search

oschwengers / asap

A scalable bacterial genome assembly, annotation and analysis pipeline
https://doi.org/10.1371/journal.pcbi.1007134
GNU General Public License v3.0
70 stars 19 forks source link

failed virulence factors and phylogeny analysis #2

Closed pavlo888 closed 5 years ago

pavlo888 commented 5 years ago

Hi,

First of, I just wanna say this pipeline is off the hook! it's truly amazing you have managed to streamline such a complete analysis!

However, I tested the pipeline with my own data but unfortunately the taxonomy classifcation failed, the MLST is empty, no virulence factors were detected, and phylogeny tabs present errors.

Additionally, the Annotation and Core/Pan Genome tabs show no results even though output files have been produced (I can see the files individually in the output folder). I am using a Safari browser running in Mac OS. I have tried opening the report files in Mozilla and apparently the files for Annotation and Core/Pan Genome cannot be found :(

I checked the log files for each sub-analysis and they state the following:

Taxonomy classification --> Error: Argument "num_threads". Illegal value, expected (>=1 and =<2):4' Error: (CArgException::eConstraint) Argument "num_threads". Illegal value, expected (>=1 and =<2): `4'

22:47:28.862 [main] ERROR asap-taxonomy - could not exec blastn!`

MLST --> 22:46:42.614 [main] INFO asap-mlst - exec: [/asap/share/blast/bin/blastn, -query, /data/scaffolds/Agrobacterium_rhizogenes_MAFF210265/Agrobacterium_rhizogenes_MAFF210265.fasta, -db, /asap/db/mlst/mlst, -num_threads, 1, -dust, no, -word_size, 32, -ungapped, -max_target_seqs, 100000, -perc_identity, 99, -outfmt, 6 sseqid slen length nident] 22:46:42.622 [main] INFO asap-mlst - ---------------------------------------------------------------------------------------------- 22:46:47.889 [main] INFO asap-mlst -

Virulence factors --> 23:09:34.790 [main] INFO asap-vf - exec: [/asap/share/blast/bin/blastp, -query, /data/annotations/Agrobacterium_rhizogenes_MAFF210265/Agrobacterium_rhizogenes_MAFF210265.faa, -db, /asap/db/sequences/vfdb, -num_threads, 1, -culling_limit, 2, -outfmt, 6 qseqid sseqid qcovs pident evalue bitscore stitle] 23:09:34.792 [main] INFO asap-vf - ---------------------------------------------------------------------------------------------- 23:11:18.192 [main] INFO asap-vf - ---------------------------------------------------------------------------------------------- 23:11:18.841 [main] DEBUG asap-vf - delete tmp-dir

Phylogeny --> 20:34:35.820 [main] ERROR asap-phylogeny - could not exec fasttreeMP!

Would you please help me solve these issues?

Thank you very much in advance. And again, killer pipeline!

Cheers, Pablo

oschwengers commented 5 years ago

Hi @pavlo888 , thanks a lot. Nice to hear that our pipeline might fit your needs!

Could you please provide some more information in order to debug?

If many analysis steps failed it's very likely, that a preceding step failed, e.g. assembly, scaffolding, annotation). To figure out which one failed I need the complete main log file.

pavlo888 commented 5 years ago

Hi @oschwengers,

I am using Docker version 2.1.0.1. Below you can find the complete log files:

