[2023-03-15 13:20:53,610] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:53,610] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:53,610] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d76a631-acbe-46e3-a331-caf6a9f17469/dqc_reference
[2023-03-15 13:20:54,869] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:54,869] [INFO] Task started: Prodigal
[2023-03-15 13:20:54,870] [INFO] Running command: cat /var/lib/cwl/stg6281519d-2a2f-4d77-acb6-f095dde08930/OceanDNA-b30122.fa | prodigal -d OceanDNA-b30122/cds.fna -a OceanDNA-b30122/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:21:16,144] [INFO] Task succeeded: Prodigal
[2023-03-15 13:21:16,144] [INFO] Task started: HMMsearch
[2023-03-15 13:21:16,144] [INFO] Running command: hmmsearch --tblout OceanDNA-b30122/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d76a631-acbe-46e3-a331-caf6a9f17469/dqc_reference/reference_markers.hmm OceanDNA-b30122/protein.faa > /dev/null
[2023-03-15 13:21:16,398] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:21:16,399] [INFO] Found 6/6 markers.
[2023-03-15 13:21:16,420] [INFO] Query marker FASTA was written to OceanDNA-b30122/markers.fasta
[2023-03-15 13:21:16,421] [INFO] Task started: Blastn
[2023-03-15 13:21:16,421] [INFO] Running command: blastn -query OceanDNA-b30122/markers.fasta -db /var/lib/cwl/stg3d76a631-acbe-46e3-a331-caf6a9f17469/dqc_reference/reference_markers.fasta -out OceanDNA-b30122/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:17,323] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:17,324] [INFO] Selected 22 target genomes.
[2023-03-15 13:21:17,324] [INFO] Target genome list was writen to OceanDNA-b30122/target_genomes.txt
[2023-03-15 13:21:17,340] [INFO] Task started: fastANI
[2023-03-15 13:21:17,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg6281519d-2a2f-4d77-acb6-f095dde08930/OceanDNA-b30122.fa --refList OceanDNA-b30122/target_genomes.txt --output OceanDNA-b30122/fastani_result.tsv --threads 1
[2023-03-15 13:21:35,185] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:35,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d76a631-acbe-46e3-a331-caf6a9f17469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:35,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d76a631-acbe-46e3-a331-caf6a9f17469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:35,199] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 13:21:35,199] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 13:21:35,199] [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 nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	96.9524	1005	1101	95	conclusive
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	82.2024	721	1101	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	80.455	656	1101	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	79.5956	526	1101	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	79.5633	534	1101	95	below_threshold
Roseovarius mucosus	strain=DSM 17069	GCA_000768555.3	215743	215743	type	True	79.4253	582	1101	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	79.2161	501	1101	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	79.1918	548	1101	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.8187	509	1101	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	78.7704	466	1101	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.7207	436	1101	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.5612	438	1101	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	78.4679	385	1101	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	78.4339	373	1101	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.3717	448	1101	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	78.0942	398	1101	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	78.0718	394	1101	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.8559	345	1101	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.5232	327	1101	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.4855	328	1101	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.4775	308	1101	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	77.2819	298	1101	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:21:35,200] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30122/tc_result.tsv
[2023-03-15 13:21:35,200] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:35,200] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:35,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d76a631-acbe-46e3-a331-caf6a9f17469/dqc_reference/checkm_data
[2023-03-15 13:21:35,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:35,206] [INFO] Task started: CheckM
[2023-03-15 13:21:35,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30122/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30122/checkm_input OceanDNA-b30122/checkm_result
[2023-03-15 13:22:29,442] [INFO] Task succeeded: CheckM
[2023-03-15 13:22:29,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:22:29,446] [INFO] ===== Completeness check finished =====
[2023-03-15 13:22:29,446] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:22:29,446] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30122/markers.fasta)
[2023-03-15 13:22:29,448] [INFO] Task started: Blastn
[2023-03-15 13:22:29,448] [INFO] Running command: blastn -query OceanDNA-b30122/markers.fasta -db /var/lib/cwl/stg3d76a631-acbe-46e3-a331-caf6a9f17469/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30122/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:22:31,202] [INFO] Task succeeded: Blastn
[2023-03-15 13:22:31,203] [INFO] Selected 10 target genomes.
[2023-03-15 13:22:31,203] [INFO] Target genome list was writen to OceanDNA-b30122/target_genomes_gtdb.txt
[2023-03-15 13:22:31,234] [INFO] Task started: fastANI
[2023-03-15 13:22:31,234] [INFO] Running command: fastANI --query /var/lib/cwl/stg6281519d-2a2f-4d77-acb6-f095dde08930/OceanDNA-b30122.fa --refList OceanDNA-b30122/target_genomes_gtdb.txt --output OceanDNA-b30122/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:22:39,305] [INFO] Task succeeded: fastANI
[2023-03-15 13:22:39,312] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:22:39,312] [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_002925845.1	s__Roseovarius nitratireducens	96.9524	1005	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.60	96.60	0.90	0.90	2	conclusive
GCA_016278295.1	s__Roseovarius sp016278295	93.1493	717	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002421985.1	s__Roseovarius sp002421985	83.8139	627	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720475.1	s__Roseovarius sp002720475	82.8119	512	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.80	99.74	0.82	0.71	3	-
GCA_014359765.1	s__Roseovarius sp014359765	82.4627	579	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109855.1	s__Roseovarius tolerans	82.1845	723	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.73	96.73	0.86	0.86	2	-
GCF_002072155.1	s__Roseovarius sp002072155	81.8917	723	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842985.1	s__Roseovarius sp002842985	81.8914	702	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069895.1	s__Roseovarius sp018069895	81.7247	680	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.42	99.42	0.86	0.86	2	-
GCF_003651245.1	s__Roseovarius spongiae	79.569	532	1101	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:22:39,313] [INFO] GTDB search result was written to OceanDNA-b30122/result_gtdb.tsv
[2023-03-15 13:22:39,313] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:22:39,315] [INFO] DFAST_QC result json was written to OceanDNA-b30122/dqc_result.json
[2023-03-15 13:22:39,315] [INFO] DFAST_QC completed!
[2023-03-15 13:22:39,315] [INFO] Total running time: 0h1m46s