[2023-03-18 00:41:30,568] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:41:30,568] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:41:30,568] [INFO] DQC Reference Directory: /var/lib/cwl/stg005e8cf0-0c5d-4dc7-bab3-c94e6bbd6388/dqc_reference
[2023-03-18 00:41:31,664] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:41:31,665] [INFO] Task started: Prodigal
[2023-03-18 00:41:31,665] [INFO] Running command: cat /var/lib/cwl/stgdf1843a7-ed31-4882-90bb-b73dca9faf1b/OceanDNA-b30447.fa | prodigal -d OceanDNA-b30447/cds.fna -a OceanDNA-b30447/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:41:55,460] [INFO] Task succeeded: Prodigal
[2023-03-18 00:41:55,460] [INFO] Task started: HMMsearch
[2023-03-18 00:41:55,460] [INFO] Running command: hmmsearch --tblout OceanDNA-b30447/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg005e8cf0-0c5d-4dc7-bab3-c94e6bbd6388/dqc_reference/reference_markers.hmm OceanDNA-b30447/protein.faa > /dev/null
[2023-03-18 00:41:55,687] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:41:55,687] [INFO] Found 6/6 markers.
[2023-03-18 00:41:55,721] [INFO] Query marker FASTA was written to OceanDNA-b30447/markers.fasta
[2023-03-18 00:41:55,722] [INFO] Task started: Blastn
[2023-03-18 00:41:55,722] [INFO] Running command: blastn -query OceanDNA-b30447/markers.fasta -db /var/lib/cwl/stg005e8cf0-0c5d-4dc7-bab3-c94e6bbd6388/dqc_reference/reference_markers.fasta -out OceanDNA-b30447/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:41:56,787] [INFO] Task succeeded: Blastn
[2023-03-18 00:41:56,790] [INFO] Selected 24 target genomes.
[2023-03-18 00:41:56,790] [INFO] Target genome list was writen to OceanDNA-b30447/target_genomes.txt
[2023-03-18 00:41:56,800] [INFO] Task started: fastANI
[2023-03-18 00:41:56,801] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf1843a7-ed31-4882-90bb-b73dca9faf1b/OceanDNA-b30447.fa --refList OceanDNA-b30447/target_genomes.txt --output OceanDNA-b30447/fastani_result.tsv --threads 1
[2023-03-18 00:42:15,264] [INFO] Task succeeded: fastANI
[2023-03-18 00:42:15,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg005e8cf0-0c5d-4dc7-bab3-c94e6bbd6388/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:42:15,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg005e8cf0-0c5d-4dc7-bab3-c94e6bbd6388/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:42:15,278] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:42:15,278] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:42:15,278] [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
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	90.2099	1093	1204	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	90.1747	1094	1204	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	79.064	592	1204	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	78.6979	505	1204	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	78.5183	446	1204	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.404	529	1204	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	78.3913	419	1204	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.3908	504	1204	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	78.3809	417	1204	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	78.1555	459	1204	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.073	400	1204	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	78.0155	458	1204	95	below_threshold
Tateyamaria pelophila	strain=DSM 17270	GCA_019966495.1	328415	328415	type	True	77.9733	377	1204	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	77.9211	401	1204	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	77.7621	386	1204	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	77.7146	412	1204	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	77.6839	383	1204	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	77.6576	392	1204	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	77.6489	387	1204	95	below_threshold
Thalassobius gelatinovorus	strain=DSM 5887	GCA_900111045.1	53501	53501	type	True	77.6306	352	1204	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.3258	340	1204	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.2302	340	1204	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.0751	257	1204	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.9224	285	1204	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:42:15,282] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30447/tc_result.tsv
[2023-03-18 00:42:15,282] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:42:15,282] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:42:15,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg005e8cf0-0c5d-4dc7-bab3-c94e6bbd6388/dqc_reference/checkm_data
[2023-03-18 00:42:15,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:42:15,327] [INFO] Task started: CheckM
[2023-03-18 00:42:15,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30447/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30447/checkm_input OceanDNA-b30447/checkm_result
[2023-03-18 00:43:18,884] [INFO] Task succeeded: CheckM
[2023-03-18 00:43:18,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:43:18,924] [INFO] ===== Completeness check finished =====
[2023-03-18 00:43:18,924] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:43:18,925] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30447/markers.fasta)
[2023-03-18 00:43:18,926] [INFO] Task started: Blastn
[2023-03-18 00:43:18,926] [INFO] Running command: blastn -query OceanDNA-b30447/markers.fasta -db /var/lib/cwl/stg005e8cf0-0c5d-4dc7-bab3-c94e6bbd6388/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30447/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:43:20,519] [INFO] Task succeeded: Blastn
[2023-03-18 00:43:20,520] [INFO] Selected 12 target genomes.
[2023-03-18 00:43:20,520] [INFO] Target genome list was writen to OceanDNA-b30447/target_genomes_gtdb.txt
[2023-03-18 00:43:20,716] [INFO] Task started: fastANI
[2023-03-18 00:43:20,717] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf1843a7-ed31-4882-90bb-b73dca9faf1b/OceanDNA-b30447.fa --refList OceanDNA-b30447/target_genomes_gtdb.txt --output OceanDNA-b30447/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:43:31,597] [INFO] Task succeeded: fastANI
[2023-03-18 00:43:31,604] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:43:31,604] [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_000620505.1	s__Ascidiaceihabitans sp000620505	90.5333	1098	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	90.1747	1094	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	87.7198	966	1204	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	85.4489	959	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_001650875.1	s__Sulfitobacter sp001650875	79.3507	606	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	79.0568	593	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	78.6983	505	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_009857745.1	s__Thalassobius mangrovi	78.3761	506	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886735.1	s__Sulfitobacter alexandrii	78.33	543	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188035.1	s__Puniceibacterium sediminis	77.9043	403	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342065.1	s__Primorskyibacter sedentarius	77.7707	385	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352065.1	s__Sulfitobacter sp003352065	77.6448	361	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:43:31,605] [INFO] GTDB search result was written to OceanDNA-b30447/result_gtdb.tsv
[2023-03-18 00:43:31,605] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:43:31,607] [INFO] DFAST_QC result json was written to OceanDNA-b30447/dqc_result.json
[2023-03-18 00:43:31,607] [INFO] DFAST_QC completed!
[2023-03-18 00:43:31,607] [INFO] Total running time: 0h2m1s