[2023-03-17 11:19:47,580] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:19:47,580] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:19:47,580] [INFO] DQC Reference Directory: /var/lib/cwl/stg0dd0e6d0-6b98-459e-981b-2e048f756a83/dqc_reference
[2023-03-17 11:19:48,709] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:19:48,710] [INFO] Task started: Prodigal
[2023-03-17 11:19:48,710] [INFO] Running command: cat /var/lib/cwl/stgd04d322c-a7ca-43fb-8a6c-fb038acd8075/OceanDNA-b23947.fa | prodigal -d OceanDNA-b23947/cds.fna -a OceanDNA-b23947/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:20:08,588] [INFO] Task succeeded: Prodigal
[2023-03-17 11:20:08,588] [INFO] Task started: HMMsearch
[2023-03-17 11:20:08,588] [INFO] Running command: hmmsearch --tblout OceanDNA-b23947/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0dd0e6d0-6b98-459e-981b-2e048f756a83/dqc_reference/reference_markers.hmm OceanDNA-b23947/protein.faa > /dev/null
[2023-03-17 11:20:08,778] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:20:08,779] [INFO] Found 6/6 markers.
[2023-03-17 11:20:08,800] [INFO] Query marker FASTA was written to OceanDNA-b23947/markers.fasta
[2023-03-17 11:20:08,801] [INFO] Task started: Blastn
[2023-03-17 11:20:08,801] [INFO] Running command: blastn -query OceanDNA-b23947/markers.fasta -db /var/lib/cwl/stg0dd0e6d0-6b98-459e-981b-2e048f756a83/dqc_reference/reference_markers.fasta -out OceanDNA-b23947/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:20:09,610] [INFO] Task succeeded: Blastn
[2023-03-17 11:20:09,611] [INFO] Selected 19 target genomes.
[2023-03-17 11:20:09,611] [INFO] Target genome list was writen to OceanDNA-b23947/target_genomes.txt
[2023-03-17 11:20:09,621] [INFO] Task started: fastANI
[2023-03-17 11:20:09,621] [INFO] Running command: fastANI --query /var/lib/cwl/stgd04d322c-a7ca-43fb-8a6c-fb038acd8075/OceanDNA-b23947.fa --refList OceanDNA-b23947/target_genomes.txt --output OceanDNA-b23947/fastani_result.tsv --threads 1
[2023-03-17 11:20:24,586] [INFO] Task succeeded: fastANI
[2023-03-17 11:20:24,587] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0dd0e6d0-6b98-459e-981b-2e048f756a83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:20:24,587] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0dd0e6d0-6b98-459e-981b-2e048f756a83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:20:24,598] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 11:20:24,599] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 11:20:24,599] [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
Maricaulis alexandrii	strain=LZ-16-1	GCA_005871165.1	2570354	2570354	type	True	97.2839	963	1060	95	conclusive
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	80.4451	627	1060	95	below_threshold
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	78.8614	463	1060	95	below_threshold
Hyphobacterium indicum	strain=2ED5	GCA_003129605.1	2162714	2162714	type	True	78.2142	227	1060	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	77.5144	194	1060	95	below_threshold
Glycocaulis alkaliphilus	strain=6B-8	GCA_004000605.1	1434191	1434191	type	True	77.4537	198	1060	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	77.4004	229	1060	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	77.3984	231	1060	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	76.7094	102	1060	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	76.3888	130	1060	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	76.2708	83	1060	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.2133	94	1060	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	76.1637	127	1060	95	below_threshold
Mesorhizobium australicum	strain=WSM2073	GCA_000230995.3	536018	536018	type	True	76.1448	93	1060	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	76.1228	108	1060	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	76.1074	122	1060	95	below_threshold
Bradyrhizobium icense	strain=LMTR 13	GCA_001693385.1	1274631	1274631	type	True	76.0812	89	1060	95	below_threshold
Xanthobacter agilis	strain=LMG 16336	GCA_021730435.1	47492	47492	type	True	75.8662	88	1060	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.8267	68	1060	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:20:24,599] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23947/tc_result.tsv
[2023-03-17 11:20:24,599] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:20:24,599] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:20:24,599] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0dd0e6d0-6b98-459e-981b-2e048f756a83/dqc_reference/checkm_data
[2023-03-17 11:20:24,600] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:20:24,604] [INFO] Task started: CheckM
[2023-03-17 11:20:24,605] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23947/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23947/checkm_input OceanDNA-b23947/checkm_result
[2023-03-17 11:21:27,665] [INFO] Task succeeded: CheckM
[2023-03-17 11:21:27,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:21:27,668] [INFO] ===== Completeness check finished =====
[2023-03-17 11:21:27,668] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:21:27,668] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23947/markers.fasta)
[2023-03-17 11:21:27,669] [INFO] Task started: Blastn
[2023-03-17 11:21:27,669] [INFO] Running command: blastn -query OceanDNA-b23947/markers.fasta -db /var/lib/cwl/stg0dd0e6d0-6b98-459e-981b-2e048f756a83/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23947/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:21:29,251] [INFO] Task succeeded: Blastn
[2023-03-17 11:21:29,252] [INFO] Selected 9 target genomes.
[2023-03-17 11:21:29,252] [INFO] Target genome list was writen to OceanDNA-b23947/target_genomes_gtdb.txt
[2023-03-17 11:21:29,418] [INFO] Task started: fastANI
[2023-03-17 11:21:29,418] [INFO] Running command: fastANI --query /var/lib/cwl/stgd04d322c-a7ca-43fb-8a6c-fb038acd8075/OceanDNA-b23947.fa --refList OceanDNA-b23947/target_genomes_gtdb.txt --output OceanDNA-b23947/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:21:35,629] [INFO] Task succeeded: fastANI
[2023-03-17 11:21:35,636] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:21:35,636] [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_005871165.1	s__Maricaulis sp005871165	97.2839	963	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002694345.1	s__Maricaulis sp002694345	87.5397	518	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016817355.1	s__Maricaulis parjimensis	86.7182	853	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642925.1	s__Maricaulis sp017642925	81.9343	693	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707795.1	s__Maricaulis sp002707795	81.9149	488	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.42	99.36	0.71	0.69	3	-
GCA_015665295.1	s__Maricaulis sp015665295	80.7212	581	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634045.1	s__Maricaulis maris	80.4548	626	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.04	98.04	0.96	0.96	2	-
GCF_000014745.1	s__Maricaulis maris_A	80.4239	578	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.51	98.49	0.94	0.92	3	-
GCA_905480005.1	s__Maricaulis sp905480005	80.2467	531	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:21:35,636] [INFO] GTDB search result was written to OceanDNA-b23947/result_gtdb.tsv
[2023-03-17 11:21:35,636] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:21:35,638] [INFO] DFAST_QC result json was written to OceanDNA-b23947/dqc_result.json
[2023-03-17 11:21:35,638] [INFO] DFAST_QC completed!
[2023-03-17 11:21:35,638] [INFO] Total running time: 0h1m48s