This is the log for the annotation of one genome: [05:10:26] This is prokka 1.12 [05:10:26] Written by Torsten Seemann <torsten.seemann@gmail.com> [05:10:26] Homepage is https://github.com/tseemann/prokka [05:10:26] Local time is Tue Aug 27 05:10:26 2019 [05:10:26] You are not telling me who you are! [05:10:26] Operating system is linux [05:10:26] You have BioPerl 1.006924 [05:10:26] System has 2 cores. [05:10:26] Option --cpu asked for 8 cores, but system only has 2 [05:10:26] Will use maximum of 2 cores. [05:10:26] Annotating as >>> Bacteria <<< [05:10:26] Re-using existing --outdir /data/annotations/Agrobacterium_rhizogenes_ST15-16-021 [05:10:26] Using filename prefix: Agrobacterium_rhizogenes_ST15-16-021.XXX [05:10:26] Setting HMMER_NCPU=1 [05:10:26] Writing log to: /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.log [05:10:26] Command: /asap/share/prokka/bin/prokka --genus Agrobacterium --species rhizogenes --strain ST15-16-021 --prefix Agrobacterium_rhizogenes_ST15-16-021 --locustag Arhiz_ST15-16-021 --centre JLU --cpus 8 --outdir /data/annotations/Agrobacterium_rhizogenes_ST15-16-021 --proteins /asap/db/sequences/asap-proteins.faa --usegenus --force --addgenes --rfam --rawproduct /data/scaffolds/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021-pseudo.fasta [05:10:26] Appending to PATH: /asap/share/prokka-1.12/bin/../binaries/linux [05:10:26] Appending to PATH: /asap/share/prokka-1.12/bin/../binaries/linux/../common [05:10:26] Appending to PATH: /asap/share/prokka-1.12/bin [05:10:26] Looking for 'aragorn' - found /asap/share/prokka-1.12/bin/../binaries/linux/aragorn [05:10:26] Determined aragorn version is 1.2 [05:10:26] Looking for 'barrnap' - found /asap/share/barrnap/bin/barrnap [05:10:26] Determined barrnap version is 0.8 [05:10:26] Looking for 'blastp' - found /usr/bin/blastp [05:10:27] Determined blastp version is 2.2 [05:10:27] Looking for 'cmpress' - found /usr/bin/cmpress [05:10:27] Determined cmpress version is 1.1 [05:10:27] Looking for 'cmscan' - found /usr/bin/cmscan [05:10:27] Determined cmscan version is 1.1 [05:10:27] Looking for 'egrep' - found /bin/egrep [05:10:27] Looking for 'find' - found /usr/bin/find [05:10:27] Looking for 'grep' - found /bin/grep [05:10:27] Looking for 'hmmpress' - found /usr/bin/hmmpress [05:10:27] Determined hmmpress version is 3.1 [05:10:27] Looking for 'hmmscan' - found /usr/bin/hmmscan [05:10:27] Determined hmmscan version is 3.1 [05:10:27] Looking for 'java' - found /usr/bin/java [05:10:27] Looking for 'less' - found /usr/bin/less [05:10:27] Looking for 'makeblastdb' - found /usr/bin/makeblastdb [05:10:28] Determined makeblastdb version is 2.2 [05:10:28] Looking for 'minced' - found /asap/share/prokka-1.12/bin/../binaries/linux/../common/minced [05:10:29] Determined minced version is 2.0 [05:10:29] Looking for 'parallel' - found /usr/bin/parallel [05:10:29] Determined parallel version is 20161222 [05:10:29] Looking for 'prodigal' - found /asap/share/prokka-1.12/bin/../binaries/linux/prodigal [05:10:29] Determined prodigal version is 2.6 [05:10:29] Looking for 'prokka-genbank_to_fasta_db' - found /asap/share/prokka/bin/prokka-genbank_to_fasta_db [05:10:29] Looking for 'sed' - found /bin/sed [05:10:29] Looking for 'tbl2asn' - found /asap/share/prokka-1.12/bin/../binaries/linux/tbl2asn [05:10:30] Determined tbl2asn version is 25.6 [05:10:30] Using genetic code table 11. [05:10:30] Loading and checking input file: /data/scaffolds/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021-pseudo.fasta [05:10:31] Wrote 1 contigs totalling 5307354 bp. [05:10:31] Predicting tRNAs and tmRNAs [05:10:31] Running: aragorn -l -gc11 -w \/data\/annotations\/Agrobacterium_rhizogenes_ST15\-16\-021\/Agrobacterium_rhizogenes_ST15\-16\-021\.fna [05:10:41] 1 tRNA-Pro [31216,31292] 35 (ggg) [05:10:41] 2 tRNA-Asn [35327,35401] 33 (gtt) [05:10:41] 3 tRNA-Arg c[37388,37464] 35 (tct) [05:10:41] 4 tRNA-Leu c[86210,86295] 35 (taa) [05:10:41] 5 tRNA-Ser [193697,193786] 35 (tga) [05:10:41] 6 tRNA-Arg [226898,226993] 34 (gcg) [05:10:41] 7 tRNA-Asp c[432790,432866] 35 (gtc) [05:10:41] 8 tRNA-Asp c[432908,432984] 35 (gtc) [05:10:41] 9 tRNA-Val [433432,433507] 34 (tac) [05:10:41] 10 tRNA-Cys [435179,435252] 33 (gca) [05:10:41] 11 tRNA-Leu [503691,503773] 35 (tag) [05:10:41] 12 tRNA-Lys c[542433,542508] 34 (ctt) [05:10:41] 13 tRNA-Glu c[592753,592827] 34 (ttc) [05:10:41] 14 tRNA-Glu c[593277,593351] 34 (ttc) [05:10:41] 15 tRNA-Leu [615913,615997] 35 (gag) [05:10:41] 16 tRNA-Arg [782877,782953] 35 (ccg) [05:10:41] 17 tRNA-Met c[784041,784117] 35 (cat) [05:10:41] 18 tRNA-Val c[1036226,1036300] 33 (gac) [05:10:41] 19 tRNA-Met c[1146216,1146292] 35 (cat) [05:10:41] 20 tRNA-Ala [1242664,1242739] 34 (ggc) [05:10:41] 21 tRNA-Gln [1345274,1345347] 33 (ctg) [05:10:41] 22 tRNA-Pro c[1348928,1349004] 35 (cgg) [05:10:41] 23 tRNA-Gln c[1352617,1352691] 33 (ttg) [05:10:41] 24 tRNA-His c[1550614,1550690] 35 (gtg) [05:10:41] 25 tRNA-Thr c[1628190,1628264] 33 (ggt) [05:10:41] 26 tRNA-Phe c[1690420,1690495] 34 (gaa) [05:10:41] 27 tRNA-Gly c[1722656,1722729] 33 (ccc) [05:10:41] 28 tRNA-Thr [1742291,1742366] 34 (cgt) [05:10:41] 29 tRNA-Arg c[1769938,1770014] 35 (acg) [05:10:41] 30 tRNA-Lys [1905592,1905667] 34 (ttt) [05:10:41] 31 tRNA-Pro c[1912482,1912558] 35 (tgg) [05:10:41] 32 tRNA-Arg [1913181,1913257] 35 (tct) [05:10:41] 33 tRNA-Trp c[2059538,2059613] 34 (cca) [05:10:41] 34 tRNA-Gly c[2066075,2066148] 33 (tcc) [05:10:41] 35 tRNA-Tyr c[2066174,2066258] 35 (gta) [05:10:41] 36 tRNA-Thr c[2079699,2079774] 34 (tgt) [05:10:41] 37 tmRNA* [2128293,2128643] 219,260 ANDNNAKEYALAA* [05:10:41] 38 tRNA-Met c[2306063,2306138] 34 (cat) [05:10:41] 39 tRNA-Leu c[2686149,2686243] 33 (gag) [05:10:41] 40 tRNA-Tyr c[2974093,2974182] 32 (gta) [05:10:41] 41 tRNA-Ile [3367979,3368055] 35 (gat) [05:10:41] 42 tRNA-Ala [3368115,3368190] 34 (tgc) [05:10:41] 43 tRNA-Met [3372517,3372593] 35 (cat) [05:10:41] 44 tRNA-Met [3373378,3373454] 35 (cat) [05:10:41] 45 tRNA-Ser c[3438452,3438541] 35 (gga) [05:10:41] 46 tRNA-Leu c[3538056,3538142] 35 (cag) [05:10:41] 47 tRNA-Gly c[3683775,3683849] 33 (gcc) [05:10:41] 48 tRNA-Leu c[3809075,3809159] 35 (caa) [05:10:41] 49 tRNA-Ser [4238750,4238840] 35 (gct) [05:10:41] 50 tRNA-Gly [4355724,4355798] 33 (gcc) [05:10:41] 51 tRNA-Met c[4433177,4433253] 35 (cat) [05:10:41] 52 tRNA-Ser c[4924556,4924645] 35 (cga) [05:10:41] Found 52 tRNAs [05:10:41] Predicting Ribosomal RNAs [05:10:41] Running Barrnap with 2 threads [05:10:49] 1 gnl|JLU|Arhiz_ST15-16-021_1 3366187 16S ribosomal RNA [05:10:49] 2 gnl|JLU|Arhiz_ST15-16-021_1 3368693 23S ribosomal RNA [05:10:49] 3 gnl|JLU|Arhiz_ST15-16-021_1 3372151 5S ribosomal RNA [05:10:49] Found 3 rRNAs [05:10:49] Scanning for ncRNAs... please be patient. [05:10:49] Running: cmscan --rfam --cpu 2 -E 1e-06 --tblout /dev/stdout -o /dev/null --noali /asap/share/prokka-1.12/bin/../db/cm/Bacteria \/data\/annotations\/Agrobacterium_rhizogenes_ST15\-16\-021\/Agrobacterium_rhizogenes_ST15\-16\-021\.fna [05:23:10] 1 ncRNA RNaseP_bact_a gnl|JLU|Arhiz_ST15-16-021_1 2193331..2192929 [05:23:10] 2 ncRNA alpha_tmRNA gnl|JLU|Arhiz_ST15-16-021_1 2128265..2128639 [05:23:10] 3 ncRNA Atu_L1 gnl|JLU|Arhiz_ST15-16-021_1 1285685..1285512 [05:23:10] 4 ncRNA Atu_C9 gnl|JLU|Arhiz_ST15-16-021_1 2206397..2206576 [05:23:10] 5 ncRNA Atu_C3 gnl|JLU|Arhiz_ST15-16-021_1 3626353..3626509 [05:23:10] 6 ncRNA Atu_C7 gnl|JLU|Arhiz_ST15-16-021_1 345571..345723 [05:23:10] 7 ncRNA ar45 gnl|JLU|Arhiz_ST15-16-021_1 2922312..2922165 [05:23:10] 8 ncRNA Cobalamin gnl|JLU|Arhiz_ST15-16-021_1 4983908..4984099 [05:23:10] 9 ncRNA Cobalamin gnl|JLU|Arhiz_ST15-16-021_1 2690377..2690592 [05:23:10] 10 ncRNA Cobalamin gnl|JLU|Arhiz_ST15-16-021_1 4106806..4107034 [05:23:10] 11 ncRNA speF gnl|JLU|Arhiz_ST15-16-021_1 2922155..2922005 [05:23:10] 12 ncRNA Cobalamin gnl|JLU|Arhiz_ST15-16-021_1 3904180..3904415 [05:23:10] 13 ncRNA 5_ureB_sRNA gnl|JLU|Arhiz_ST15-16-021_1 4284458..4284747 [05:23:10] 14 ncRNA Cobalamin gnl|JLU|Arhiz_ST15-16-021_1 527440..527624 [05:23:10] 15 ncRNA Cobalamin gnl|JLU|Arhiz_ST15-16-021_1 3380866..3381090 [05:23:11] 16 ncRNA FMN gnl|JLU|Arhiz_ST15-16-021_1 1997537..1997687 [05:23:11] 17 ncRNA Atu_C8 gnl|JLU|Arhiz_ST15-16-021_1 2117033..2116914 [05:23:11] 18 ncRNA ar35 gnl|JLU|Arhiz_ST15-16-021_1 2868407..2868550 [05:23:11] 19 ncRNA Atu_C10 gnl|JLU|Arhiz_ST15-16-021_1 3216919..3216831 [05:23:11] 20 ncRNA ar15 gnl|JLU|Arhiz_ST15-16-021_1 2339410..2339523 [05:23:11] 21 ncRNA ar15 gnl|JLU|Arhiz_ST15-16-021_1 5072708..5072596 [05:23:11] 22 ncRNA ar9 gnl|JLU|Arhiz_ST15-16-021_1 413186..413333 [05:23:11] 23 ncRNA ar14 gnl|JLU|Arhiz_ST15-16-021_1 3419169..3419290 [05:23:11] 24 ncRNA Atu_Ti3 gnl|JLU|Arhiz_ST15-16-021_1 656432..656522 [05:23:11] 25 ncRNA ar7 gnl|JLU|Arhiz_ST15-16-021_1 3422728..3422589 [05:23:11] 26 ncRNA ar14 gnl|JLU|Arhiz_ST15-16-021_1 1233546..1233425 [05:23:11] 27 ncRNA Atu_C4 gnl|JLU|Arhiz_ST15-16-021_1 4225867..4225798 [05:23:11] 28 ncRNA Atu_At1 gnl|JLU|Arhiz_ST15-16-021_1 1200907..1201014 [05:23:11] 29 ncRNA SAM_alpha gnl|JLU|Arhiz_ST15-16-021_1 1723957..1724035 [05:23:11] 30 ncRNA ar14 gnl|JLU|Arhiz_ST15-16-021_1 4705927..4705803 [05:23:11] 31 ncRNA RcsR1 gnl|JLU|Arhiz_ST15-16-021_1 715886..715981 [05:23:11] 32 ncRNA ctRNA_p42d gnl|JLU|Arhiz_ST15-16-021_1 3070237..3070282 [05:23:11] 33 ncRNA SAM_alpha gnl|JLU|Arhiz_ST15-16-021_1 2796987..2796911 [05:23:11] 34 ncRNA S-element gnl|JLU|Arhiz_ST15-16-021_1 5033141..5033074 [05:23:11] 35 ncRNA TPP gnl|JLU|Arhiz_ST15-16-021_1 3342800..3342911 [05:23:11] 36 ncRNA ctRNA_p42d gnl|JLU|Arhiz_ST15-16-021_1 5033184..5033227 [05:23:11] 37 ncRNA TPP gnl|JLU|Arhiz_ST15-16-021_1 3027199..3027301 [05:23:11] 38 ncRNA Atu_Ti1 gnl|JLU|Arhiz_ST15-16-021_1 5049396..5049487 [05:23:11] 39 ncRNA beta_tmRNA gnl|JLU|Arhiz_ST15-16-021_1 2128231..2128577 [05:23:11] 40 ncRNA 6S gnl|JLU|Arhiz_ST15-16-021_1 844383..844225 [05:23:11] 41 ncRNA ctRNA_p42d gnl|JLU|Arhiz_ST15-16-021_1 1082451..1082495 [05:23:11] 42 ncRNA Bacteria_small_SRP gnl|JLU|Arhiz_ST15-16-021_1 3411221..3411125 [05:23:11] 43 ncRNA Atu_C6 gnl|JLU|Arhiz_ST15-16-021_1 400105..399996 [05:23:11] 44 ncRNA RNaseP_bact_b gnl|JLU|Arhiz_ST15-16-021_1 2193327..2192940 [05:23:11] 45 ncRNA suhB gnl|JLU|Arhiz_ST15-16-021_1 1037932..1037863 [05:23:11] 46 ncRNA Glycine gnl|JLU|Arhiz_ST15-16-021_1 243784..243871 [05:23:11] 47 ncRNA ar15 gnl|JLU|Arhiz_ST15-16-021_1 2339610..2339708 [05:23:11] 48 ncRNA TPP gnl|JLU|Arhiz_ST15-16-021_1 2800095..2800205 [05:23:11] 49 ncRNA isrG gnl|JLU|Arhiz_ST15-16-021_1 4239540..4239781 [05:23:11] 50 ncRNA S-element gnl|JLU|Arhiz_ST15-16-021_1 1082410..1082341 [05:23:11] 51 ncRNA ffh gnl|JLU|Arhiz_ST15-16-021_1 3202208..3202157 [05:23:11] 52 ncRNA RNaseP_arch gnl|JLU|Arhiz_ST15-16-021_1 2193332..2192932 [05:23:11] 53 ncRNA ybhL gnl|JLU|Arhiz_ST15-16-021_1 3218934..3218867 [05:23:11] 54 ncRNA cspA gnl|JLU|Arhiz_ST15-16-021_1 3419379..3419667 [05:23:11] 55 ncRNA suhB gnl|JLU|Arhiz_ST15-16-021_1 2339453..2339532 [05:23:11] 56 ncRNA BASRCI27 gnl|JLU|Arhiz_ST15-16-021_1 1545312..1545142 [05:23:11] 57 ncRNA S-element gnl|JLU|Arhiz_ST15-16-021_1 3070196..3070130 [05:23:11] 58 ncRNA serC gnl|JLU|Arhiz_ST15-16-021_1 791537..791486 [05:23:11] 59 ncRNA suhB gnl|JLU|Arhiz_ST15-16-021_1 2339639..2339718 [05:23:11] Found 59 ncRNAs. [05:23:11] Total of 54 tRNA + rRNA features [05:23:11] Searching for CRISPR repeats [05:23:12] Found 0 CRISPRs [05:23:12] Predicting coding sequences [05:23:12] Contigs total 5307354 bp, so using single mode [05:23:12] Running: prodigal -i \/data\/annotations\/Agrobacterium_rhizogenes_ST15\-16\-021\/Agrobacterium_rhizogenes_ST15\-16\-021\.fna -c -m -g 11 -p single -f sco -q [05:23:24] Excluding CDS which overlaps existing RNA (tRNA) at gnl|JLU|Arhiz_ST15-16-021_1:225965..227329 on + strand [05:23:25] Excluding CDS which overlaps existing RNA (tRNA) at gnl|JLU|Arhiz_ST15-16-021_1:1144574..1146259 on + strand [05:23:27] Excluding CDS which overlaps existing RNA (tRNA) at gnl|JLU|Arhiz_ST15-16-021_1:2684911..2686188 on + strand [05:23:27] Excluding CDS which overlaps existing RNA (tRNA) at gnl|JLU|Arhiz_ST15-16-021_1:2686170..2687216 on - strand [05:23:28] Excluding CDS which overlaps existing RNA (tRNA) at gnl|JLU|Arhiz_ST15-16-021_1:2973099..2974298 on + strand [05:23:30] Found 4994 CDS [05:23:30] Connecting features back to sequences [05:23:30] Using custom Agrobacterium database for annotation [05:23:30] Preparing user-supplied primary BLAST annotation source: /asap/db/sequences/asap-proteins.faa [05:23:31] Guessed source was in fasta format. [05:23:31] Running: makeblastdb -dbtype prot -in \/asap\/db\/sequences\/asap\-proteins\.faa -out \/data\/annotations\/Agrobacterium_rhizogenes_ST15\-16\-021\/proteins -logfile /dev/null [05:23:31] Using /inference source as 'asap-proteins.faa' [05:23:31] Annotating CDS, please be patient. [05:23:31] Will use 2 CPUs for similarity searching. [05:23:39] There are still 4994 unannotated CDS left (started with 4994) [05:23:39] Will use blast to search against /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/proteins with 2 CPUs [05:23:39] Running: cat \/data\/annotations\/Agrobacterium_rhizogenes_ST15\-16\-021\/proteins\.faa | parallel --gnu --plain -j 2 --block 395957 --recstart '>' --pipe blastp -query - -db /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/proteins -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/data\/annotations\/Agrobacterium_rhizogenes_ST15\-16\-021\/proteins\.blast 2> /dev/null [05:24:47] Deleting unwanted file: /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/proteins.faa [05:24:47] Deleting unwanted file: /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/proteins.blast [05:24:53] There are still 4005 unannotated CDS left (started with 4994) [05:24:53] Will use blast to search against /asap/share/prokka-1.12/bin/../db/genus/Agrobacterium with 2 CPUs [05:24:53] Running: cat \/data\/annotations\/Agrobacterium_rhizogenes_ST15\-16\-021\/Agrobacterium\.faa | parallel --gnu --plain -j 2 --block 294325 --recstart '>' --pipe blastp -query - -db /asap/share/prokka-1.12/bin/../db/genus/Agrobacterium -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/data\/annotations\/Agrobacterium_rhizogenes_ST15\-16\-021\/Agrobacterium\.blast 2> /dev/null [05:27:15] Deleting unwanted file: /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium.faa [05:27:15] Deleting unwanted file: /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium.blast [05:27:17] There are still 1224 unannotated CDS left (started with 4994) [05:27:17] Will use blast to search against /asap/share/prokka-1.12/bin/../db/kingdom/Bacteria/sprot with 2 CPUs [05:27:17] Running: cat \/data\/annotations\/Agrobacterium_rhizogenes_ST15\-16\-021\/sprot\.faa | parallel --gnu --plain -j 2 --block 63343 --recstart '>' --pipe blastp -query - -db /asap/share/prokka-1.12/bin/../db/kingdom/Bacteria/sprot -evalue 1e-06 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > \/data\/annotations\/Agrobacterium_rhizogenes_ST15\-16\-021\/sprot\.blast 2> /dev/null [05:27:52] Deleting unwanted file: /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/sprot.faa [05:27:52] Deleting unwanted file: /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/sprot.blast [05:27:54] There are still 1153 unannotated CDS left (started with 4994) [05:27:54] Will use hmmer3 to search against /asap/share/prokka-1.12/bin/../db/hmm/HAMAP.hmm with 2 CPUs [05:27:54] Running: cat \/data\/annotations\/Agrobacterium_rhizogenes_ST15\-16\-021\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 2 --block 57509 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /asap/share/prokka-1.12/bin/../db/hmm/HAMAP.hmm /dev/stdin > \/data\/annotations\/Agrobacterium_rhizogenes_ST15\-16\-021\/HAMAP\.hmm\.hmmer3 2> /dev/null [05:31:46] Deleting unwanted file: /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/HAMAP.hmm.faa [05:31:46] Deleting unwanted file: /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/HAMAP.hmm.hmmer3 [05:31:46] Deleting unwanted file: /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/proteins.psq [05:31:46] Deleting unwanted file: /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/proteins.phr [05:31:46] Deleting unwanted file: /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/proteins.pin [05:31:46] Labelling remaining 1138 proteins as 'hypothetical protein' [05:31:46] Possible /pseudo 'iron(III) ABC transporter, ATP-binding protein ' at gnl|JLU|Arhiz_ST15-16-021_1 position 79511 [05:31:46] Possible /pseudo 'ABC transporter, membrane spanning protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 81612 [05:31:46] Possible /pseudo 'RhtB family transporter' at gnl|JLU|Arhiz_ST15-16-021_1 position 98033 [05:31:46] Possible /pseudo 'glyoxalase/bleomycin resistance protein/dioxygenase superfamily protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 161417 [05:31:46] Possible /pseudo 'colibactin polyketide synthase ClbI ' at gnl|JLU|Arhiz_ST15-16-021_1 position 220114 [05:31:46] Possible /pseudo 'ABC transporter, membrane spanning protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 307544 [05:31:46] Possible /pseudo 'twitching motility protein PilH ' at gnl|JLU|Arhiz_ST15-16-021_1 position 401910 [05:31:46] Possible /pseudo 'SEC-independent protein translocase protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 466975 [05:31:46] Possible /pseudo 'SEC-independent protein translocase protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 467709 [05:31:46] Possible /pseudo 'peptidyl prolyl cis-trans isomerase' at gnl|JLU|Arhiz_ST15-16-021_1 position 490625 [05:31:46] Possible /pseudo 'capsular polysaccharide biosynthesis fatty acid synthase' at gnl|JLU|Arhiz_ST15-16-021_1 position 582503 [05:31:46] Possible /pseudo 'ABC transporter, membrane spanning protein (amino acid)' at gnl|JLU|Arhiz_ST15-16-021_1 position 595600 [05:31:46] Possible /pseudo 'transposase' at gnl|JLU|Arhiz_ST15-16-021_1 position 652395 [05:31:46] Possible /pseudo 'MutT/nudix family protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 831280 [05:31:46] Possible /pseudo 'diguanylate cyclase' at gnl|JLU|Arhiz_ST15-16-021_1 position 891827 [05:31:46] Possible /pseudo 'resistance-nodulation-cell division (RND) antibiotic efflux pump' at gnl|JLU|Arhiz_ST15-16-021_1 position 933652 [05:31:46] Possible /pseudo 'resistance-nodulation-cell division (RND) antibiotic efflux pump' at gnl|JLU|Arhiz_ST15-16-021_1 position 934737 [05:31:46] Possible /pseudo 'ABC transporter membrane spanning protein (sugar)' at gnl|JLU|Arhiz_ST15-16-021_1 position 1019956 [05:31:46] Possible /pseudo 'sugar ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 1047364 [05:31:46] Possible /pseudo 'iron(III) ABC transporter, ATP-binding protein ' at gnl|JLU|Arhiz_ST15-16-021_1 position 1049316 [05:31:46] Possible /pseudo 'cytochrome-c oxidase subunit III protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 1101187 [05:31:46] Possible /pseudo 'permease component of C4 dicarboxylate transporter' at gnl|JLU|Arhiz_ST15-16-021_1 position 1114294 [05:31:46] Possible /pseudo 'amino acid ABC transporter' at gnl|JLU|Arhiz_ST15-16-021_1 position 1133017 [05:31:46] Possible /pseudo 'two component sensor kinase' at gnl|JLU|Arhiz_ST15-16-021_1 position 1182258 [05:31:46] Possible /pseudo 'branched chain amino acid ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 1216935 [05:31:46] Possible /pseudo 'dipeptide ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 1229133 [05:31:46] Possible /pseudo 'succinoglycan biosynthesis protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 1294277 [05:31:46] Possible /pseudo 'sugar ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 1320151 [05:31:46] Possible /pseudo 'Lectin-like protein BA14k' at gnl|JLU|Arhiz_ST15-16-021_1 position 1431005 [05:31:46] Possible /pseudo 'iron(III) ABC transporter, permease protein ' at gnl|JLU|Arhiz_ST15-16-021_1 position 1556833 [05:31:46] Possible /pseudo 'flagellin ' at gnl|JLU|Arhiz_ST15-16-021_1 position 1625856 [05:31:46] Possible /pseudo 'flagellin ' at gnl|JLU|Arhiz_ST15-16-021_1 position 1627060 [05:31:46] Possible /pseudo 'N-acyl-homoserine lactone dependent regulatory protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 1644924 [05:31:46] Possible /pseudo 'pH adaption potassium efflux system protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 1659594 [05:31:46] Possible /pseudo 'ABC transporter, membrane spanning protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 1734379 [05:31:46] Possible /pseudo 'ABC transporter, membrane spanning protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 1767403 [05:31:46] Possible /pseudo 'ABC transporter, membrane spanning protein (sugar)' at gnl|JLU|Arhiz_ST15-16-021_1 position 1898612 [05:31:46] Possible /pseudo 'ATP-binding cassette (ABC) antibiotic efflux pump' at gnl|JLU|Arhiz_ST15-16-021_1 position 1921968 [05:31:46] Possible /pseudo 'ATP-binding