023-03-19 01:39:23,444] [INFO] GTDB search result was written to OceanDNA-b42991/result_gtdb.tsv
[2023-03-19 01:39:23,445] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:39:23,447] [INFO] DFAST_QC result json was written to OceanDNA-b42991/dqc_result.json
[2023-03-19 01:39:23,447] [INFO] DFAST_QC completed!
[2023-03-19 01:39:23,447] [INFO] Total running time: 0h0m29s