[2023-03-17 04:15:14,729] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:14,730] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:14,730] [INFO] DQC Reference Directory: /var/lib/cwl/stgf62388af-2e30-4a7c-8b40-63706e02dff4/dqc_reference
[2023-03-17 04:15:16,100] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:16,100] [INFO] Task started: Prodigal
[2023-03-17 04:15:16,100] [INFO] Running command: cat /var/lib/cwl/stgf873714b-93dc-47dd-ad59-b9008a8b0b59/OceanDNA-b28042.fa | prodigal -d OceanDNA-b28042/cds.fna -a OceanDNA-b28042/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:33,093] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:33,093] [INFO] Task started: HMMsearch
[2023-03-17 04:15:33,093] [INFO] Running command: hmmsearch --tblout OceanDNA-b28042/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf62388af-2e30-4a7c-8b40-63706e02dff4/dqc_reference/reference_markers.hmm OceanDNA-b28042/protein.faa > /dev/null
[2023-03-17 04:15:33,314] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:33,315] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf873714b-93dc-47dd-ad59-b9008a8b0b59/OceanDNA-b28042.fa]
[2023-03-17 04:15:33,335] [INFO] Query marker FASTA was written to OceanDNA-b28042/markers.fasta
[2023-03-17 04:15:33,336] [INFO] Task started: Blastn
[2023-03-17 04:15:33,336] [INFO] Running command: blastn -query OceanDNA-b28042/markers.fasta -db /var/lib/cwl/stgf62388af-2e30-4a7c-8b40-63706e02dff4/dqc_reference/reference_markers.fasta -out OceanDNA-b28042/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:33,885] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:33,886] [INFO] Selected 25 target genomes.
[2023-03-17 04:15:33,887] [INFO] Target genome list was writen to OceanDNA-b28042/target_genomes.txt
[2023-03-17 04:15:33,899] [INFO] Task started: fastANI
[2023-03-17 04:15:33,899] [INFO] Running command: fastANI --query /var/lib/cwl/stgf873714b-93dc-47dd-ad59-b9008a8b0b59/OceanDNA-b28042.fa --refList OceanDNA-b28042/target_genomes.txt --output OceanDNA-b28042/fastani_result.tsv --threads 1
[2023-03-17 04:15:51,378] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:51,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf62388af-2e30-4a7c-8b40-63706e02dff4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:15:51,378] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf62388af-2e30-4a7c-8b40-63706e02dff4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:15:51,390] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:15:51,390] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 04:15:51,390] [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
Ascidiaceihabitans donghaensis	strain=CECT 8599	GCA_900302465.1	1510460	1510460	type	True	76.8391	208	885	95	below_threshold
Octadecabacter arcticus	strain=238	GCA_000155735.2	53946	53946	type	True	76.4052	98	885	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.2313	121	885	95	below_threshold
Pelagicola litoralis	strain=CL-ES2	GCA_005518135.1	420403	420403	type	True	76.1196	68	885	95	below_threshold
Sulfitobacter brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	76.092	96	885	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	76.0335	99	885	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.0106	118	885	95	below_threshold
Loktanella ponticola	strain=DSM 101064	GCA_014199395.1	1524255	1524255	type	True	76.0076	79	885	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	75.9923	121	885	95	below_threshold
Tateyamaria pelophila	strain=DSM 17270	GCA_019966495.1	328415	328415	type	True	75.9887	84	885	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	75.9813	92	885	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	75.9529	126	885	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	75.9484	128	885	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	75.9342	50	885	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	75.9199	87	885	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	75.85	94	885	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	75.8486	94	885	95	below_threshold
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	75.736	77	885	95	below_threshold
Puniceibacterium antarcticum	strain=SM1211	GCA_002760615.1	1206336	1206336	type	True	75.7337	55	885	95	below_threshold
Yoonia maricola	strain=DSM 29128	GCA_002797915.1	420999	420999	type	True	75.5267	62	885	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:15:51,390] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28042/tc_result.tsv
[2023-03-17 04:15:51,391] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:15:51,391] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:15:51,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf62388af-2e30-4a7c-8b40-63706e02dff4/dqc_reference/checkm_data
[2023-03-17 04:15:51,391] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:15:51,396] [INFO] Task started: CheckM
[2023-03-17 04:15:51,397] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28042/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28042/checkm_input OceanDNA-b28042/checkm_result
[2023-03-17 04:16:35,988] [INFO] Task succeeded: CheckM
[2023-03-17 04:16:35,988] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:16:35,991] [INFO] ===== Completeness check finished =====
[2023-03-17 04:16:35,991] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:16:35,991] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28042/markers.fasta)
[2023-03-17 04:16:35,991] [INFO] Task started: Blastn
[2023-03-17 04:16:35,991] [INFO] Running command: blastn -query OceanDNA-b28042/markers.fasta -db /var/lib/cwl/stgf62388af-2e30-4a7c-8b40-63706e02dff4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28042/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:16:36,812] [INFO] Task succeeded: Blastn
[2023-03-17 04:16:36,813] [INFO] Selected 15 target genomes.
[2023-03-17 04:16:36,813] [INFO] Target genome list was writen to OceanDNA-b28042/target_genomes_gtdb.txt
[2023-03-17 04:16:37,032] [INFO] Task started: fastANI
[2023-03-17 04:16:37,033] [INFO] Running command: fastANI --query /var/lib/cwl/stgf873714b-93dc-47dd-ad59-b9008a8b0b59/OceanDNA-b28042.fa --refList OceanDNA-b28042/target_genomes_gtdb.txt --output OceanDNA-b28042/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:16:45,776] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:45,785] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:16:45,785] [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_905182355.1	s__Ascidiaceihabitans sp905182355	80.6374	545	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478745.1	s__Ascidiaceihabitans sp002478745	78.5962	354	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.75	99.75	0.89	0.89	2	-
GCA_905182105.1	s__Ascidiaceihabitans sp905182105	78.5348	350	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647275.1	s__Ascidiaceihabitans sp018647275	78.1929	209	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302465.1	s__Ascidiaceihabitans donghaensis	76.8391	208	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	76.3254	118	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCA_017854675.1	s__Sulfitobacter sp017854675	76.3161	105	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	76.2963	103	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	76.208	122	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103185.1	s__Sulfitobacter litoralis	76.0335	99	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	-
GCF_900106935.1	s__Sulfitobacter pontiacus	75.9813	92	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_000622325.1	s__Sulfitobacter geojensis	75.9529	126	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_003201935.1	s__Yoonia sp003201935	75.9367	61	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002760615.1	s__Puniceibacterium antarcticum	75.7337	55	885	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:16:45,785] [INFO] GTDB search result was written to OceanDNA-b28042/result_gtdb.tsv
[2023-03-17 04:16:45,785] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:16:45,787] [INFO] DFAST_QC result json was written to OceanDNA-b28042/dqc_result.json
[2023-03-17 04:16:45,787] [INFO] DFAST_QC completed!
[2023-03-17 04:16:45,787] [INFO] Total running time: 0h1m31s