[2023-03-19 02:20:30,902] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:20:30,903] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:20:30,903] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc6a2eb9-1ae3-4e43-8b72-74bcdd03c338/dqc_reference
[2023-03-19 02:20:32,056] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:20:32,056] [INFO] Task started: Prodigal
[2023-03-19 02:20:32,057] [INFO] Running command: cat /var/lib/cwl/stg4b3cf938-a9cd-4bf1-9cf1-1d566c06822e/OceanDNA-b30042.fa | prodigal -d OceanDNA-b30042/cds.fna -a OceanDNA-b30042/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:20:58,876] [INFO] Task succeeded: Prodigal
[2023-03-19 02:20:58,876] [INFO] Task started: HMMsearch
[2023-03-19 02:20:58,877] [INFO] Running command: hmmsearch --tblout OceanDNA-b30042/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc6a2eb9-1ae3-4e43-8b72-74bcdd03c338/dqc_reference/reference_markers.hmm OceanDNA-b30042/protein.faa > /dev/null
[2023-03-19 02:20:59,092] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:20:59,093] [INFO] Found 6/6 markers.
[2023-03-19 02:20:59,121] [INFO] Query marker FASTA was written to OceanDNA-b30042/markers.fasta
[2023-03-19 02:20:59,122] [INFO] Task started: Blastn
[2023-03-19 02:20:59,122] [INFO] Running command: blastn -query OceanDNA-b30042/markers.fasta -db /var/lib/cwl/stgcc6a2eb9-1ae3-4e43-8b72-74bcdd03c338/dqc_reference/reference_markers.fasta -out OceanDNA-b30042/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:20:59,945] [INFO] Task succeeded: Blastn
[2023-03-19 02:20:59,946] [INFO] Selected 27 target genomes.
[2023-03-19 02:20:59,947] [INFO] Target genome list was writen to OceanDNA-b30042/target_genomes.txt
[2023-03-19 02:20:59,965] [INFO] Task started: fastANI
[2023-03-19 02:20:59,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b3cf938-a9cd-4bf1-9cf1-1d566c06822e/OceanDNA-b30042.fa --refList OceanDNA-b30042/target_genomes.txt --output OceanDNA-b30042/fastani_result.tsv --threads 1
[2023-03-19 02:21:23,163] [INFO] Task succeeded: fastANI
[2023-03-19 02:21:23,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc6a2eb9-1ae3-4e43-8b72-74bcdd03c338/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:21:23,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc6a2eb9-1ae3-4e43-8b72-74bcdd03c338/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:21:23,179] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:21:23,179] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:21:23,179] [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
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	80.4157	701	1408	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	80.0514	676	1408	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	80.0329	653	1408	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	79.9936	713	1408	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	79.8938	707	1408	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	79.8263	711	1408	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	79.6771	627	1408	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	79.6565	669	1408	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	79.6272	671	1408	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	79.6253	709	1408	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	79.5293	605	1408	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	79.5152	595	1408	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	79.5029	652	1408	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	79.4828	596	1408	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.3029	533	1408	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	79.1979	544	1408	95	below_threshold
Roseivivax halotolerans	strain=JCM 10271	GCA_900115815.1	93684	93684	type	True	79.066	531	1408	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	79.0331	599	1408	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	78.8542	494	1408	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.8034	518	1408	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	78.8027	521	1408	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	78.6586	514	1408	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.5809	455	1408	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	78.5206	452	1408	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	78.4234	532	1408	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	78.2067	418	1408	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.169	448	1408	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:21:23,180] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30042/tc_result.tsv
[2023-03-19 02:21:23,181] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:21:23,181] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:21:23,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc6a2eb9-1ae3-4e43-8b72-74bcdd03c338/dqc_reference/checkm_data
[2023-03-19 02:21:23,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:21:23,321] [INFO] Task started: CheckM
[2023-03-19 02:21:23,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30042/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30042/checkm_input OceanDNA-b30042/checkm_result
[2023-03-19 02:22:31,756] [INFO] Task succeeded: CheckM
[2023-03-19 02:22:31,756] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:22:31,765] [INFO] ===== Completeness check finished =====
[2023-03-19 02:22:31,766] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:22:31,766] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30042/markers.fasta)
[2023-03-19 02:22:31,767] [INFO] Task started: Blastn
[2023-03-19 02:22:31,767] [INFO] Running command: blastn -query OceanDNA-b30042/markers.fasta -db /var/lib/cwl/stgcc6a2eb9-1ae3-4e43-8b72-74bcdd03c338/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30042/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:22:33,186] [INFO] Task succeeded: Blastn
[2023-03-19 02:22:33,189] [INFO] Selected 21 target genomes.
[2023-03-19 02:22:33,189] [INFO] Target genome list was writen to OceanDNA-b30042/target_genomes_gtdb.txt
[2023-03-19 02:22:33,204] [INFO] Task started: fastANI
[2023-03-19 02:22:33,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b3cf938-a9cd-4bf1-9cf1-1d566c06822e/OceanDNA-b30042.fa --refList OceanDNA-b30042/target_genomes_gtdb.txt --output OceanDNA-b30042/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:22:52,921] [INFO] Task succeeded: fastANI
[2023-03-19 02:22:52,933] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:22:52,933] [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_003344785.1	s__Puniceibacterium profundi	98.0261	1307	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900156805.1	s__Roseivivax lentus	80.4328	699	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184945.1	s__Maliponia aquimaris	80.0511	737	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969385.1	s__Salipiger profundus	80.0489	675	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_900102075.1	s__Salipiger thiooxidans	80.0276	708	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_000153725.1	s__Salipiger bermudensis	79.9081	704	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_900107235.1	s__Citreimonas salinaria	79.9056	638	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	79.8989	705	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	79.8896	687	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	79.8228	711	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923445.1	s__Puniceibacterium confluentis	79.64	707	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003111685.1	s__Salipiger pacificus_A	79.5832	655	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
GCF_002814095.1	s__Sagittula sp002814095	79.5721	726	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054175.1	s__Allosediminivita pacifica	79.4617	599	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Allosediminivita	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.2992	556	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	79.1309	414	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169415.1	s__Sagittula stellata	79.1026	621	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188035.1	s__Puniceibacterium sediminis	79.0484	597	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	78.9799	494	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002786295.1	s__Pseudooceanicola marinus	78.8075	518	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003072125.1	s__Roseovarius sediminicola	78.1855	446	1408	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:22:52,935] [INFO] GTDB search result was written to OceanDNA-b30042/result_gtdb.tsv
[2023-03-19 02:22:52,939] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:22:52,942] [INFO] DFAST_QC result json was written to OceanDNA-b30042/dqc_result.json
[2023-03-19 02:22:52,942] [INFO] DFAST_QC completed!
[2023-03-19 02:22:52,942] [INFO] Total running time: 0h2m22s