[2023-03-19 00:01:03,385] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:01:03,385] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:01:03,385] [INFO] DQC Reference Directory: /var/lib/cwl/stga6f91a24-3dfc-4474-956c-f08fc2b39914/dqc_reference
[2023-03-19 00:01:04,505] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:01:04,505] [INFO] Task started: Prodigal
[2023-03-19 00:01:04,506] [INFO] Running command: cat /var/lib/cwl/stg540355bc-7ffc-4ce2-b1cb-637909189711/OceanDNA-b22799.fa | prodigal -d OceanDNA-b22799/cds.fna -a OceanDNA-b22799/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:01:17,765] [INFO] Task succeeded: Prodigal
[2023-03-19 00:01:17,765] [INFO] Task started: HMMsearch
[2023-03-19 00:01:17,765] [INFO] Running command: hmmsearch --tblout OceanDNA-b22799/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6f91a24-3dfc-4474-956c-f08fc2b39914/dqc_reference/reference_markers.hmm OceanDNA-b22799/protein.faa > /dev/null
[2023-03-19 00:01:17,996] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:01:17,997] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg540355bc-7ffc-4ce2-b1cb-637909189711/OceanDNA-b22799.fa]
[2023-03-19 00:01:18,018] [INFO] Query marker FASTA was written to OceanDNA-b22799/markers.fasta
[2023-03-19 00:01:18,019] [INFO] Task started: Blastn
[2023-03-19 00:01:18,019] [INFO] Running command: blastn -query OceanDNA-b22799/markers.fasta -db /var/lib/cwl/stga6f91a24-3dfc-4474-956c-f08fc2b39914/dqc_reference/reference_markers.fasta -out OceanDNA-b22799/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:18,478] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:18,478] [INFO] Selected 13 target genomes.
[2023-03-19 00:01:18,479] [INFO] Target genome list was writen to OceanDNA-b22799/target_genomes.txt
[2023-03-19 00:01:18,485] [INFO] Task started: fastANI
[2023-03-19 00:01:18,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg540355bc-7ffc-4ce2-b1cb-637909189711/OceanDNA-b22799.fa --refList OceanDNA-b22799/target_genomes.txt --output OceanDNA-b22799/fastani_result.tsv --threads 1
[2023-03-19 00:01:32,978] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:32,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6f91a24-3dfc-4474-956c-f08fc2b39914/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:01:32,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6f91a24-3dfc-4474-956c-f08fc2b39914/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:01:32,985] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:01:32,985] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:01:32,986] [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
Alienimonas californiensis	strain=CA12	GCA_007743815.1	2527989	2527989	type	True	75.4717	176	738	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.3466	59	738	95	below_threshold
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	75.2689	73	738	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.1407	129	738	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.0467	179	738	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.9661	136	738	95	below_threshold
Dactylosporangium siamense	strain=NBRC 106093	GCA_016862795.1	685454	685454	type	True	74.6384	178	738	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	74.6055	202	738	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_000716715.1	35754	35754	type	True	74.6046	200	738	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:01:32,986] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22799/tc_result.tsv
[2023-03-19 00:01:32,986] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:01:32,986] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:01:32,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6f91a24-3dfc-4474-956c-f08fc2b39914/dqc_reference/checkm_data
[2023-03-19 00:01:32,987] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:01:32,992] [INFO] Task started: CheckM
[2023-03-19 00:01:32,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22799/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22799/checkm_input OceanDNA-b22799/checkm_result
[2023-03-19 00:02:08,367] [INFO] Task succeeded: CheckM
[2023-03-19 00:02:08,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:02:08,370] [INFO] ===== Completeness check finished =====
[2023-03-19 00:02:08,370] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:02:08,370] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22799/markers.fasta)
[2023-03-19 00:02:08,370] [INFO] Task started: Blastn
[2023-03-19 00:02:08,370] [INFO] Running command: blastn -query OceanDNA-b22799/markers.fasta -db /var/lib/cwl/stga6f91a24-3dfc-4474-956c-f08fc2b39914/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22799/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:02:08,875] [INFO] Task succeeded: Blastn
[2023-03-19 00:02:08,876] [INFO] Selected 18 target genomes.
[2023-03-19 00:02:08,876] [INFO] Target genome list was writen to OceanDNA-b22799/target_genomes_gtdb.txt
[2023-03-19 00:02:08,896] [INFO] Task started: fastANI
[2023-03-19 00:02:08,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg540355bc-7ffc-4ce2-b1cb-637909189711/OceanDNA-b22799.fa --refList OceanDNA-b22799/target_genomes_gtdb.txt --output OceanDNA-b22799/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:02:23,695] [INFO] Task succeeded: fastANI
[2023-03-19 00:02:23,701] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:02:23,702] [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_007743815.1	s__Alienimonas californiensis	75.4525	183	738	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Alienimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813775.1	s__JACCRE01 sp013813775	75.452	61	738	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JACCRE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795125.1	s__JAEUIG01 sp016795125	75.3601	64	738	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007745175.1	s__Caulifigura coniformis	75.2689	73	738	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Caulifigura	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001610895.1	s__Paludisphaera sp001610895	75.0735	112	738	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008087625.1	s__Aquisphaera giovannonii	75.0563	180	738	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Aquisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702655.1	s__GCA-2702655 sp002702655	75.0403	77	738	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__GCA-2702655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191115.1	s__JACPPG01 sp016191115	75.0092	57	738	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__JACPPG01;g__JACPPG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872955.1	s__QWPN01 sp016872955	74.9797	55	738	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901538445.1	s__Gemmata sp901538445	74.7635	148	738	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218765.1	s__JAAZOP01 sp016218765	74.5469	94	738	d__Bacteria;p__Myxococcota;c__Polyangia;o__DRWM01;f__JAAZOP01;g__JAAZOP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:02:23,702] [INFO] GTDB search result was written to OceanDNA-b22799/result_gtdb.tsv
[2023-03-19 00:02:23,702] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:02:23,703] [INFO] DFAST_QC result json was written to OceanDNA-b22799/dqc_result.json
[2023-03-19 00:02:23,703] [INFO] DFAST_QC completed!
[2023-03-19 00:02:23,703] [INFO] Total running time: 0h1m20s