[2023-03-17 22:37:12,600] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:37:12,601] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:37:12,601] [INFO] DQC Reference Directory: /var/lib/cwl/stgd07bddf5-ea40-489e-8688-6a7c06d80a46/dqc_reference
[2023-03-17 22:37:14,348] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:37:14,349] [INFO] Task started: Prodigal
[2023-03-17 22:37:14,349] [INFO] Running command: cat /var/lib/cwl/stgdab8b152-502a-40f4-842e-fe200d538c0d/OceanDNA-b29285.fa | prodigal -d OceanDNA-b29285/cds.fna -a OceanDNA-b29285/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:37:31,080] [INFO] Task succeeded: Prodigal
[2023-03-17 22:37:31,080] [INFO] Task started: HMMsearch
[2023-03-17 22:37:31,080] [INFO] Running command: hmmsearch --tblout OceanDNA-b29285/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd07bddf5-ea40-489e-8688-6a7c06d80a46/dqc_reference/reference_markers.hmm OceanDNA-b29285/protein.faa > /dev/null
[2023-03-17 22:37:31,277] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:37:31,278] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdab8b152-502a-40f4-842e-fe200d538c0d/OceanDNA-b29285.fa]
[2023-03-17 22:37:31,305] [INFO] Query marker FASTA was written to OceanDNA-b29285/markers.fasta
[2023-03-17 22:37:31,306] [INFO] Task started: Blastn
[2023-03-17 22:37:31,306] [INFO] Running command: blastn -query OceanDNA-b29285/markers.fasta -db /var/lib/cwl/stgd07bddf5-ea40-489e-8688-6a7c06d80a46/dqc_reference/reference_markers.fasta -out OceanDNA-b29285/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:37:31,868] [INFO] Task succeeded: Blastn
[2023-03-17 22:37:31,869] [INFO] Selected 33 target genomes.
[2023-03-17 22:37:31,870] [INFO] Target genome list was writen to OceanDNA-b29285/target_genomes.txt
[2023-03-17 22:37:31,886] [INFO] Task started: fastANI
[2023-03-17 22:37:31,887] [INFO] Running command: fastANI --query /var/lib/cwl/stgdab8b152-502a-40f4-842e-fe200d538c0d/OceanDNA-b29285.fa --refList OceanDNA-b29285/target_genomes.txt --output OceanDNA-b29285/fastani_result.tsv --threads 1
[2023-03-17 22:37:51,348] [INFO] Task succeeded: fastANI
[2023-03-17 22:37:51,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd07bddf5-ea40-489e-8688-6a7c06d80a46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:37:51,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd07bddf5-ea40-489e-8688-6a7c06d80a46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:37:51,356] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:37:51,356] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 22:37:51,356] [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
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	76.5011	65	755	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	76.0795	64	755	95	below_threshold
Pelagimonas phthalicica	strain=DSM 26923	GCA_004364805.1	1037362	1037362	type	True	76.0499	59	755	95	below_threshold
Pseudophaeobacter leonis	strain=306	GCA_002087335.1	1144477	1144477	type	True	76.0149	64	755	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	75.9263	55	755	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	75.9254	51	755	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	75.8987	56	755	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	75.6477	64	755	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	75.6166	52	755	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	75.6166	52	755	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	75.5702	51	755	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 22:37:51,357] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29285/tc_result.tsv
[2023-03-17 22:37:51,357] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:37:51,357] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:37:51,357] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd07bddf5-ea40-489e-8688-6a7c06d80a46/dqc_reference/checkm_data
[2023-03-17 22:37:51,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:37:51,365] [INFO] Task started: CheckM
[2023-03-17 22:37:51,365] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29285/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29285/checkm_input OceanDNA-b29285/checkm_result
[2023-03-17 22:38:36,544] [INFO] Task succeeded: CheckM
[2023-03-17 22:38:36,545] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 5.15%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-17 22:38:36,548] [INFO] ===== Completeness check finished =====
[2023-03-17 22:38:36,548] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:38:36,548] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29285/markers.fasta)
[2023-03-17 22:38:36,549] [INFO] Task started: Blastn
[2023-03-17 22:38:36,549] [INFO] Running command: blastn -query OceanDNA-b29285/markers.fasta -db /var/lib/cwl/stgd07bddf5-ea40-489e-8688-6a7c06d80a46/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29285/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:38:37,342] [INFO] Task succeeded: Blastn
[2023-03-17 22:38:37,343] [INFO] Selected 23 target genomes.
[2023-03-17 22:38:37,343] [INFO] Target genome list was writen to OceanDNA-b29285/target_genomes_gtdb.txt
[2023-03-17 22:38:37,417] [INFO] Task started: fastANI
[2023-03-17 22:38:37,417] [INFO] Running command: fastANI --query /var/lib/cwl/stgdab8b152-502a-40f4-842e-fe200d538c0d/OceanDNA-b29285.fa --refList OceanDNA-b29285/target_genomes_gtdb.txt --output OceanDNA-b29285/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:38:51,037] [INFO] Task succeeded: fastANI
[2023-03-17 22:38:51,046] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 22:38:51,046] [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_002684375.1	s__CPC320 sp002684375	98.5702	601	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CPC320	95.0	98.52	98.26	0.79	0.72	8	conclusive
GCA_002336405.1	s__CPC320 sp002336405	87.0744	525	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CPC320	95.0	98.74	97.78	0.79	0.51	9	-
GCF_900115165.1	s__Roseovarius lutimaris	76.5011	65	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366795.1	s__UBA3069 sp002366795	76.4755	59	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3069	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205515.1	s__Litorivita pollutaquae	76.3639	55	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorivita	95.0	98.23	98.23	0.93	0.93	2	-
GCF_900110775.1	s__Litorimicrobium taeanense	76.2938	62	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054325.1	s__Sulfitobacter mediterraneus	76.0795	64	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
GCF_001458355.1	s__Thalassobius gelatinovorus	75.9348	61	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	100.00	99.99	0.99	0.99	3	-
GCA_017854855.1	s__Sulfitobacter sp017854855	75.7965	54	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112755.1	s__Sulfitobacter brevis	75.7359	50	755	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	75.7187	60	755	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	75.6166	52	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_900116285.1	s__Sulfitobacter marinus	75.5702	51	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203975.2	s__Leisingera sp000203975	75.545	51	755	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
--------------------------------------------------------------------------------
[2023-03-17 22:38:51,046] [INFO] GTDB search result was written to OceanDNA-b29285/result_gtdb.tsv
[2023-03-17 22:38:51,046] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:38:51,048] [INFO] DFAST_QC result json was written to OceanDNA-b29285/dqc_result.json
[2023-03-17 22:38:51,048] [INFO] DFAST_QC completed!
[2023-03-17 22:38:51,048] [INFO] Total running time: 0h1m38s