[2023-03-18 21:08:04,366] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:08:04,366] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:08:04,366] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a909963-9e4f-4062-9a5c-b77767759958/dqc_reference
[2023-03-18 21:08:05,487] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:08:05,488] [INFO] Task started: Prodigal
[2023-03-18 21:08:05,488] [INFO] Running command: cat /var/lib/cwl/stg80c9e2bc-9a13-4a06-9a52-e9dcaf5d7abb/OceanDNA-b30046.fa | prodigal -d OceanDNA-b30046/cds.fna -a OceanDNA-b30046/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:08:17,877] [INFO] Task succeeded: Prodigal
[2023-03-18 21:08:17,877] [INFO] Task started: HMMsearch
[2023-03-18 21:08:17,878] [INFO] Running command: hmmsearch --tblout OceanDNA-b30046/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a909963-9e4f-4062-9a5c-b77767759958/dqc_reference/reference_markers.hmm OceanDNA-b30046/protein.faa > /dev/null
[2023-03-18 21:08:18,084] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:08:18,085] [INFO] Found 6/6 markers.
[2023-03-18 21:08:18,117] [INFO] Query marker FASTA was written to OceanDNA-b30046/markers.fasta
[2023-03-18 21:08:18,118] [INFO] Task started: Blastn
[2023-03-18 21:08:18,118] [INFO] Running command: blastn -query OceanDNA-b30046/markers.fasta -db /var/lib/cwl/stg8a909963-9e4f-4062-9a5c-b77767759958/dqc_reference/reference_markers.fasta -out OceanDNA-b30046/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:08:18,940] [INFO] Task succeeded: Blastn
[2023-03-18 21:08:18,941] [INFO] Selected 28 target genomes.
[2023-03-18 21:08:18,941] [INFO] Target genome list was writen to OceanDNA-b30046/target_genomes.txt
[2023-03-18 21:08:18,956] [INFO] Task started: fastANI
[2023-03-18 21:08:18,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg80c9e2bc-9a13-4a06-9a52-e9dcaf5d7abb/OceanDNA-b30046.fa --refList OceanDNA-b30046/target_genomes.txt --output OceanDNA-b30046/fastani_result.tsv --threads 1
[2023-03-18 21:08:37,840] [INFO] Task succeeded: fastANI
[2023-03-18 21:08:37,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a909963-9e4f-4062-9a5c-b77767759958/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:08:37,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a909963-9e4f-4062-9a5c-b77767759958/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:08:37,855] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:08:37,856] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:08:37,856] [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
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	78.0385	167	586	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	78.0376	152	586	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	78.0163	171	586	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	77.9771	187	586	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	77.9529	178	586	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	77.9255	155	586	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	77.9209	179	586	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.9114	157	586	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	77.8235	162	586	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	77.8224	129	586	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.7902	137	586	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	77.7675	204	586	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	77.729	175	586	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	77.6639	180	586	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	77.6089	184	586	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	77.5517	159	586	95	below_threshold
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	77.3781	61	586	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	77.3311	148	586	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	77.1919	128	586	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.1459	123	586	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.1192	146	586	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	77.0727	126	586	95	below_threshold
Aliiroseovarius zhejiangensis	strain=KCTC 42443	GCA_014656375.1	1632025	1632025	type	True	77.0487	107	586	95	below_threshold
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	76.9797	84	586	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.9075	130	586	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.8714	130	586	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.6256	109	586	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:08:37,856] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30046/tc_result.tsv
[2023-03-18 21:08:37,856] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:08:37,856] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:08:37,856] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a909963-9e4f-4062-9a5c-b77767759958/dqc_reference/checkm_data
[2023-03-18 21:08:37,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:08:37,863] [INFO] Task started: CheckM
[2023-03-18 21:08:37,863] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30046/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30046/checkm_input OceanDNA-b30046/checkm_result
[2023-03-18 21:09:12,278] [INFO] Task succeeded: CheckM
[2023-03-18 21:09:12,278] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:09:12,298] [INFO] ===== Completeness check finished =====
[2023-03-18 21:09:12,298] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:09:12,298] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30046/markers.fasta)
[2023-03-18 21:09:12,299] [INFO] Task started: Blastn
[2023-03-18 21:09:12,299] [INFO] Running command: blastn -query OceanDNA-b30046/markers.fasta -db /var/lib/cwl/stg8a909963-9e4f-4062-9a5c-b77767759958/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30046/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:09:13,790] [INFO] Task succeeded: Blastn
[2023-03-18 21:09:13,791] [INFO] Selected 21 target genomes.
[2023-03-18 21:09:13,791] [INFO] Target genome list was writen to OceanDNA-b30046/target_genomes_gtdb.txt
[2023-03-18 21:09:13,840] [INFO] Task started: fastANI
[2023-03-18 21:09:13,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg80c9e2bc-9a13-4a06-9a52-e9dcaf5d7abb/OceanDNA-b30046.fa --refList OceanDNA-b30046/target_genomes_gtdb.txt --output OceanDNA-b30046/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:09:31,928] [INFO] Task succeeded: fastANI
[2023-03-18 21:09:31,940] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:09:31,940] [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
GCA_002701395.1	s__Rhodobacter_B sp002701395	99.9184	585	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017792445.1	s__Rhodobacter_B sp017792445	87.0126	483	586	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_013184805.1	s__Rhodobacter_B sp013184805	79.4851	266	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	78.6972	192	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.0677	198	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882975.1	s__Maritimibacter harenae	78.0376	152	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969385.1	s__Salipiger profundus	78.0159	171	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_000153725.1	s__Salipiger bermudensis	77.9753	187	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	77.9529	178	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004343075.1	s__Rhodovulum marinum	77.844	161	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	77.8026	174	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	77.7958	130	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	77.7512	205	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_900101505.1	s__Mameliella alba	77.6869	178	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_015223355.1	s__Salipiger pacificus_B	77.6757	203	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142295.1	s__Vannielia litorea	77.5797	150	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001078595.1	s__Rhodobacter_B lobularis	77.2998	156	586	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_005870025.1	s__Mangrovicoccus sp005870025	77.1927	176	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008555.2	s__Pukyongiella litopenaei	77.1726	160	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711185.1	s__Paracoccus limosus	77.0727	126	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	76.8714	130	586	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
--------------------------------------------------------------------------------
[2023-03-18 21:09:31,940] [INFO] GTDB search result was written to OceanDNA-b30046/result_gtdb.tsv
[2023-03-18 21:09:31,940] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:09:31,943] [INFO] DFAST_QC result json was written to OceanDNA-b30046/dqc_result.json
[2023-03-18 21:09:31,943] [INFO] DFAST_QC completed!
[2023-03-18 21:09:31,943] [INFO] Total running time: 0h1m28s