[2023-03-15 15:18:22,102] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:18:22,102] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:18:22,103] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b1eb299-92ae-42ca-b61d-f1dd8f7ed030/dqc_reference
[2023-03-15 15:18:23,235] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:18:23,235] [INFO] Task started: Prodigal
[2023-03-15 15:18:23,235] [INFO] Running command: cat /var/lib/cwl/stg890c3ead-3ad8-4575-bf92-5bb5ff8f9b53/OceanDNA-b30773.fa | prodigal -d OceanDNA-b30773/cds.fna -a OceanDNA-b30773/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:18:45,632] [INFO] Task succeeded: Prodigal
[2023-03-15 15:18:45,632] [INFO] Task started: HMMsearch
[2023-03-15 15:18:45,632] [INFO] Running command: hmmsearch --tblout OceanDNA-b30773/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b1eb299-92ae-42ca-b61d-f1dd8f7ed030/dqc_reference/reference_markers.hmm OceanDNA-b30773/protein.faa > /dev/null
[2023-03-15 15:18:45,844] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:18:45,845] [INFO] Found 6/6 markers.
[2023-03-15 15:18:45,872] [INFO] Query marker FASTA was written to OceanDNA-b30773/markers.fasta
[2023-03-15 15:18:45,873] [INFO] Task started: Blastn
[2023-03-15 15:18:45,873] [INFO] Running command: blastn -query OceanDNA-b30773/markers.fasta -db /var/lib/cwl/stg5b1eb299-92ae-42ca-b61d-f1dd8f7ed030/dqc_reference/reference_markers.fasta -out OceanDNA-b30773/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:18:46,756] [INFO] Task succeeded: Blastn
[2023-03-15 15:18:46,760] [INFO] Selected 33 target genomes.
[2023-03-15 15:18:46,760] [INFO] Target genome list was writen to OceanDNA-b30773/target_genomes.txt
[2023-03-15 15:18:46,782] [INFO] Task started: fastANI
[2023-03-15 15:18:46,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg890c3ead-3ad8-4575-bf92-5bb5ff8f9b53/OceanDNA-b30773.fa --refList OceanDNA-b30773/target_genomes.txt --output OceanDNA-b30773/fastani_result.tsv --threads 1
[2023-03-15 15:19:13,172] [INFO] Task succeeded: fastANI
[2023-03-15 15:19:13,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b1eb299-92ae-42ca-b61d-f1dd8f7ed030/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:19:13,173] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b1eb299-92ae-42ca-b61d-f1dd8f7ed030/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:19:13,190] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:19:13,190] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 15:19:13,191] [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
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.8391	257	1206	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.8294	190	1206	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.7806	201	1206	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	76.7687	239	1206	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.5954	217	1206	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	76.5813	211	1206	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.5698	225	1206	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.5439	188	1206	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.5275	202	1206	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.4986	248	1206	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.4324	262	1206	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.4196	265	1206	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	76.3974	153	1206	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	76.3485	217	1206	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_008630015.1	140057	140057	type	True	76.333	160	1206	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014197855.1	140057	140057	type	True	76.3196	158	1206	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014203135.1	140057	140057	type	True	76.3164	157	1206	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.2476	200	1206	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	76.2151	157	1206	95	below_threshold
Fodinicurvata sediminis	strain=DSM 21159	GCA_000420625.1	1121832	1121832	type	True	76.2109	58	1206	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	76.1855	189	1206	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	76.1194	258	1206	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	76.1071	216	1206	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	76.0656	214	1206	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	76.033	203	1206	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.0329	159	1206	95	below_threshold
Methylobacterium currus	strain=PR1016A	GCA_003058325.1	2051553	2051553	type	True	76.0133	201	1206	95	below_threshold
Methylobacterium ajmalii	strain=IF7SW-B2	GCA_016613415.1	2738439	2738439	type	True	75.9364	225	1206	95	below_threshold
Telmatospirillum siberiense	strain=26-4b1	GCA_002845745.1	382514	382514	type	True	75.9156	164	1206	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	75.7046	190	1206	95	below_threshold
Elstera cyanobacteriorum	strain=CGMCC 1.15802	GCA_014643715.1	2022747	2022747	type	True	75.5154	82	1206	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.354	123	1206	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.1683	113	1206	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:19:13,192] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30773/tc_result.tsv
[2023-03-15 15:19:13,196] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:19:13,196] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:19:13,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b1eb299-92ae-42ca-b61d-f1dd8f7ed030/dqc_reference/checkm_data
[2023-03-15 15:19:13,196] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:19:13,206] [INFO] Task started: CheckM
[2023-03-15 15:19:13,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30773/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30773/checkm_input OceanDNA-b30773/checkm_result
[2023-03-15 15:20:07,992] [INFO] Task succeeded: CheckM
[2023-03-15 15:20:07,993] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:20:08,055] [INFO] ===== Completeness check finished =====
[2023-03-15 15:20:08,055] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:20:08,055] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30773/markers.fasta)
[2023-03-15 15:20:08,056] [INFO] Task started: Blastn
[2023-03-15 15:20:08,056] [INFO] Running command: blastn -query OceanDNA-b30773/markers.fasta -db /var/lib/cwl/stg5b1eb299-92ae-42ca-b61d-f1dd8f7ed030/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30773/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:20:09,825] [INFO] Task succeeded: Blastn
[2023-03-15 15:20:09,829] [INFO] Selected 27 target genomes.
