[2023-03-16 03:23:49,693] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:49,693] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:49,693] [INFO] DQC Reference Directory: /var/lib/cwl/stg60b285e6-d5d8-4d8e-b520-e976035f5dea/dqc_reference
[2023-03-16 03:23:50,862] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:50,862] [INFO] Task started: Prodigal
[2023-03-16 03:23:50,862] [INFO] Running command: cat /var/lib/cwl/stg19ebdad1-40ba-4beb-ad93-cfbcb2e39925/OceanDNA-b28083.fa | prodigal -d OceanDNA-b28083/cds.fna -a OceanDNA-b28083/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:24:06,337] [INFO] Task succeeded: Prodigal
[2023-03-16 03:24:06,338] [INFO] Task started: HMMsearch
[2023-03-16 03:24:06,338] [INFO] Running command: hmmsearch --tblout OceanDNA-b28083/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60b285e6-d5d8-4d8e-b520-e976035f5dea/dqc_reference/reference_markers.hmm OceanDNA-b28083/protein.faa > /dev/null
[2023-03-16 03:24:06,578] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:24:06,579] [INFO] Found 6/6 markers.
[2023-03-16 03:24:06,600] [INFO] Query marker FASTA was written to OceanDNA-b28083/markers.fasta
[2023-03-16 03:24:06,600] [INFO] Task started: Blastn
[2023-03-16 03:24:06,600] [INFO] Running command: blastn -query OceanDNA-b28083/markers.fasta -db /var/lib/cwl/stg60b285e6-d5d8-4d8e-b520-e976035f5dea/dqc_reference/reference_markers.fasta -out OceanDNA-b28083/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:07,204] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:07,205] [INFO] Selected 28 target genomes.
[2023-03-16 03:24:07,205] [INFO] Target genome list was writen to OceanDNA-b28083/target_genomes.txt
[2023-03-16 03:24:07,223] [INFO] Task started: fastANI
[2023-03-16 03:24:07,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg19ebdad1-40ba-4beb-ad93-cfbcb2e39925/OceanDNA-b28083.fa --refList OceanDNA-b28083/target_genomes.txt --output OceanDNA-b28083/fastani_result.tsv --threads 1
[2023-03-16 03:24:24,693] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:24,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60b285e6-d5d8-4d8e-b520-e976035f5dea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:24,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60b285e6-d5d8-4d8e-b520-e976035f5dea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:24,706] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:24,707] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:24:24,707] [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
Boseongicola aestuarii	strain=CECT 8489	GCA_900184815.1	1470561	1470561	type	True	77.556	247	803	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	76.7941	131	803	95	below_threshold
Aliiroseovarius zhejiangensis	strain=KCTC 42443	GCA_014656375.1	1632025	1632025	type	True	76.3564	66	803	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	76.3562	59	803	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	76.3282	60	803	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	76.3126	89	803	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	76.2939	78	803	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	76.2909	90	803	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	76.2749	79	803	95	below_threshold
Ruegeria denitrificans	strain=CECT 5091	GCA_001458295.1	1715692	1715692	type	True	76.1188	58	803	95	below_threshold
Tateyamaria pelophila	strain=DSM 17270	GCA_019966495.1	328415	328415	type	True	76.0259	53	803	95	below_threshold
Ruegeria meonggei	strain=CECT 8411	GCA_900172215.1	1446476	1446476	type	True	76.0127	57	803	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	75.9442	59	803	95	below_threshold
Pseudopuniceibacterium sediminis	strain=CY03	GCA_003575965.1	2211117	2211117	type	True	75.9407	56	803	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	75.9156	70	803	95	below_threshold
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	75.8876	67	803	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	75.8681	57	803	95	below_threshold
Thalassobius mediterraneus	strain=CECT 5383	GCA_001458435.1	340021	340021	type	True	75.8193	67	803	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	75.7573	73	803	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	75.7541	50	803	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	75.672	68	803	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	75.6623	61	803	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	75.6442	66	803	95	below_threshold
Yoonia maricola	strain=DSM 29128	GCA_002797915.1	420999	420999	type	True	75.4859	52	803	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:24:24,707] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28083/tc_result.tsv
