[2023-03-18 00:56:43,494] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:56:43,494] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:56:43,494] [INFO] DQC Reference Directory: /var/lib/cwl/stg7395dcab-0532-4bd2-93a4-b7836ceb9930/dqc_reference
[2023-03-18 00:56:44,566] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:56:44,567] [INFO] Task started: Prodigal
[2023-03-18 00:56:44,567] [INFO] Running command: cat /var/lib/cwl/stg043efa9f-5d90-4d65-87ea-ef8a2fcf0425/OceanDNA-b28102.fa | prodigal -d OceanDNA-b28102/cds.fna -a OceanDNA-b28102/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:57:01,234] [INFO] Task succeeded: Prodigal
[2023-03-18 00:57:01,235] [INFO] Task started: HMMsearch
[2023-03-18 00:57:01,235] [INFO] Running command: hmmsearch --tblout OceanDNA-b28102/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7395dcab-0532-4bd2-93a4-b7836ceb9930/dqc_reference/reference_markers.hmm OceanDNA-b28102/protein.faa > /dev/null
[2023-03-18 00:57:01,417] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:57:01,417] [INFO] Found 6/6 markers.
[2023-03-18 00:57:01,438] [INFO] Query marker FASTA was written to OceanDNA-b28102/markers.fasta
[2023-03-18 00:57:01,439] [INFO] Task started: Blastn
[2023-03-18 00:57:01,439] [INFO] Running command: blastn -query OceanDNA-b28102/markers.fasta -db /var/lib/cwl/stg7395dcab-0532-4bd2-93a4-b7836ceb9930/dqc_reference/reference_markers.fasta -out OceanDNA-b28102/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:57:02,175] [INFO] Task succeeded: Blastn
[2023-03-18 00:57:02,176] [INFO] Selected 31 target genomes.
[2023-03-18 00:57:02,176] [INFO] Target genome list was writen to OceanDNA-b28102/target_genomes.txt
[2023-03-18 00:57:02,203] [INFO] Task started: fastANI
[2023-03-18 00:57:02,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg043efa9f-5d90-4d65-87ea-ef8a2fcf0425/OceanDNA-b28102.fa --refList OceanDNA-b28102/target_genomes.txt --output OceanDNA-b28102/fastani_result.tsv --threads 1
[2023-03-18 00:57:20,174] [INFO] Task succeeded: fastANI
[2023-03-18 00:57:20,174] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7395dcab-0532-4bd2-93a4-b7836ceb9930/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:57:20,174] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7395dcab-0532-4bd2-93a4-b7836ceb9930/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:57:20,190] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:57:20,190] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:57:20,191] [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
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	78.9656	390	899	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.123	155	899	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.1173	156	899	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.9381	152	899	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	76.9345	193	899	95	below_threshold
Boseongicola aestuarii	strain=CECT 8489	GCA_900184815.1	1470561	1470561	type	True	76.9224	189	899	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	76.9191	196	899	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	76.8268	122	899	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	76.8025	157	899	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.8004	150	899	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	76.7028	132	899	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	76.6415	161	899	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	76.6336	158	899	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	76.6286	157	899	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	76.6004	148	899	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	76.5264	146	899	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	76.5219	143	899	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	76.5211	143	899	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	76.475	115	899	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	76.4612	148	899	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	76.318	114	899	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.3089	120	899	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.3089	120	899	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	76.3047	70	899	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	76.2572	68	899	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	76.256	97	899	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	76.256	97	899	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001404195.1	481446	481446	type	True	76.256	97	899	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	76.2041	105	899	95	below_threshold
Shimia abyssi	strain=DSM 100673	GCA_003014475.1	1662395	1662395	type	True	76.0711	67	899	95	below_threshold
Haematobacter massiliensis	strain=CCUG 47968	GCA_000740795.1	195105	195105	type	True	75.6168	67	899	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:57:20,191] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28102/tc_result.tsv
[2023-03-18 00:57:20,192] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:57:20,192] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:57:20,192] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7395dcab-0532-4bd2-93a4-b7836ceb9930/dqc_reference/checkm_data
[2023-03-18 00:57:20,193] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:57:20,198] [INFO] Task started: CheckM
[2023-03-18 00:57:20,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28102/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28102/checkm_input OceanDNA-b28102/checkm_result
[2023-03-18 00:58:03,690] [INFO] Task succeeded: CheckM
[2023-03-18 00:58:03,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:58:03,696] [INFO] ===== Completeness check finished =====
[2023-03-18 00:58:03,696] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:58:03,696] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28102/markers.fasta)
[2023-03-18 00:58:03,697] [INFO] Task started: Blastn
[2023-03-18 00:58:03,697] [INFO] Running command: blastn -query OceanDNA-b28102/markers.fasta -db /var/lib/cwl/stg7395dcab-0532-4bd2-93a4-b7836ceb9930/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28102/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:58:04,973] [INFO] Task succeeded: Blastn
[2023-03-18 00:58:04,975] [INFO] Selected 29 target genomes.