cassette (ABC) antibiotic efflux pump' at gnl|JLU|Arhiz_ST15-16-021_1 position 1922677 [05:31:46] Possible /pseudo 'ABC transporter, membrane spanning protein (amino acid)' at gnl|JLU|Arhiz_ST15-16-021_1 position 1987239 [05:31:46] Possible /pseudo 'tetracycline-resistant ribosomal protection protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 2041641 [05:31:46] Possible /pseudo 'resistance-nodulation-cell division (RND) antibiotic efflux pump' at gnl|JLU|Arhiz_ST15-16-021_1 position 2141392 [05:31:46] Possible /pseudo 'cell division protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 2172474 [05:31:46] Possible /pseudo 'cell division protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 2173802 [05:31:46] Possible /pseudo 'sarcosine oxidase' at gnl|JLU|Arhiz_ST15-16-021_1 position 2194638 [05:31:46] Possible /pseudo 'small multidrug resistance (SMR) antibiotic efflux pump' at gnl|JLU|Arhiz_ST15-16-021_1 position 2215995 [05:31:46] Possible /pseudo 'ABC transporter, membrane spanning protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 2233307 [05:31:46] Possible /pseudo 'enoyl-CoA hydratase' at gnl|JLU|Arhiz_ST15-16-021_1 position 2382429 [05:31:46] Possible /pseudo 'ATP-binding cassette (ABC) antibiotic efflux pump' at gnl|JLU|Arhiz_ST15-16-021_1 position 2389818 [05:31:46] Possible /pseudo 'sugar ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 2466015 [05:31:46] Possible /pseudo 'ATP-binding cassette (ABC) antibiotic efflux pump' at gnl|JLU|Arhiz_ST15-16-021_1 position 2499092 [05:31:46] Possible /pseudo 'ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 2519465 [05:31:46] Possible /pseudo 'IS3 family transposase' at gnl|JLU|Arhiz_ST15-16-021_1 position 2553496 [05:31:46] Possible /pseudo 'amino acid ABC transporter' at gnl|JLU|Arhiz_ST15-16-021_1 position 2578948 [05:31:46] Possible /pseudo 'acetyltransferase' at gnl|JLU|Arhiz_ST15-16-021_1 position 2712667 [05:31:46] Possible /pseudo 'spermidine/putrescine ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 2828948 [05:31:46] Possible /pseudo 'sn-glycerol-3-phosphate ABC transporter membrane protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 2840321 [05:31:46] Possible /pseudo 'sugar ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 2858425 [05:31:46] Possible /pseudo 'cold shock protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 2867274 [05:31:46] Possible /pseudo 'sugar ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 2877282 [05:31:46] Possible /pseudo 'sugar ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 2891664 [05:31:46] Possible /pseudo 'sugar ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 2900347 [05:31:46] Possible /pseudo 'glycerol-3-phosphate ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 2914386 [05:31:46] Possible /pseudo 'resistance-nodulation-cell division (RND) antibiotic efflux pump' at gnl|JLU|Arhiz_ST15-16-021_1 position 2927944 [05:31:46] Possible /pseudo 'resistance-nodulation-cell division (RND) antibiotic efflux pump' at gnl|JLU|Arhiz_ST15-16-021_1 position 2931091 [05:31:46] Possible /pseudo 'oligopeptide ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 2945392 [05:31:46] Possible /pseudo 'iron(III) ABC transporter, ATP-binding protein ' at gnl|JLU|Arhiz_ST15-16-021_1 position 2947019 [05:31:46] Possible /pseudo 'sugar ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 2970595 [05:31:46] Possible /pseudo 'bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 2981173 [05:31:46] Possible /pseudo 'resistance-nodulation-cell division (RND) antibiotic efflux pump' at gnl|JLU|Arhiz_ST15-16-021_1 position 3010945 [05:31:46] Possible /pseudo 'sugar ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 3021372 [05:31:46] Possible /pseudo 'cellulose synthesis protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 3046103 [05:31:46] Possible /pseudo 'integrase IntA' at gnl|JLU|Arhiz_ST15-16-021_1 position 3075924 [05:31:46] Possible /pseudo 'plasmid partitioning protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 3089285 [05:31:46] Possible /pseudo 'ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 3154405 [05:31:46] Possible /pseudo 'sugar ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 3189734 [05:31:46] Possible /pseudo 'ABC transporter, membrane spanning protein (oligopeptide)' at gnl|JLU|Arhiz_ST15-16-021_1 position 3318704 [05:31:46] Possible /pseudo 'ABC transporter, membrane spanning protein (sugar/ribonucleotide)' at gnl|JLU|Arhiz_ST15-16-021_1 position 3443718 [05:31:46] Possible /pseudo 'biopolymer transport protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 3477887 [05:31:46] Possible /pseudo 'ABC transporter, membrane spanning protein (phosphonate)' at gnl|JLU|Arhiz_ST15-16-021_1 position 3486464 [05:31:46] Possible /pseudo 'ABC transporter, membrane spanning protein (peptide)' at gnl|JLU|Arhiz_ST15-16-021_1 position 3502639 [05:31:46] Possible /pseudo 'components of type IV pilus' at gnl|JLU|Arhiz_ST15-16-021_1 position 3529129 [05:31:46] Possible /pseudo 'type IV pilus protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 3532973 [05:31:46] Possible /pseudo 'oxidoreductase' at gnl|JLU|Arhiz_ST15-16-021_1 position 3568351 [05:31:46] Possible /pseudo 'octopine ABC transporter' at gnl|JLU|Arhiz_ST15-16-021_1 position 3655233 [05:31:47] Possible /pseudo 'IS426 transposase' at gnl|JLU|Arhiz_ST15-16-021_1 position 3660269 [05:31:47] Possible /pseudo 'IS3 family transposase' at gnl|JLU|Arhiz_ST15-16-021_1 position 3663929 [05:31:47] Possible /pseudo 'dioxygenase' at gnl|JLU|Arhiz_ST15-16-021_1 position 3668176 [05:31:47] Possible /pseudo 'sugar ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 3678447 [05:31:47] Possible /pseudo 'ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 3800584 [05:31:47] Possible /pseudo 'iron(III) ABC transporter, permease protein ' at gnl|JLU|Arhiz_ST15-16-021_1 position 3831452 [05:31:47] Possible /pseudo 'ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 3843906 [05:31:47] Possible /pseudo 'ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 3876932 [05:31:47] Possible /pseudo 'iron(III) ABC transporter, ATP-binding protein ' at gnl|JLU|Arhiz_ST15-16-021_1 position 3878660 [05:31:47] Possible /pseudo 'ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 3888106 [05:31:47] Possible /pseudo 'ABC transporter substrate-binding protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 3910083 [05:31:47] Possible /pseudo 'probable oxidoreductase ' at gnl|JLU|Arhiz_ST15-16-021_1 position 3924608 [05:31:47] Possible /pseudo 'probable oxidoreductase ' at gnl|JLU|Arhiz_ST15-16-021_1 position 3925621 [05:31:47] Possible /pseudo 'sugar ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 3929006 [05:31:47] Possible /pseudo 'TRAP mannitol/C4-dicarboxylate transporter' at gnl|JLU|Arhiz_ST15-16-021_1 position 3957315 [05:31:47] Possible /pseudo 'amino acid ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 3966817 [05:31:47] Possible /pseudo 'sorbitol/mannitol ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 3972831 [05:31:47] Possible /pseudo 'Manganese transport system membrane protein MntB' at gnl|JLU|Arhiz_ST15-16-021_1 position 3988461 [05:31:47] Possible /pseudo 'trehalose/maltose ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 4024715 [05:31:47] Possible /pseudo 'iron(III) ABC transporter, permease protein ' at gnl|JLU|Arhiz_ST15-16-021_1 position 4049790 [05:31:47] Possible /pseudo 'ErfK/YbiS/YcfS/YnhG family protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 4076466 [05:31:47] Possible /pseudo 'Na+/H+ antiporter' at gnl|JLU|Arhiz_ST15-16-021_1 position 4130315 [05:31:47] Possible /pseudo 'Na+/H+ antiporter' at gnl|JLU|Arhiz_ST15-16-021_1 position 4130734 [05:31:47] Possible /pseudo 'Na+/H+ antiporter' at gnl|JLU|Arhiz_ST15-16-021_1 position 4131131 [05:31:47] Possible /pseudo 'Na+/H+ antiporter' at gnl|JLU|Arhiz_ST15-16-021_1 position 4132705 [05:31:47] Possible /pseudo 'Na+/H+ antiporter' at gnl|JLU|Arhiz_ST15-16-021_1 position 4133181 [05:31:47] Possible /pseudo 'Na+/H+ antiporter' at gnl|JLU|Arhiz_ST15-16-021_1 position 4133564 [05:31:47] Possible /pseudo 'porin outer membrane protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 4239653 [05:31:47] Possible /pseudo 'ABC transporter, membrane spanning protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 4249212 [05:31:47] Possible /pseudo 'ABC transporter, membrane spanning protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 4271680 [05:31:47] Possible /pseudo 'resistance-nodulation-cell division (RND) antibiotic efflux pump' at gnl|JLU|Arhiz_ST15-16-021_1 position 4275134 [05:31:47] Possible /pseudo 'urease alpha subunit UreA ' at gnl|JLU|Arhiz_ST15-16-021_1 position 4286690 [05:31:47] Possible /pseudo 'ABC transporter, membrane spanning protein (urea/amide)' at gnl|JLU|Arhiz_ST15-16-021_1 position 4292187 [05:31:47] Possible /pseudo 'tricarboxylic transport membrane protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 4347868 [05:31:47] Possible /pseudo 'resistance-nodulation-cell division (RND) antibiotic efflux pump' at gnl|JLU|Arhiz_ST15-16-021_1 position 4359155 [05:31:47] Possible /pseudo 'iron(III) ABC transporter, ATP-binding protein ' at gnl|JLU|Arhiz_ST15-16-021_1 position 4396327 [05:31:47] Possible /pseudo 'ABC transporter, membrane spanning protein (dipeptide)' at gnl|JLU|Arhiz_ST15-16-021_1 position 4398060 [05:31:47] Possible /pseudo 'iron ABC transporter substrate-binding protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 4426651 [05:31:47] Possible /pseudo 'resistance-nodulation-cell division (RND) antibiotic efflux pump' at gnl|JLU|Arhiz_ST15-16-021_1 position 4428620 [05:31:47] Possible /pseudo 'heme permease protein ChuU ' at gnl|JLU|Arhiz_ST15-16-021_1 position 4461850 [05:31:47] Possible /pseudo 'oligopeptide ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 4485540 [05:31:47] Possible /pseudo 'iron(III) ABC transporter, ATP-binding protein ' at gnl|JLU|Arhiz_ST15-16-021_1 position 4487302 [05:31:47] Possible /pseudo 'oligopeptide transport system permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 4496558 [05:31:47] Possible /pseudo 'branched chain amino acid ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 4538671 [05:31:47] Possible /pseudo 'ABC transporter substrate binding protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 4565112 [05:31:47] Possible /pseudo 'sugar ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 4582090 [05:31:47] Possible /pseudo 'amino acid ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 4626043 [05:31:47] Possible /pseudo 'iron(III) ABC transporter, ATP-binding protein ' at gnl|JLU|Arhiz_ST15-16-021_1 position 4674129 [05:31:47] Possible /pseudo 'amino acid ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 4689679 [05:31:47] Possible /pseudo 'amino acid ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 4698736 [05:31:47] Possible /pseudo 'oligopeptide ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 4716767 [05:31:47] Possible /pseudo 'sugar ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 4730239 [05:31:47] Possible /pseudo 'branched-chain amino acid ABC transporter' at gnl|JLU|Arhiz_ST15-16-021_1 position 4741864 [05:31:47] Possible /pseudo 'dipeptide ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 4773367 [05:31:47] Possible /pseudo 'iron(III) ABC transporter, ATP-binding protein ' at gnl|JLU|Arhiz_ST15-16-021_1 position 4775095 [05:31:47] Possible /pseudo 'iron(III) ABC transporter, ATP-binding protein ' at gnl|JLU|Arhiz_ST15-16-021_1 position 4775929 [05:31:47] Possible /pseudo 'sugar ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 4777831 [05:31:47] Possible /pseudo 'transposase' at gnl|JLU|Arhiz_ST15-16-021_1 position 4814438 [05:31:47] Possible /pseudo 'permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 4833160 [05:31:47] Possible /pseudo 'major facilitator superfamily (MFS) antibiotic efflux pump' at gnl|JLU|Arhiz_ST15-16-021_1 position 4852753 [05:31:47] Possible /pseudo 'oligopeptide ABC transporter, membrane spanning protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 4928295 [05:31:47] Possible /pseudo 'sugar ABC transporter permease' at gnl|JLU|Arhiz_ST15-16-021_1 position 4957302 [05:31:47] Possible /pseudo 'resistance-nodulation-cell division (RND) antibiotic efflux pump' at gnl|JLU|Arhiz_ST15-16-021_1 position 5004949 [05:31:47] Possible /pseudo 'transposase' at gnl|JLU|Arhiz_ST15-16-021_1 position 5020364 [05:31:47] Possible /pseudo 'sugar ABC transporter' at gnl|JLU|Arhiz_ST15-16-021_1 position 5025459 [05:31:47] Possible /pseudo 'conjugal transfer protein Dtr system' at gnl|JLU|Arhiz_ST15-16-021_1 position 5054372 [05:31:47] Possible /pseudo 'sarcosine oxidase alpha subunit' at gnl|JLU|Arhiz_ST15-16-021_1 position 5143125 [05:31:47] Possible /pseudo 'sarcosine oxidase alpha subunit' at gnl|JLU|Arhiz_ST15-16-021_1 position 5144398 [05:31:47] Possible /pseudo 'nucleotidyltransferase protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 5211711 [05:31:47] Possible /pseudo 'iron(III) ABC transporter, ATP-binding protein ' at gnl|JLU|Arhiz_ST15-16-021_1 position 5242423 [05:31:47] Possible /pseudo 'conjugal transfer protein' at gnl|JLU|Arhiz_ST15-16-021_1 position 5276446 [05:31:47] Found 1555 unique /gene codes. [05:31:47] Fixed 9 duplicate /gene - arlR_1 arlR_2 arlR_3 arlR_4 arlR_5 arlR_6 arlR_7 arlR_8 arlR_9 [05:31:47] Fixed 2 duplicate /gene - hasC_1 hasC_2 [05:31:47] Fixed 3 duplicate /gene - glpK_1 glpK_2 glpK_3 [05:31:47] Fixed 2 duplicate /gene - TaeA_1 TaeA_2 [05:31:47] Fixed 2 duplicate /gene - guaA_1 guaA_2 [05:31:47] Fixed 2 duplicate /gene - entD_1 entD_2 [05:31:47] Fixed 2 duplicate /gene - sun_1 sun_2 [05:31:47] Fixed 3 duplicate /gene - hlyB_1 hlyB_2 hlyB_3 [05:31:47] Fixed 2 duplicate /gene - ppiB_1 ppiB_2 [05:31:47] Fixed 2 duplicate /gene - kdgA_1 kdgA_2 [05:31:47] Fixed 3 duplicate /gene - pvdS_1 pvdS_2 pvdS_3 [05:31:47] Fixed 3 duplicate /gene - repB_1 repB_2 repB_3 [05:31:47] Fixed 2 duplicate /gene - livJ_1 livJ_2 [05:31:47] Fixed 2 duplicate /gene - livH_1 livH_2 [05:31:47] Fixed 2 duplicate /gene - melA_1 melA_2 [05:31:47] Fixed 4 duplicate /gene - ilvD_1 ilvD_2 ilvD_3 ilvD_4 [05:31:47] Fixed 2 duplicate /gene - proX_1 proX_2 [05:31:47] Fixed 2 duplicate /gene - AAC(6')-Ic_1 AAC(6')-Ic_2 [05:31:47] Fixed 5 duplicate /gene - pilR_1 pilR_2 pilR_3 pilR_4 pilR_5 [05:31:47] Fixed 2 duplicate /gene - virB1_1 virB1_2 [05:31:47] Fixed 10 duplicate /gene - allS_1 allS_2 allS_3 allS_4 allS_5 allS_6 allS_7 allS_8 allS_9 allS_10 [05:31:47] Fixed 2 duplicate /gene - adeF_1 adeF_2 [05:31:47] Fixed 3 duplicate /gene - fpvA_1 fpvA_2 fpvA_3 [05:31:47] Fixed 5 duplicate /gene - wcbP_1 wcbP_2 wcbP_3 wcbP_4 wcbP_5 [05:31:47] Fixed 2 duplicate /gene - nikB_1 nikB_2 [05:31:47] Fixed 3 duplicate /gene - gnd_1 gnd_2 gnd_3 [05:31:47] Fixed 3 duplicate /gene - allD_1 allD_2 allD_3 [05:31:47] Fixed 3 duplicate /gene - clbB_1 clbB_2 clbB_3 [05:31:47] Fixed 2 duplicate /gene - dac_1 dac_2 [05:31:47] Fixed 13 duplicate /gene - fbpB_1 fbpB_2 fbpB_3 fbpB_4 fbpB_5 fbpB_6 fbpB_7 fbpB_8 fbpB_9 fbpB_10 fbpB_11 fbpB_12 fbpB_13 [05:31:47] Fixed 2 duplicate /gene - vanD_1 vanD_2 [05:31:47] Fixed 2 duplicate /gene - gidA_1 gidA_2 [05:31:47] Fixed 57 duplicate /gene - fbpC_1 fbpC_2 fbpC_3 fbpC_4 fbpC_5 fbpC_6 fbpC_7 fbpC_8 fbpC_9 fbpC_10 fbpC_11 fbpC_12 fbpC_13 fbpC_14 fbpC_15 fbpC_16 fbpC_17 fbpC_18 fbpC_19 fbpC_20 fbpC_21 fbpC_22 fbpC_23 fbpC_24 fbpC_25 fbpC_26 fbpC_27 fbpC_28 fbpC_29 fbpC_30 fbpC_31 fbpC_32 fbpC_33 fbpC_34 fbpC_35 fbpC_36 fbpC_37 fbpC_38 fbpC_39 fbpC_40 fbpC_41 fbpC_42 fbpC_43 fbpC_44 fbpC_45 fbpC_46 fbpC_47 fbpC_48 fbpC_49 fbpC_50 fbpC_51 fbpC_52 fbpC_53 fbpC_54 fbpC_55 fbpC_56 fbpC_57 [05:31:47] Fixed 7 duplicate /gene - chuU_1 chuU_2 chuU_3 chuU_4 chuU_5 chuU_6 chuU_7 [05:31:47] Fixed 2 duplicate /gene - fptA_1 fptA_2 [05:31:47] Fixed 2 duplicate /gene - nuoF_1 nuoF_2 [05:31:47] Fixed 6 duplicate /gene - glnA_1 glnA_2 glnA_3 glnA_4 glnA_5 glnA_6 [05:31:47] Fixed 2 duplicate /gene - purC_1 purC_2 [05:31:47] Fixed 2 duplicate /gene - phnE_1 phnE_2 [05:31:47] Fixed 11 duplicate /gene - patA_1 patA_2 patA_3 patA_4 patA_5 patA_6 patA_7 patA_8 patA_9 patA_10 patA_11 [05:31:47] Fixed 2 duplicate /gene - adsA_1 adsA_2 [05:31:47] Fixed 3 duplicate /gene - wbkA_1 wbkA_2 wbkA_3 [05:31:47] Fixed 2 duplicate /gene - MuxC_1 MuxC_2 [05:31:47] Fixed 2 duplicate /gene - ybtA_1 ybtA_2 [05:31:47] Fixed 3 duplicate /gene - hutH_1 hutH_2 hutH_3 [05:31:47] Fixed 2 duplicate /gene - lpdA_1 lpdA_2 [05:31:47] Fixed 2 duplicate /gene - dep_1 dep_2 [05:31:47] Fixed 4 duplicate /gene - bcrA_1 bcrA_2 bcrA_3 bcrA_4 [05:31:47] Fixed 2 duplicate /gene - mntC_1 mntC_2 [05:31:47] Fixed 2 duplicate /gene - bepA_1 bepA_2 [05:31:47] Fixed 2 duplicate /gene - parB_1 parB_2 [05:31:47] Fixed 2 duplicate /gene - fdhF_1 fdhF_2 [05:31:47] Fixed 2 duplicate /gene - pchD_1 pchD_2 [05:31:47] Fixed 2 duplicate /gene - thiG_1 thiG_2 [05:31:47] Fixed 3 duplicate /gene - phoP_1 phoP_2 phoP_3 [05:31:47] Fixed 3 duplicate /gene - bspR2_1 bspR2_2 bspR2_3 [05:31:47] Fixed 2 duplicate /gene - tetT_1 tetT_2 [05:31:47] Fixed 2 duplicate /gene - mtrR_1 mtrR_2 [05:31:47] Fixed 2 duplicate /gene - virB2_1 virB2_2 [05:31:47] Fixed 4 duplicate /gene - oleC_1 oleC_2 oleC_3 oleC_4 [05:31:47] Fixed 3 duplicate /gene - tetS_1 tetS_2 tetS_3 [05:31:47] Fixed 3 duplicate /gene - bauF_1 bauF_2 bauF_3 [05:31:47] Fixed 3 duplicate /gene - clpP_1 clpP_2 clpP_3 [05:31:47] Fixed 4 duplicate /gene - basS_1 basS_2 basS_3 basS_4 [05:31:47] Fixed 2 duplicate /gene - emrY_1 emrY_2 [05:31:47] Fixed 3 duplicate /gene - metF_1 metF_2 metF_3 [05:31:47] Fixed 2 duplicate /gene - ureA_1 ureA_2 [05:31:47] Fixed 2 duplicate /gene - rosB_1 rosB_2 [05:31:47] Fixed 5 duplicate /gene - ugpA_1 ugpA_2 ugpA_3 ugpA_4 ugpA_5 [05:31:47] Fixed 2 duplicate /gene - smeS_1 smeS_2 [05:31:47] Fixed 2 duplicate /gene - rfaE_1 rfaE_2 [05:31:47] Fixed 2 duplicate /gene - flaA_1 flaA_2 [05:31:47] Fixed 2 duplicate /gene - arlS_1 arlS_2 [05:31:47] Fixed 2 duplicate /gene - sodB_1 sodB_2 [05:31:47] Fixed 2 duplicate /gene - rpsU_1 rpsU_2 [05:31:47] Fixed 12 duplicate /gene - pebA_1 pebA_2 pebA_3 pebA_4 pebA_5 pebA_6 pebA_7 pebA_8 pebA_9 pebA_10 pebA_11 pebA_12 [05:31:47] Fixed 2 duplicate /gene - clbD_1 clbD_2 [05:31:47] Fixed 3 duplicate /gene - Cj1437c_1 Cj1437c_2 Cj1437c_3 [05:31:47] Fixed 2 duplicate /gene - bauB_1 bauB_2 [05:31:47] Fixed 2 duplicate /gene - emrA_1 emrA_2 [05:31:47] Fixed 5 duplicate /gene - soxD_1 soxD_2 soxD_3 soxD_4 soxD_5 [05:31:47] Fixed 4 duplicate /gene - fimE_1 fimE_2 fimE_3 fimE_4 [05:31:47] Fixed 2 duplicate /gene - nifS_1 nifS_2 [05:31:47] Fixed 16 duplicate /gene - bopD_1 bopD_2 bopD_3 bopD_4 bopD_5 bopD_6 bopD_7 bopD_8 bopD_9 bopD_10 bopD_11 bopD_12 bopD_13 bopD_14 bopD_15 bopD_16 [05:31:47] Fixed 2 duplicate /gene - fabZ_1 fabZ_2 [05:31:47] Fixed 4 duplicate /gene - glyA_1 glyA_2 glyA_3 glyA_4 [05:31:47] Fixed 5 duplicate /gene - fimB_1 fimB_2 fimB_3 fimB_4 fimB_5 [05:31:47] Fixed 4 duplicate /gene - vanRF_1 vanRF_2 vanRF_3 vanRF_4 [05:31:47] Fixed 4 duplicate /gene - mntB_1 mntB_2 mntB_3 mntB_4 [05:31:47] Fixed 3 duplicate /gene - optrA_1 optrA_2 optrA_3 [05:31:47] Fixed 3 duplicate /gene - abeS_1 abeS_2 abeS_3 [05:31:47] Fixed 2 duplicate /gene - uxuB_1 uxuB_2 [05:31:47] Fixed 2 duplicate /gene - rolB_1 rolB_2 [05:31:47] Fixed 3 duplicate /gene - bprB_1 bprB_2 bprB_3 [05:31:47] Fixed 4 duplicate /gene - cspA_1 cspA_2 cspA_3 cspA_4 [05:31:47] Fixed 2 duplicate /gene - Cj1427c_1 Cj1427c_2 [05:31:47] Fixed 2 duplicate /gene - clpE_1 clpE_2 [05:31:47] Fixed 2 duplicate /gene - gpmB_1 gpmB_2 [05:31:47] Fixed 3 duplicate /gene - glpD_1 glpD_2 glpD_3 [05:31:47] Fixed 2 duplicate /gene - uvrD_1 uvrD_2 [05:31:47] Fixed 2 duplicate /gene - flgG_1 flgG_2 [05:31:47] Fixed 13 duplicate /gene - tetA(48)_1 tetA(48)_2 tetA(48)_3 tetA(48)_4 tetA(48)_5 tetA(48)_6 tetA(48)_7 tetA(48)_8 tetA(48)_9 tetA(48)_10 tetA(48)_11 tetA(48)_12 tetA(48)_13 [05:31:47] Fixed 2 duplicate /gene - pmlR_1 pmlR_2 [05:31:47] Fixed 3 duplicate /gene - bauE_1 bauE_2 bauE_3 [05:31:47] Fixed 2 duplicate /gene - exoM_1 exoM_2 [05:31:47] Fixed 3 duplicate /gene - wza_1 wza_2 wza_3 [05:31:47] Fixed 2 duplicate /gene - purF_1 purF_2 [05:31:47] Fixed 3 duplicate /gene - gltB_1 gltB_2 gltB_3 [05:31:47] Fixed 5 duplicate /gene - bplH_1 bplH_2 bplH_3 bplH_4 bplH_5 [05:31:47] Fixed 4 duplicate /gene - hlyD_1 hlyD_2 hlyD_3 hlyD_4 [05:31:47] Fixed 2 duplicate /gene - traA_1 traA_2 [05:31:47] Fixed 2 duplicate /gene - def_1 def_2 [05:31:47] Fixed 2 duplicate /gene - pntB_1 pntB_2 [05:31:47] Fixed 22 duplicate /gene - tsr_1 tsr_2 tsr_3 tsr_4 tsr_5 tsr_6 tsr_7 tsr_8 tsr_9 tsr_10 tsr_11 tsr_12 tsr_13 tsr_14 tsr_15 tsr_16 tsr_17 tsr_18 tsr_19 tsr_20 tsr_21 tsr_22 [05:31:47] Fixed 4 duplicate /gene - golS_1 golS_2 golS_3 golS_4 [05:31:47] Fixed 2 duplicate /gene - ftsZ1_1 