[2023-03-16 03:24:24,707] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:24,707] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:24,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60b285e6-d5d8-4d8e-b520-e976035f5dea/dqc_reference/checkm_data
[2023-03-16 03:24:24,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:24,713] [INFO] Task started: CheckM
[2023-03-16 03:24:24,713] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28083/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28083/checkm_input OceanDNA-b28083/checkm_result
[2023-03-16 03:25:05,930] [INFO] Task succeeded: CheckM
[2023-03-16 03:25:05,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.17%
Contamintation: 8.33%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-16 03:25:05,933] [INFO] ===== Completeness check finished =====
[2023-03-16 03:25:05,934] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:25:05,934] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28083/markers.fasta)
[2023-03-16 03:25:05,934] [INFO] Task started: Blastn
[2023-03-16 03:25:05,934] [INFO] Running command: blastn -query OceanDNA-b28083/markers.fasta -db /var/lib/cwl/stg60b285e6-d5d8-4d8e-b520-e976035f5dea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28083/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:25:06,818] [INFO] Task succeeded: Blastn
[2023-03-16 03:25:06,819] [INFO] Selected 22 target genomes.
[2023-03-16 03:25:06,819] [INFO] Target genome list was writen to OceanDNA-b28083/target_genomes_gtdb.txt
[2023-03-16 03:25:07,069] [INFO] Task started: fastANI
[2023-03-16 03:25:07,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg19ebdad1-40ba-4beb-ad93-cfbcb2e39925/OceanDNA-b28083.fa --refList OceanDNA-b28083/target_genomes_gtdb.txt --output OceanDNA-b28083/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:25:20,737] [INFO] Task succeeded: fastANI
[2023-03-16 03:25:20,748] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:25:20,749] [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_900184815.1	s__Boseongicola aestuarii	77.556	247	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479635.1	s__Boseongicola sp905479635	77.4184	139	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042105.1	s__Boseongicola sp013042105	77.3427	206	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	99.16	99.16	0.85	0.85	2	-
GCA_013042895.1	s__Boseongicola sp013042895	77.239	123	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	98.28	98.28	0.61	0.61	2	-
GCA_009830125.1	s__GH1-50 sp009830125	76.7758	132	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014075275.1	s__Boseongicola sp014075275	76.715	123	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	99.87	99.87	0.99	0.99	2	-
GCA_013002465.1	s__JABDJO01 sp013002465	76.5815	94	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	76.3132	76	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768315.1	s__Pseudooceanicola atlanticus	76.3055	64	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.92	0.92	2	-
GCF_002285415.1	s__Actibacterium pelagium	76.2939	78	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013003245.1	s__JABDJX01 sp013003245	76.2043	93	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031355.1	s__Ruegeria arenilitoris_C	76.1297	71	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.51	99.51	0.98	0.98	2	-
GCF_000744955.1	s__Actibacterium sp000744955	76.1218	64	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458295.1	s__Ruegeria denitrificans	76.1188	58	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	76.0717	65	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000203975.2	s__Leisingera sp000203975	75.9477	69	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	75.9304	61	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001205715.1	s__Pseudaestuariivita atlantica	75.9177	84	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudaestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803475.1	s__Aliishimia ponticola	75.7767	72	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	75.6442	66	803	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
--------------------------------------------------------------------------------
[2023-03-16 03:25:20,749] [INFO] GTDB search result was written to OceanDNA-b28083/result_gtdb.tsv
[2023-03-16 03:25:20,749] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:25:20,751] [INFO] DFAST_QC result json was written to OceanDNA-b28083/dqc_result.json
[2023-03-16 03:25:20,751] [INFO] DFAST_QC completed!
[2023-03-16 03:25:20,751] [INFO] Total running time: 0h1m31s