[2023-03-15 08:55:06,627] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:55:06,627] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:55:06,627] [INFO] DQC Reference Directory: /var/lib/cwl/stgceddf455-e230-4bf2-948b-e9c11ed74d9c/dqc_reference
[2023-03-15 08:55:08,347] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:55:08,348] [INFO] Task started: Prodigal
[2023-03-15 08:55:08,348] [INFO] Running command: cat /var/lib/cwl/stgeed72ebb-174a-4711-b785-9fbb74510805/OceanDNA-b4064.fa | prodigal -d OceanDNA-b4064/cds.fna -a OceanDNA-b4064/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:55:38,437] [INFO] Task succeeded: Prodigal
[2023-03-15 08:55:38,437] [INFO] Task started: HMMsearch
[2023-03-15 08:55:38,437] [INFO] Running command: hmmsearch --tblout OceanDNA-b4064/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgceddf455-e230-4bf2-948b-e9c11ed74d9c/dqc_reference/reference_markers.hmm OceanDNA-b4064/protein.faa > /dev/null
[2023-03-15 08:55:38,683] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:55:38,684] [INFO] Found 6/6 markers.
[2023-03-15 08:55:38,709] [INFO] Query marker FASTA was written to OceanDNA-b4064/markers.fasta
[2023-03-15 08:55:38,709] [INFO] Task started: Blastn
[2023-03-15 08:55:38,710] [INFO] Running command: blastn -query OceanDNA-b4064/markers.fasta -db /var/lib/cwl/stgceddf455-e230-4bf2-948b-e9c11ed74d9c/dqc_reference/reference_markers.fasta -out OceanDNA-b4064/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:39,265] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:39,266] [INFO] Selected 19 target genomes.
[2023-03-15 08:55:39,266] [INFO] Target genome list was writen to OceanDNA-b4064/target_genomes.txt
[2023-03-15 08:55:39,274] [INFO] Task started: fastANI
[2023-03-15 08:55:39,275] [INFO] Running command: fastANI --query /var/lib/cwl/stgeed72ebb-174a-4711-b785-9fbb74510805/OceanDNA-b4064.fa --refList OceanDNA-b4064/target_genomes.txt --output OceanDNA-b4064/fastani_result.tsv --threads 1
[2023-03-15 08:55:53,755] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:53,756] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgceddf455-e230-4bf2-948b-e9c11ed74d9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:55:53,756] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgceddf455-e230-4bf2-948b-e9c11ed74d9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:55:53,763] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 08:55:53,763] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 08:55:53,763] [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
Roseivirga thermotolerans	strain=CGMCC 1.15111	GCA_014653175.1	1758176	1758176	type	True	98.54	1209	1320	95	conclusive
Roseivirga spongicola	strain=UST030701-084	GCA_001592965.1	333140	333140	type	True	79.1471	380	1320	95	below_threshold
Roseivirga pacifica	strain=CGMCC 1.12402	GCA_900111145.1	1267423	1267423	type	True	77.2254	196	1320	95	below_threshold
Roseivirga pacifica	strain=DSM 100771	GCA_003633845.1	1267423	1267423	type	True	77.1614	193	1320	95	below_threshold
Roseivirga misakiensis	strain=SK-8	GCA_001747105.1	1563681	1563681	type	True	76.845	87	1320	95	below_threshold
Roseivirga seohaensis	strain=SW-152	GCA_001592945.1	1914963	1914963	type	True	76.7921	124	1320	95	below_threshold
Roseivirga ehrenbergii	strain=DSM 102268	GCA_004340805.1	279360	279360	type	True	76.6572	102	1320	95	below_threshold
Roseivirga ehrenbergii	strain=KMM 6017	GCA_001593005.1	279360	279360	type	True	76.6479	103	1320	95	below_threshold
Roseivirga seohaensis subsp. aquiponti	strain=D-25	GCA_001267955.1	1566026	1914963	type	True	76.6067	110	1320	95	below_threshold
Roseivirga echinicomitans	strain=KMM 6058	GCA_001592935.1	296218	296218	type	True	76.5753	87	1320	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:55:53,794] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4064/tc_result.tsv
[2023-03-15 08:55:53,794] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:55:53,794] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:55:53,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgceddf455-e230-4bf2-948b-e9c11ed74d9c/dqc_reference/checkm_data
[2023-03-15 08:55:53,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:55:53,813] [INFO] Task started: CheckM
[2023-03-15 08:55:53,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4064/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4064/checkm_input OceanDNA-b4064/checkm_result
[2023-03-15 08:57:06,314] [INFO] Task succeeded: CheckM
[2023-03-15 08:57:06,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:57:06,317] [INFO] ===== Completeness check finished =====
[2023-03-15 08:57:06,317] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:57:06,317] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4064/markers.fasta)
[2023-03-15 08:57:06,319] [INFO] Task started: Blastn
[2023-03-15 08:57:06,319] [INFO] Running command: blastn -query OceanDNA-b4064/markers.fasta -db /var/lib/cwl/stgceddf455-e230-4bf2-948b-e9c11ed74d9c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4064/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:57:07,055] [INFO] Task succeeded: Blastn
[2023-03-15 08:57:07,056] [INFO] Selected 17 target genomes.
[2023-03-15 08:57:07,056] [INFO] Target genome list was writen to OceanDNA-b4064/target_genomes_gtdb.txt
[2023-03-15 08:57:07,168] [INFO] Task started: fastANI
[2023-03-15 08:57:07,168] [INFO] Running command: fastANI --query /var/lib/cwl/stgeed72ebb-174a-4711-b785-9fbb74510805/OceanDNA-b4064.fa --refList OceanDNA-b4064/target_genomes_gtdb.txt --output OceanDNA-b4064/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:57:19,078] [INFO] Task succeeded: fastANI
[2023-03-15 08:57:19,084] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:57:19,084] [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_014653175.1	s__Fabibacter thermotolerans	98.54	1209	1320	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	98.67	98.61	0.92	0.91	4	conclusive
GCF_001592965.1	s__Fabibacter spongicola	79.135	381	1320	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	97.73	96.54	0.93	0.88	5	-
GCA_013373005.1	s__Fabibacter sp013373005	78.0926	312	1320	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111145.1	s__Fabibacter pacificus	77.2254	196	1320	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001747095.1	s__Fabibacter sp001747095	76.9212	133	1320	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592945.1	s__Roseivirga seohaensis	76.7921	124	1320	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	97.29	97.29	0.91	0.91	2	-
GCF_001593005.1	s__Roseivirga ehrenbergii	76.6479	103	1320	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002427755.1	s__Fabibacter sp002427755	76.6242	110	1320	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592935.1	s__Roseivirga echinicomitans	76.5753	87	1320	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:57:19,085] [INFO] GTDB search result was written to OceanDNA-b4064/result_gtdb.tsv
[2023-03-15 08:57:19,085] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:57:19,086] [INFO] DFAST_QC result json was written to OceanDNA-b4064/dqc_result.json
[2023-03-15 08:57:19,087] [INFO] DFAST_QC completed!
[2023-03-15 08:57:19,087] [INFO] Total running time: 0h2m12s