[2023-03-16 01:12:29,297] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:12:29,299] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:12:29,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg591400d9-1d5f-4aa2-9fb7-0abc5e5ed518/dqc_reference
[2023-03-16 01:12:30,467] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:12:30,468] [INFO] Task started: Prodigal
[2023-03-16 01:12:30,468] [INFO] Running command: cat /var/lib/cwl/stg645aed16-e8af-4e5b-9768-7bf805ec1313/OceanDNA-b30224.fa | prodigal -d OceanDNA-b30224/cds.fna -a OceanDNA-b30224/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:12:47,517] [INFO] Task succeeded: Prodigal
[2023-03-16 01:12:47,517] [INFO] Task started: HMMsearch
[2023-03-16 01:12:47,517] [INFO] Running command: hmmsearch --tblout OceanDNA-b30224/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg591400d9-1d5f-4aa2-9fb7-0abc5e5ed518/dqc_reference/reference_markers.hmm OceanDNA-b30224/protein.faa > /dev/null
[2023-03-16 01:12:47,705] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:12:47,706] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg645aed16-e8af-4e5b-9768-7bf805ec1313/OceanDNA-b30224.fa]
[2023-03-16 01:12:47,733] [INFO] Query marker FASTA was written to OceanDNA-b30224/markers.fasta
[2023-03-16 01:12:47,733] [INFO] Task started: Blastn
[2023-03-16 01:12:47,733] [INFO] Running command: blastn -query OceanDNA-b30224/markers.fasta -db /var/lib/cwl/stg591400d9-1d5f-4aa2-9fb7-0abc5e5ed518/dqc_reference/reference_markers.fasta -out OceanDNA-b30224/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:12:48,262] [INFO] Task succeeded: Blastn
[2023-03-16 01:12:48,265] [INFO] Selected 19 target genomes.
[2023-03-16 01:12:48,266] [INFO] Target genome list was writen to OceanDNA-b30224/target_genomes.txt
[2023-03-16 01:12:48,382] [INFO] Task started: fastANI
[2023-03-16 01:12:48,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg645aed16-e8af-4e5b-9768-7bf805ec1313/OceanDNA-b30224.fa --refList OceanDNA-b30224/target_genomes.txt --output OceanDNA-b30224/fastani_result.tsv --threads 1
[2023-03-16 01:13:00,888] [INFO] Task succeeded: fastANI
[2023-03-16 01:13:00,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg591400d9-1d5f-4aa2-9fb7-0abc5e5ed518/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:13:00,888] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg591400d9-1d5f-4aa2-9fb7-0abc5e5ed518/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:13:00,899] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 01:13:00,899] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 01:13:00,900] [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
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	81.6689	527	877	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	79.2143	386	877	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	78.8657	351	877	95	below_threshold
Sulfitobacter brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	77.3796	218	877	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.2523	207	877	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	77.1677	232	877	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	77.094	185	877	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.0878	187	877	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	76.9771	192	877	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.9429	206	877	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	76.4701	102	877	95	below_threshold
Planktotalea arctica	strain=IMCC9565	GCA_002105285.1	1481893	1481893	type	True	76.3495	99	877	95	below_threshold
Pelagimonas phthalicica	strain=DSM 26923	GCA_004364805.1	1037362	1037362	type	True	76.2247	92	877	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.1328	77	877	95	below_threshold
Cognatishimia maritima	strain=DSM 28223	GCA_900129685.1	870908	870908	type	True	76.1109	61	877	95	below_threshold
Pararhodobacter oceanensis	strain=AM505	GCA_003076755.1	2172121	2172121	type	True	75.9023	59	877	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	75.8302	68	877	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	75.7072	64	877	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 01:13:00,903] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30224/tc_result.tsv
[2023-03-16 01:13:00,911] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:13:00,911] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:13:00,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg591400d9-1d5f-4aa2-9fb7-0abc5e5ed518/dqc_reference/checkm_data
[2023-03-16 01:13:00,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:13:00,927] [INFO] Task started: CheckM
[2023-03-16 01:13:00,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30224/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30224/checkm_input OceanDNA-b30224/checkm_result
[2023-03-16 01:13:46,455] [INFO] Task succeeded: CheckM
[2023-03-16 01:13:46,455] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:13:46,461] [INFO] ===== Completeness check finished =====
[2023-03-16 01:13:46,461] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:13:46,461] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30224/markers.fasta)
[2023-03-16 01:13:46,463] [INFO] Task started: Blastn
[2023-03-16 01:13:46,463] [INFO] Running command: blastn -query OceanDNA-b30224/markers.fasta -db /var/lib/cwl/stg591400d9-1d5f-4aa2-9fb7-0abc5e5ed518/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30224/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:13:47,202] [INFO] Task succeeded: Blastn
[2023-03-16 01:13:47,206] [INFO] Selected 11 target genomes.
[2023-03-16 01:13:47,206] [INFO] Target genome list was writen to OceanDNA-b30224/target_genomes_gtdb.txt
[2023-03-16 01:13:47,580] [INFO] Task started: fastANI
[2023-03-16 01:13:47,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg645aed16-e8af-4e5b-9768-7bf805ec1313/OceanDNA-b30224.fa --refList OceanDNA-b30224/target_genomes_gtdb.txt --output OceanDNA-b30224/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:13:55,111] [INFO] Task succeeded: fastANI
[2023-03-16 01:13:55,118] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 01:13:55,119] [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_013282155.1	s__Sulfitobacter sp013282155	84.5501	635	877	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCA_013139555.1	s__Sulfitobacter sp013139555	82.5236	521	877	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116285.1	s__Sulfitobacter marinus	81.6689	527	877	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156335.1	s__Sulfitobacter sp000156335	80.4544	483	877	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050655.1	s__Sulfitobacter sp011050655	79.8818	269	877	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006064855.1	s__Sulfitobacter sp006064855	79.3779	332	877	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	79.2267	385	877	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCA_002731875.1	s__Sulfitobacter sp002731875	78.4692	271	877	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.91	99.88	0.91	0.87	3	-
GCA_017854675.1	s__Sulfitobacter sp017854675	76.88	190	877	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013112245.1	s__Ruegeria sp013112245	76.0897	93	877	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.18	96.94	0.93	0.89	11	-
GCA_002166865.1	s__Roseovarius sp002166865	75.5149	59	877	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 01:13:55,120] [INFO] GTDB search result was written to OceanDNA-b30224/result_gtdb.tsv
[2023-03-16 01:13:55,120] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:13:55,124] [INFO] DFAST_QC result json was written to OceanDNA-b30224/dqc_result.json
[2023-03-16 01:13:55,124] [INFO] DFAST_QC completed!
[2023-03-16 01:13:55,124] [INFO] Total running time: 0h1m26s