[2023-03-15 15:20:09,829] [INFO] Target genome list was writen to OceanDNA-b30773/target_genomes_gtdb.txt
[2023-03-15 15:20:09,857] [INFO] Task started: fastANI
[2023-03-15 15:20:09,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg890c3ead-3ad8-4575-bf92-5bb5ff8f9b53/OceanDNA-b30773.fa --refList OceanDNA-b30773/target_genomes_gtdb.txt --output OceanDNA-b30773/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:20:26,666] [INFO] Task succeeded: fastANI
[2023-03-15 15:20:26,681] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:20:26,681] [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_016872535.1	s__2-12-FULL-67-15 sp016872535	78.3346	375	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	95.80	95.80	0.86	0.86	2	-
GCA_016187325.1	s__JACPJY01 sp016187325	77.8613	270	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693905.1	s__2-12-FULL-67-15 sp009693905	77.8508	244	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	99.79	99.79	0.72	0.72	2	-
GCA_001830475.1	s__2-12-FULL-67-15 sp001830475	77.7508	226	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002781745.1	s__UBA1479 sp002781745	77.5687	317	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	77.3996	258	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_014382345.1	s__Casp-alpha2 sp014382345	77.2377	221	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.86	99.86	0.92	0.92	2	-
GCA_009694195.1	s__SHVQ01 sp009694195	77.1223	166	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__SHVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002938075.1	s__Casp-alpha2 sp002938075	77.0934	202	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	98.70	98.63	0.78	0.77	3	-
GCF_902729435.1	s__Magnetospirillum sp902729435	77.0334	247	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001510075.1	s__Casp-alpha2 sp001510075	77.0072	104	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859895.1	s__JACZKS01 sp014859895	77.0022	250	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018432935.1	s__JAHDSF01 sp018432935	76.9966	233	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JAHDSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001511835.1	s__Phaeospirillum sp001511835	76.7989	207	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008843145.1	s__Skermanella pratensis	76.7235	223	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	76.7137	276	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204045.1	s__JABMOQ01 sp013204045	76.6019	112	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16_A;g__JABMOQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823745.1	s__Oceanibaculum sp018823745	76.5442	171	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCF_002148795.1	s__Oceanibaculum nanhaiense	76.5267	202	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903907895.1	s__CAIVPW01 sp903907895	76.4623	88	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CAIVPW01;f__CAIVPW01;g__CAIVPW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869315.1	s__VGEM01 sp016869315	76.4338	91	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__VGEM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620685.1	s__Dongia sp000620685	76.3848	151	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Dongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001830425.1	s__2-02-FULL-58-16 sp001830425	76.3037	115	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16;g__2-02-FULL-58-16	95.0	99.96	99.96	0.97	0.97	2	-
GCF_000013085.1	s__Rhodospirillum rubrum	76.2142	157	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospirillum	95.0	98.74	96.31	0.98	0.96	7	-
GCF_900103365.1	s__Bradyrhizobium sp900103365	76.0424	193	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576765.1	s__PRO6 sp003576765	76.0394	124	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__PRO6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019244115.1	s__Bradyrhizobium sp019244115	75.7293	116	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.31	99.31	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-15 15:20:26,683] [INFO] GTDB search result was written to OceanDNA-b30773/result_gtdb.tsv
[2023-03-15 15:20:26,687] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:20:26,691] [INFO] DFAST_QC result json was written to OceanDNA-b30773/dqc_result.json
[2023-03-15 15:20:26,691] [INFO] DFAST_QC completed!
[2023-03-15 15:20:26,691] [INFO] Total running time: 0h2m5s