[2023-03-16 23:05:03,825] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:05:03,825] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:05:03,825] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3c71e69-5a99-4637-bb64-e4091c0366fe/dqc_reference
[2023-03-16 23:05:05,096] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:05:05,096] [INFO] Task started: Prodigal
[2023-03-16 23:05:05,096] [INFO] Running command: cat /var/lib/cwl/stg147c6701-b0a1-4b3c-b63e-0279d571439e/OceanDNA-b7493.fa | prodigal -d OceanDNA-b7493/cds.fna -a OceanDNA-b7493/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:05:19,587] [INFO] Task succeeded: Prodigal
[2023-03-16 23:05:19,587] [INFO] Task started: HMMsearch
[2023-03-16 23:05:19,587] [INFO] Running command: hmmsearch --tblout OceanDNA-b7493/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3c71e69-5a99-4637-bb64-e4091c0366fe/dqc_reference/reference_markers.hmm OceanDNA-b7493/protein.faa > /dev/null
[2023-03-16 23:05:19,818] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:05:19,819] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg147c6701-b0a1-4b3c-b63e-0279d571439e/OceanDNA-b7493.fa]
[2023-03-16 23:05:19,835] [INFO] Query marker FASTA was written to OceanDNA-b7493/markers.fasta
[2023-03-16 23:05:19,835] [INFO] Task started: Blastn
[2023-03-16 23:05:19,835] [INFO] Running command: blastn -query OceanDNA-b7493/markers.fasta -db /var/lib/cwl/stgc3c71e69-5a99-4637-bb64-e4091c0366fe/dqc_reference/reference_markers.fasta -out OceanDNA-b7493/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:20,399] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:20,399] [INFO] Selected 23 target genomes.
[2023-03-16 23:05:20,400] [INFO] Target genome list was writen to OceanDNA-b7493/target_genomes.txt
[2023-03-16 23:05:20,412] [INFO] Task started: fastANI
[2023-03-16 23:05:20,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg147c6701-b0a1-4b3c-b63e-0279d571439e/OceanDNA-b7493.fa --refList OceanDNA-b7493/target_genomes.txt --output OceanDNA-b7493/fastani_result.tsv --threads 1
[2023-03-16 23:05:34,879] [INFO] Task succeeded: fastANI
[2023-03-16 23:05:34,879] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3c71e69-5a99-4637-bb64-e4091c0366fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:05:34,880] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3c71e69-5a99-4637-bb64-e4091c0366fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:05:34,887] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:05:34,887] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:05:34,887] [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
Leeuwenhoekiella aequorea	strain=LMG 22550	GCA_004104375.1	283736	283736	type	True	79.7141	396	735	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	79.4208	416	735	95	below_threshold
Leeuwenhoekiella marinoflava	strain=LMG 1345	GCA_004104035.1	988	988	type	True	79.1175	408	735	95	below_threshold
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	79.1065	407	735	95	below_threshold
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	78.4593	307	735	95	below_threshold
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	78.1706	324	735	95	below_threshold
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	78.1574	324	735	95	below_threshold
Leeuwenhoekiella nanhaiensis	strain=G18	GCA_002744755.1	1655491	1655491	type	True	77.9792	261	735	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	75.8361	50	735	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	75.5344	56	735	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:05:34,888] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7493/tc_result.tsv
[2023-03-16 23:05:34,888] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:05:34,888] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:05:34,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3c71e69-5a99-4637-bb64-e4091c0366fe/dqc_reference/checkm_data
[2023-03-16 23:05:34,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:05:34,896] [INFO] Task started: CheckM
[2023-03-16 23:05:34,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7493/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7493/checkm_input OceanDNA-b7493/checkm_result
[2023-03-16 23:06:13,629] [INFO] Task succeeded: CheckM
[2023-03-16 23:06:13,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:06:13,631] [INFO] ===== Completeness check finished =====
[2023-03-16 23:06:13,631] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:06:13,631] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7493/markers.fasta)
[2023-03-16 23:06:13,632] [INFO] Task started: Blastn
[2023-03-16 23:06:13,632] [INFO] Running command: blastn -query OceanDNA-b7493/markers.fasta -db /var/lib/cwl/stgc3c71e69-5a99-4637-bb64-e4091c0366fe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7493/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:06:14,392] [INFO] Task succeeded: Blastn
[2023-03-16 23:06:14,393] [INFO] Selected 17 target genomes.
[2023-03-16 23:06:14,393] [INFO] Target genome list was writen to OceanDNA-b7493/target_genomes_gtdb.txt
[2023-03-16 23:06:14,526] [INFO] Task started: fastANI
[2023-03-16 23:06:14,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg147c6701-b0a1-4b3c-b63e-0279d571439e/OceanDNA-b7493.fa --refList OceanDNA-b7493/target_genomes_gtdb.txt --output OceanDNA-b7493/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:06:25,998] [INFO] Task succeeded: fastANI
[2023-03-16 23:06:26,004] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:06:26,004] [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_000687915.1	s__Leeuwenhoekiella sp000687915	80.9178	495	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104375.1	s__Leeuwenhoekiella aequorea	79.7066	397	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104075.1	s__Leeuwenhoekiella polynyae	79.4335	404	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104055.1	s__Leeuwenhoekiella aestuarii	79.4208	416	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.75	99.75	0.97	0.97	2	-
GCF_900129005.1	s__Leeuwenhoekiella marinoflava	79.1065	407	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000152985.1	s__Leeuwenhoekiella blandensis	78.4593	307	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	-
GCF_900130045.1	s__Leeuwenhoekiella palythoae	78.1706	324	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	-
GCF_002744755.1	s__Leeuwenhoekiella nanhaiensis	77.9792	261	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.22	96.22	0.78	0.78	2	-
GCF_007827465.1	s__Dokdonia sp007827465	76.2077	52	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	76.0105	56	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
--------------------------------------------------------------------------------
[2023-03-16 23:06:26,004] [INFO] GTDB search result was written to OceanDNA-b7493/result_gtdb.tsv
[2023-03-16 23:06:26,004] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:06:26,006] [INFO] DFAST_QC result json was written to OceanDNA-b7493/dqc_result.json
[2023-03-16 23:06:26,006] [INFO] DFAST_QC completed!
[2023-03-16 23:06:26,006] [INFO] Total running time: 0h1m22s