[2023-03-15 13:03:53,440] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:03:53,440] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:03:53,441] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ffdc20a-56fb-4bb7-85a5-144d2ab53e76/dqc_reference
[2023-03-15 13:03:54,657] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:03:54,657] [INFO] Task started: Prodigal
[2023-03-15 13:03:54,657] [INFO] Running command: cat /var/lib/cwl/stg01fda8f5-da2b-428b-b61c-081ce748e70c/OceanDNA-b29587.fa | prodigal -d OceanDNA-b29587/cds.fna -a OceanDNA-b29587/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:04:07,512] [INFO] Task succeeded: Prodigal
[2023-03-15 13:04:07,513] [INFO] Task started: HMMsearch
[2023-03-15 13:04:07,513] [INFO] Running command: hmmsearch --tblout OceanDNA-b29587/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ffdc20a-56fb-4bb7-85a5-144d2ab53e76/dqc_reference/reference_markers.hmm OceanDNA-b29587/protein.faa > /dev/null
[2023-03-15 13:04:07,743] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:04:07,743] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg01fda8f5-da2b-428b-b61c-081ce748e70c/OceanDNA-b29587.fa]
[2023-03-15 13:04:07,765] [INFO] Query marker FASTA was written to OceanDNA-b29587/markers.fasta
[2023-03-15 13:04:07,765] [INFO] Task started: Blastn
[2023-03-15 13:04:07,765] [INFO] Running command: blastn -query OceanDNA-b29587/markers.fasta -db /var/lib/cwl/stg8ffdc20a-56fb-4bb7-85a5-144d2ab53e76/dqc_reference/reference_markers.fasta -out OceanDNA-b29587/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:08,352] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:08,353] [INFO] Selected 19 target genomes.
[2023-03-15 13:04:08,353] [INFO] Target genome list was writen to OceanDNA-b29587/target_genomes.txt
[2023-03-15 13:04:08,363] [INFO] Task started: fastANI
[2023-03-15 13:04:08,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg01fda8f5-da2b-428b-b61c-081ce748e70c/OceanDNA-b29587.fa --refList OceanDNA-b29587/target_genomes.txt --output OceanDNA-b29587/fastani_result.tsv --threads 1
[2023-03-15 13:04:19,820] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:19,821] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ffdc20a-56fb-4bb7-85a5-144d2ab53e76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:04:19,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ffdc20a-56fb-4bb7-85a5-144d2ab53e76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:04:19,827] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 13:04:19,827] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 13:04:19,827] [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
Octadecabacter arcticus	strain=238	GCA_000155735.2	53946	53946	type	True	97.107	551	585	95	conclusive
Octadecabacter antarcticus	strain=307	GCA_000155675.2	1217908	1217908	type	True	84.1321	502	585	95	below_threshold
Octadecabacter ascidiaceicola	strain=CECT 8868	GCA_900185015.1	1655543	1655543	type	True	78.2066	240	585	95	below_threshold
Octadecabacter temperatus	strain=SB1	GCA_001187845.1	1458307	1458307	type	True	77.977	239	585	95	below_threshold
Octadecabacter temperatus	strain=DSM 26878	GCA_900142425.1	1458307	1458307	type	True	77.9408	243	585	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	77.0401	169	585	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	76.4648	79	585	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	76.4612	78	585	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	75.6843	53	585	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:04:19,828] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29587/tc_result.tsv
[2023-03-15 13:04:19,828] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:04:19,828] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:04:19,828] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ffdc20a-56fb-4bb7-85a5-144d2ab53e76/dqc_reference/checkm_data
[2023-03-15 13:04:19,829] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:04:19,833] [INFO] Task started: CheckM
[2023-03-15 13:04:19,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29587/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29587/checkm_input OceanDNA-b29587/checkm_result
[2023-03-15 13:04:56,281] [INFO] Task succeeded: CheckM
[2023-03-15 13:04:56,281] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:04:56,284] [INFO] ===== Completeness check finished =====
[2023-03-15 13:04:56,284] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:04:56,284] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29587/markers.fasta)
[2023-03-15 13:04:56,285] [INFO] Task started: Blastn
[2023-03-15 13:04:56,285] [INFO] Running command: blastn -query OceanDNA-b29587/markers.fasta -db /var/lib/cwl/stg8ffdc20a-56fb-4bb7-85a5-144d2ab53e76/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29587/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:57,190] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:57,191] [INFO] Selected 9 target genomes.
[2023-03-15 13:04:57,191] [INFO] Target genome list was writen to OceanDNA-b29587/target_genomes_gtdb.txt
[2023-03-15 13:04:57,198] [INFO] Task started: fastANI
[2023-03-15 13:04:57,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg01fda8f5-da2b-428b-b61c-081ce748e70c/OceanDNA-b29587.fa --refList OceanDNA-b29587/target_genomes_gtdb.txt --output OceanDNA-b29587/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:05:03,373] [INFO] Task succeeded: fastANI
[2023-03-15 13:05:03,379] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:05:03,379] [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
GCF_000155735.2	s__Octadecabacter arcticus	97.107	551	585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	96.73	96.73	0.93	0.93	2	conclusive
GCA_017886375.1	s__Octadecabacter sp017886375	93.7518	493	585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	99.96	99.96	0.97	0.97	2	-
GCF_000155675.2	s__Octadecabacter antarcticus	84.1321	502	585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608045.1	s__Octadecabacter sp018608045	78.3633	223	585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	98.68	98.68	0.85	0.85	2	-
GCF_900185015.1	s__Octadecabacter ascidiaceicola	78.2066	240	585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187845.1	s__Octadecabacter temperatus	77.977	239	585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018861045.1	s__Octadecabacter sp018861045	77.5067	199	585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458435.1	s__Thalassobius mediterraneus	76.4072	54	585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015488685.1	s__Profundibacter sp015488685	75.7257	58	585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:05:03,379] [INFO] GTDB search result was written to OceanDNA-b29587/result_gtdb.tsv
[2023-03-15 13:05:03,380] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:05:03,381] [INFO] DFAST_QC result json was written to OceanDNA-b29587/dqc_result.json
[2023-03-15 13:05:03,381] [INFO] DFAST_QC completed!
[2023-03-15 13:05:03,381] [INFO] Total running time: 0h1m10s