[2023-03-18 00:35:06,575] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:35:06,575] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:35:06,575] [INFO] DQC Reference Directory: /var/lib/cwl/stg34bfdeb7-512d-4c3f-bb6f-e268eef115ed/dqc_reference
[2023-03-18 00:35:07,699] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:35:07,700] [INFO] Task started: Prodigal
[2023-03-18 00:35:07,700] [INFO] Running command: cat /var/lib/cwl/stgdb617316-6174-4a2d-b152-d62e780d19a8/OceanDNA-b23907.fa | prodigal -d OceanDNA-b23907/cds.fna -a OceanDNA-b23907/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:35:22,204] [INFO] Task succeeded: Prodigal
[2023-03-18 00:35:22,204] [INFO] Task started: HMMsearch
[2023-03-18 00:35:22,204] [INFO] Running command: hmmsearch --tblout OceanDNA-b23907/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34bfdeb7-512d-4c3f-bb6f-e268eef115ed/dqc_reference/reference_markers.hmm OceanDNA-b23907/protein.faa > /dev/null
[2023-03-18 00:35:22,429] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:35:22,430] [INFO] Found 6/6 markers.
[2023-03-18 00:35:22,447] [INFO] Query marker FASTA was written to OceanDNA-b23907/markers.fasta
[2023-03-18 00:35:22,447] [INFO] Task started: Blastn
[2023-03-18 00:35:22,447] [INFO] Running command: blastn -query OceanDNA-b23907/markers.fasta -db /var/lib/cwl/stg34bfdeb7-512d-4c3f-bb6f-e268eef115ed/dqc_reference/reference_markers.fasta -out OceanDNA-b23907/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:35:23,318] [INFO] Task succeeded: Blastn
[2023-03-18 00:35:23,319] [INFO] Selected 17 target genomes.
[2023-03-18 00:35:23,319] [INFO] Target genome list was writen to OceanDNA-b23907/target_genomes.txt
[2023-03-18 00:35:23,325] [INFO] Task started: fastANI
[2023-03-18 00:35:23,325] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb617316-6174-4a2d-b152-d62e780d19a8/OceanDNA-b23907.fa --refList OceanDNA-b23907/target_genomes.txt --output OceanDNA-b23907/fastani_result.tsv --threads 1
[2023-03-18 00:35:33,978] [INFO] Task succeeded: fastANI
[2023-03-18 00:35:33,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34bfdeb7-512d-4c3f-bb6f-e268eef115ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:35:33,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34bfdeb7-512d-4c3f-bb6f-e268eef115ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:35:33,988] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:35:33,988] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:35:33,988] [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
Hyphobacterium indicum	strain=2ED5	GCA_003129605.1	2162714	2162714	type	True	79.5303	464	782	95	below_threshold
Maricaulis alexandrii	strain=LZ-16-1	GCA_005871165.1	2570354	2570354	type	True	77.2242	207	782	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	76.8713	181	782	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	76.85	182	782	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.8085	192	782	95	below_threshold
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	76.708	214	782	95	below_threshold
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	76.7023	174	782	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_009806145.1	1133559	1133559	type	True	76.4707	167	782	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	76.438	171	782	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	76.438	171	782	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	75.8293	74	782	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	75.4688	67	782	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	75.4041	50	782	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.3233	84	782	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.3126	85	782	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	75.2887	68	782	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:35:33,989] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23907/tc_result.tsv
[2023-03-18 00:35:33,989] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:35:33,989] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:35:33,989] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34bfdeb7-512d-4c3f-bb6f-e268eef115ed/dqc_reference/checkm_data
[2023-03-18 00:35:33,990] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:35:33,994] [INFO] Task started: CheckM
[2023-03-18 00:35:33,994] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23907/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23907/checkm_input OceanDNA-b23907/checkm_result
[2023-03-18 00:36:12,498] [INFO] Task succeeded: CheckM
[2023-03-18 00:36:12,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:36:12,500] [INFO] ===== Completeness check finished =====
[2023-03-18 00:36:12,500] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:36:12,500] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23907/markers.fasta)
[2023-03-18 00:36:12,501] [INFO] Task started: Blastn
[2023-03-18 00:36:12,501] [INFO] Running command: blastn -query OceanDNA-b23907/markers.fasta -db /var/lib/cwl/stg34bfdeb7-512d-4c3f-bb6f-e268eef115ed/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23907/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:36:14,192] [INFO] Task succeeded: Blastn
[2023-03-18 00:36:14,193] [INFO] Selected 14 target genomes.
[2023-03-18 00:36:14,193] [INFO] Target genome list was writen to OceanDNA-b23907/target_genomes_gtdb.txt
[2023-03-18 00:36:14,217] [INFO] Task started: fastANI
[2023-03-18 00:36:14,217] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb617316-6174-4a2d-b152-d62e780d19a8/OceanDNA-b23907.fa --refList OceanDNA-b23907/target_genomes_gtdb.txt --output OceanDNA-b23907/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:36:21,458] [INFO] Task succeeded: fastANI
[2023-03-18 00:36:21,466] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:36:21,467] [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_003129605.1	s__Hyphobacterium indicum	79.5412	463	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124665.1	s__Hyphobacterium sp016124665	79.3748	431	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014323565.1	s__Hyphobacterium sp014323565	78.9005	397	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783385.1	s__Hyphobacterium sp002783385	78.6364	319	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124205.1	s__Hyphobacterium sp016124205	77.8335	230	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692855.1	s__Hyphobacterium sp002692855	77.7539	235	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	99.83	99.83	0.96	0.96	2	-
GCA_017642925.1	s__Maricaulis sp017642925	77.334	231	782	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	77.1977	176	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.42	99.36	0.71	0.69	3	-
GCF_003122085.1	s__WD6-1 sp003122085	76.7967	193	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__WD6-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634045.1	s__Maricaulis maris	76.708	214	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.04	98.04	0.96	0.96	2	-
GCF_008630495.1	s__Oceanicaulis satelles	76.3955	138	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050995.1	s__Glycocaulis profundi	76.356	132	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124675.1	s__Oceanicaulis sp016124675	76.2571	142	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001657295.1	s__Oceanicaulis sp001657295	76.2295	143	782	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:36:21,467] [INFO] GTDB search result was written to OceanDNA-b23907/result_gtdb.tsv
[2023-03-18 00:36:21,467] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:36:21,469] [INFO] DFAST_QC result json was written to OceanDNA-b23907/dqc_result.json
[2023-03-18 00:36:21,469] [INFO] DFAST_QC completed!
[2023-03-18 00:36:21,469] [INFO] Total running time: 0h1m15s