[2023-03-15 21:01:44,364] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,364] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,364] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3e7607f-4f78-4f38-8a56-9989b14cb3bb/dqc_reference
[2023-03-15 21:01:45,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,597] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,597] [INFO] Running command: cat /var/lib/cwl/stgdae6125b-1da8-4593-aa3d-b29d6b148f07/OceanDNA-b30001.fa | prodigal -d OceanDNA-b30001/cds.fna -a OceanDNA-b30001/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:02:03,142] [INFO] Task succeeded: Prodigal
[2023-03-15 21:02:03,142] [INFO] Task started: HMMsearch
[2023-03-15 21:02:03,142] [INFO] Running command: hmmsearch --tblout OceanDNA-b30001/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3e7607f-4f78-4f38-8a56-9989b14cb3bb/dqc_reference/reference_markers.hmm OceanDNA-b30001/protein.faa > /dev/null
[2023-03-15 21:02:03,325] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:02:03,326] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgdae6125b-1da8-4593-aa3d-b29d6b148f07/OceanDNA-b30001.fa]
[2023-03-15 21:02:03,347] [INFO] Query marker FASTA was written to OceanDNA-b30001/markers.fasta
[2023-03-15 21:02:03,347] [INFO] Task started: Blastn
[2023-03-15 21:02:03,348] [INFO] Running command: blastn -query OceanDNA-b30001/markers.fasta -db /var/lib/cwl/stgc3e7607f-4f78-4f38-8a56-9989b14cb3bb/dqc_reference/reference_markers.fasta -out OceanDNA-b30001/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:03,902] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:03,902] [INFO] Selected 19 target genomes.
[2023-03-15 21:02:03,902] [INFO] Target genome list was writen to OceanDNA-b30001/target_genomes.txt
[2023-03-15 21:02:03,912] [INFO] Task started: fastANI
[2023-03-15 21:02:03,912] [INFO] Running command: fastANI --query /var/lib/cwl/stgdae6125b-1da8-4593-aa3d-b29d6b148f07/OceanDNA-b30001.fa --refList OceanDNA-b30001/target_genomes.txt --output OceanDNA-b30001/fastani_result.tsv --threads 1
[2023-03-15 21:02:14,636] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:14,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3e7607f-4f78-4f38-8a56-9989b14cb3bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:14,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3e7607f-4f78-4f38-8a56-9989b14cb3bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:14,646] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:14,646] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:02:14,646] [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
Planktotalea frisia	strain=DSM 23709	GCA_003254185.1	696762	696762	type	True	80.0117	508	910	95	below_threshold
Planktotalea frisia	strain=SH6-1	GCA_001890925.1	696762	696762	type	True	79.98	513	910	95	below_threshold
Planktotalea arctica	strain=IMCC9565	GCA_002105285.1	1481893	1481893	type	True	78.3871	403	910	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.1165	58	910	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.9382	65	910	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.9122	86	910	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	76.8624	86	910	95	below_threshold
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	76.7906	57	910	95	below_threshold
Cognatishimia activa	strain=CECT 5113	GCA_001458335.1	1715691	1715691	type	True	76.5112	71	910	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	76.3729	74	910	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	76.2914	76	910	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	76.1191	62	910	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	76.0673	55	910	95	below_threshold
Salipiger aestuarii	strain=DSM 22011	GCA_003259905.1	568098	568098	type	True	76.0653	55	910	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	76.0634	75	910	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	76.0606	75	910	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:02:14,655] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30001/tc_result.tsv
[2023-03-15 21:02:14,655] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:14,655] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:14,655] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3e7607f-4f78-4f38-8a56-9989b14cb3bb/dqc_reference/checkm_data
[2023-03-15 21:02:14,656] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:14,661] [INFO] Task started: CheckM
[2023-03-15 21:02:14,661] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30001/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30001/checkm_input OceanDNA-b30001/checkm_result
[2023-03-15 21:03:00,912] [INFO] Task succeeded: CheckM
[2023-03-15 21:03:00,912] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.95%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 21:03:00,915] [INFO] ===== Completeness check finished =====
[2023-03-15 21:03:00,915] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:03:00,915] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30001/markers.fasta)
[2023-03-15 21:03:00,915] [INFO] Task started: Blastn
[2023-03-15 21:03:00,915] [INFO] Running command: blastn -query OceanDNA-b30001/markers.fasta -db /var/lib/cwl/stgc3e7607f-4f78-4f38-8a56-9989b14cb3bb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30001/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:03:01,793] [INFO] Task succeeded: Blastn
[2023-03-15 21:03:01,794] [INFO] Selected 8 target genomes.
[2023-03-15 21:03:01,794] [INFO] Target genome list was writen to OceanDNA-b30001/target_genomes_gtdb.txt
[2023-03-15 21:03:01,972] [INFO] Task started: fastANI
[2023-03-15 21:03:01,972] [INFO] Running command: fastANI --query /var/lib/cwl/stgdae6125b-1da8-4593-aa3d-b29d6b148f07/OceanDNA-b30001.fa --refList OceanDNA-b30001/target_genomes_gtdb.txt --output OceanDNA-b30001/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:03:07,793] [INFO] Task succeeded: fastANI
[2023-03-15 21:03:07,798] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:03:07,799] [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_000156115.1	s__Planktotalea sp000156115	99.7972	907	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	99.77	99.74	0.95	0.90	3	conclusive
GCA_018607995.1	s__Planktotalea sp018607995	92.1581	707	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001890925.1	s__Planktotalea frisia	79.9905	512	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	99.35	98.99	0.94	0.89	4	-
GCA_018607965.1	s__Planktotalea sp018607965	78.841	351	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105285.1	s__Planktotalea arctica	78.3773	404	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107355.1	s__Lentibacter algarum	77.4605	79	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900327775.1	s__Roseovarius sp900327775	76.4423	76	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743735.1	s__Shimia sp017743735	76.4405	87	910	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
--------------------------------------------------------------------------------
[2023-03-15 21:03:07,799] [INFO] GTDB search result was written to OceanDNA-b30001/result_gtdb.tsv
[2023-03-15 21:03:07,799] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:03:07,800] [INFO] DFAST_QC result json was written to OceanDNA-b30001/dqc_result.json
[2023-03-15 21:03:07,800] [INFO] DFAST_QC completed!
[2023-03-15 21:03:07,801] [INFO] Total running time: 0h1m23s