[2023-03-18 00:58:04,975] [INFO] Target genome list was writen to OceanDNA-b28102/target_genomes_gtdb.txt
[2023-03-18 00:58:04,998] [INFO] Task started: fastANI
[2023-03-18 00:58:04,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg043efa9f-5d90-4d65-87ea-ef8a2fcf0425/OceanDNA-b28102.fa --refList OceanDNA-b28102/target_genomes_gtdb.txt --output OceanDNA-b28102/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:58:23,492] [INFO] Task succeeded: fastANI
[2023-03-18 00:58:23,507] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:58:23,508] [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_009830125.1	s__GH1-50 sp009830125	78.9769	388	899	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_017792445.1	s__Rhodobacter_B sp017792445	77.0826	181	899	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	76.9977	170	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116585.1	s__Albibacillus kandeliae	76.9512	161	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148765.1	s__Silicimonas algicola	76.9479	192	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Silicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900184815.1	s__Boseongicola aestuarii	76.9352	188	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002973535.1	s__Albidovulum denitrificans	76.8289	127	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	76.807	192	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	76.7471	153	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	76.7418	143	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002465.1	s__JABDJO01 sp013002465	76.7188	155	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152625.1	s__Roseovarius nubinhibens	76.7028	132	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCA_015487335.1	s__S012-89 sp015487335	76.6848	86	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__S012-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042105.1	s__Boseongicola sp013042105	76.6706	127	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	99.16	99.16	0.85	0.85	2	-
GCA_014762635.1	s__JABURR01 sp014762635	76.6614	169	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABURR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701395.1	s__Rhodobacter_B sp002701395	76.6531	177	899	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_015223355.1	s__Salipiger pacificus_B	76.6333	160	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500245.1	s__Ruegeria_B sp010500245	76.6172	166	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	76.5368	124	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379485.1	s__Wenxinia marina	76.5085	144	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_003789055.1	s__Oceanicola lentulus	76.5021	157	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018145.1	s__Dinoroseobacter shibae	76.4747	147	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Dinoroseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014075275.1	s__Boseongicola sp014075275	76.469	112	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	99.87	99.87	0.99	0.99	2	-
GCF_900110775.1	s__Litorimicrobium taeanense	76.4658	104	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142295.1	s__Vannielia litorea	76.3386	125	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116005.1	s__Poseidonocella sedimentorum	76.3035	143	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Poseidonocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114635.1	s__Shimia aestuarii	76.2126	127	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652355.1	s__Gemmobacter lanyuensis	76.2041	105	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006351965.1	s__Vannielia sp006351965	76.173	126	899	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:58:23,509] [INFO] GTDB search result was written to OceanDNA-b28102/result_gtdb.tsv
[2023-03-18 00:58:23,510] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:58:23,514] [INFO] DFAST_QC result json was written to OceanDNA-b28102/dqc_result.json
[2023-03-18 00:58:23,514] [INFO] DFAST_QC completed!
[2023-03-18 00:58:23,514] [INFO] Total running time: 0h1m40s