ftsZ1_2 [05:31:47] Fixed 2 duplicate /gene - pgm_1 pgm_2 [05:31:47] Fixed 2 duplicate /gene - macA_1 macA_2 [05:31:47] Fixed 3 duplicate /gene - ada_1 ada_2 ada_3 [05:31:47] Fixed 2 duplicate /gene - virB5_1 virB5_2 [05:31:47] Fixed 5 duplicate /gene - rbsC_1 rbsC_2 rbsC_3 rbsC_4 rbsC_5 [05:31:47] Fixed 2 duplicate /gene - mdtC_1 mdtC_2 [05:31:47] Fixed 2 duplicate /gene - nolR_1 nolR_2 [05:31:47] Fixed 2 duplicate /gene - adhP_1 adhP_2 [05:31:47] Fixed 2 duplicate /gene - mprF_1 mprF_2 [05:31:47] Fixed 9 duplicate /gene - tnp_1 tnp_2 tnp_3 tnp_4 tnp_5 tnp_6 tnp_7 tnp_8 tnp_9 [05:31:47] Fixed 5 duplicate /gene - purU_1 purU_2 purU_3 purU_4 purU_5 [05:31:47] Fixed 2 duplicate /gene - gloA_1 gloA_2 [05:31:47] Fixed 3 duplicate /gene - uxuA_1 uxuA_2 uxuA_3 [05:31:47] Fixed 2 duplicate /gene - pccA_1 pccA_2 [05:31:47] Fixed 2 duplicate /gene - mgtE_1 mgtE_2 [05:31:47] Fixed 6 duplicate /gene - allR_1 allR_2 allR_3 allR_4 allR_5 allR_6 [05:31:47] Fixed 3 duplicate /gene - parA_1 parA_2 parA_3 [05:31:47] Fixed 2 duplicate /gene - ibeA_1 ibeA_2 [05:31:47] Fixed 3 duplicate /gene - exoQ_1 exoQ_2 exoQ_3 [05:31:47] Fixed 4 duplicate /gene - clbL_1 clbL_2 clbL_3 clbL_4 [05:31:47] Fixed 2 duplicate /gene - cfa_1 cfa_2 [05:31:47] Fixed 2 duplicate /gene - motB_1 motB_2 [05:31:47] Fixed 15 duplicate /gene - NmcR_1 NmcR_2 NmcR_3 NmcR_4 NmcR_5 NmcR_6 NmcR_7 NmcR_8 NmcR_9 NmcR_10 NmcR_11 NmcR_12 NmcR_13 NmcR_14 NmcR_15 [05:31:47] Fixed 2 duplicate /gene - frcR_1 frcR_2 [05:31:47] Fixed 2 duplicate /gene - parD1_1 parD1_2 [05:31:47] Fixed 4 duplicate /gene - dppB_1 dppB_2 dppB_3 dppB_4 [05:31:47] Fixed 3 duplicate /gene - repA_1 repA_2 repA_3 [05:31:47] Fixed 2 duplicate /gene - lasI_1 lasI_2 [05:31:47] Fixed 2 duplicate /gene - dnaA_1 dnaA_2 [05:31:47] Fixed 2 duplicate /gene - glmS_1 glmS_2 [05:31:47] Fixed 3 duplicate /gene - virB10_1 virB10_2 virB10_3 [05:31:47] Fixed 2 duplicate /gene - thuF_1 thuF_2 [05:31:47] Fixed 3 duplicate /gene - MexL_1 MexL_2 MexL_3 [05:31:47] Fixed 2 duplicate /gene - cysJ_1 cysJ_2 [05:31:47] Fixed 3 duplicate /gene - lrp_1 lrp_2 lrp_3 [05:31:47] Fixed 2 duplicate /gene - allB_1 allB_2 [05:31:47] Fixed 2 duplicate /gene - virB6_1 virB6_2 [05:31:47] Fixed 4 duplicate /gene - cyaA_1 cyaA_2 cyaA_3 cyaA_4 [05:31:47] Fixed 3 duplicate /gene - hutC_1 hutC_2 hutC_3 [05:31:47] Fixed 2 duplicate /gene - atpC_1 atpC_2 [05:31:47] Fixed 8 duplicate /gene - soxB_1 soxB_2 soxB_3 soxB_4 soxB_5 soxB_6 soxB_7 soxB_8 [05:31:47] Fixed 2 duplicate /gene - wbcA_1 wbcA_2 [05:31:47] Fixed 2 duplicate /gene - wbkC_1 wbkC_2 [05:31:47] Fixed 12 duplicate /gene - macB_1 macB_2 macB_3 macB_4 macB_5 macB_6 macB_7 macB_8 macB_9 macB_10 macB_11 macB_12 [05:31:47] Fixed 2 duplicate /gene - ves_1 ves_2 [05:31:47] Fixed 5 duplicate /gene - mgtB_1 mgtB_2 mgtB_3 mgtB_4 mgtB_5 [05:31:47] Fixed 2 duplicate /gene - dhbK_1 dhbK_2 [05:31:47] Fixed 2 duplicate /gene - aglA_1 aglA_2 [05:31:47] Fixed 2 duplicate /gene - vdh_1 vdh_2 [05:31:47] Fixed 2 duplicate /gene - wcsT_1 wcsT_2 [05:31:47] Fixed 2 duplicate /gene - mbtA_1 mbtA_2 [05:31:47] Fixed 4 duplicate /gene - ordL_1 ordL_2 ordL_3 ordL_4 [05:31:47] Fixed 3 duplicate /gene - dadA_1 dadA_2 dadA_3 [05:31:47] Fixed 2 duplicate /gene - intX_1 intX_2 [05:31:47] Fixed 10 duplicate /gene - chpD_1 chpD_2 chpD_3 chpD_4 chpD_5 chpD_6 chpD_7 chpD_8 chpD_9 chpD_10 [05:31:47] Fixed 7 duplicate /gene - wcbR_1 wcbR_2 wcbR_3 wcbR_4 wcbR_5 wcbR_6 wcbR_7 [05:31:47] Fixed 2 duplicate /gene - malG_1 malG_2 [05:31:47] Fixed 3 duplicate /gene - soxG_1 soxG_2 soxG_3 [05:31:47] Fixed 2 duplicate /gene - vanHA_1 vanHA_2 [05:31:47] Fixed 2 duplicate /gene - sfaX_1 sfaX_2 [05:31:47] Fixed 2 duplicate /gene - MexJ_1 MexJ_2 [05:31:47] Fixed 3 duplicate /gene - ameR_1 ameR_2 ameR_3 [05:31:47] Fixed 4 duplicate /gene - cps4D_1 cps4D_2 cps4D_3 cps4D_4 [05:31:47] Fixed 17 duplicate /gene - bplA_1 bplA_2 bplA_3 bplA_4 bplA_5 bplA_6 bplA_7 bplA_8 bplA_9 bplA_10 bplA_11 bplA_12 bplA_13 bplA_14 bplA_15 bplA_16 bplA_17 [05:31:47] Fixed 3 duplicate /gene - mntA_1 mntA_2 mntA_3 [05:31:47] Fixed 3 duplicate /gene - galE_1 galE_2 galE_3 [05:31:47] Fixed 7 duplicate /gene - virD4_1 virD4_2 virD4_3 virD4_4 virD4_5 virD4_6 virD4_7 [05:31:47] Fixed 5 duplicate /gene - lap_1 lap_2 lap_3 lap_4 lap_5 [05:31:47] Fixed 2 duplicate /gene - chuW_1 chuW_2 [05:31:47] Fixed 2 duplicate /gene - ramA_1 ramA_2 [05:31:47] Fixed 2 duplicate /gene - ftsH_1 ftsH_2 [05:31:47] Fixed 12 duplicate /gene - evgS_1 evgS_2 evgS_3 evgS_4 evgS_5 evgS_6 evgS_7 evgS_8 evgS_9 evgS_10 evgS_11 evgS_12 [05:31:47] Fixed 2 duplicate /gene - copC_1 copC_2 [05:31:47] Fixed 2 duplicate /gene - vanTG_1 vanTG_2 [05:31:47] Fixed 2 duplicate /gene - ybaK_1 ybaK_2 [05:31:47] Fixed 2 duplicate /gene - clpS_1 clpS_2 [05:31:47] Fixed 2 duplicate /gene - flhF_1 flhF_2 [05:31:47] Fixed 2 duplicate /gene - zinT_1 zinT_2 [05:31:47] Fixed 2 duplicate /gene - etfA_1 etfA_2 [05:31:47] Fixed 2 duplicate /gene - gmk_1 gmk_2 [05:31:47] Fixed 2 duplicate /gene - clbI_1 clbI_2 [05:31:47] Fixed 3 duplicate /gene - fbpA_1 fbpA_2 fbpA_3 [05:31:47] Fixed 10 duplicate /gene - soxA_1 soxA_2 soxA_3 soxA_4 soxA_5 soxA_6 soxA_7 soxA_8 soxA_9 soxA_10 [05:31:47] Fixed 2 duplicate /gene - tet(V)_1 tet(V)_2 [05:31:47] Fixed 2 duplicate /gene - adk_1 adk_2 [05:31:47] Fixed 2 duplicate /gene - nrdE_1 nrdE_2 [05:31:47] Fixed 22 duplicate /gene - adeL_1 adeL_2 adeL_3 adeL_4 adeL_5 adeL_6 adeL_7 adeL_8 adeL_9 adeL_10 adeL_11 adeL_12 adeL_13 adeL_14 adeL_15 adeL_16 adeL_17 adeL_18 adeL_19 adeL_20 adeL_21 adeL_22 [05:31:47] Fixed 2 duplicate /gene - shuV_1 shuV_2 [05:31:47] Fixed 2 duplicate /gene - arsB_1 arsB_2 [05:31:47] Fixed 2 duplicate /gene - icaR_1 icaR_2 [05:31:47] Fixed 2 duplicate /gene - lpg2370_1 lpg2370_2 [05:31:47] Fixed 2 duplicate /gene - tet(H)_1 tet(H)_2 [05:31:47] Fixed 2 duplicate /gene - lipA_1 lipA_2 [05:31:47] Fixed 2 duplicate /gene - phzS_1 phzS_2 [05:31:47] Fixed 2 duplicate /gene - ilvA_1 ilvA_2 [05:31:47] Fixed 6 duplicate /gene - msbA_1 msbA_2 msbA_3 msbA_4 msbA_5 msbA_6 [05:31:47] Fixed 2 duplicate /gene - plsC_1 plsC_2 [05:31:47] Fixed 4 duplicate /gene - cpxA_1 cpxA_2 cpxA_3 cpxA_4 [05:31:47] Fixed 2 duplicate /gene - pcm_1 pcm_2 [05:31:47] Fixed 7 duplicate /gene - clbF_1 clbF_2 clbF_3 clbF_4 clbF_5 clbF_6 clbF_7 [05:31:47] Fixed 2 duplicate /gene - cobS_1 cobS_2 [05:31:47] Fixed 3 duplicate /gene - gcvT_1 gcvT_2 gcvT_3 [05:31:47] Fixed 2 duplicate /gene - alaS_1 alaS_2 [05:31:47] Fixed 2 duplicate /gene - mntH_1 mntH_2 [05:31:47] Fixed 2 duplicate /gene - cyaB_1 cyaB_2 [05:31:47] Fixed 2 duplicate /gene - plcD_1 plcD_2 [05:31:47] Fixed 6 duplicate /gene - fepC_1 fepC_2 fepC_3 fepC_4 fepC_5 fepC_6 [05:31:47] Fixed 3 duplicate /gene - dnaJ_1 dnaJ_2 dnaJ_3 [05:31:47] Fixed 2 duplicate /gene - lysA_1 lysA_2 [05:31:47] Fixed 2 duplicate /gene - etfB_1 etfB_2 [05:31:47] Fixed 2 duplicate /gene - hutI_1 hutI_2 [05:31:47] Fixed 3 duplicate /gene - wcbT_1 wcbT_2 wcbT_3 [05:31:47] Fixed 2 duplicate /gene - serS_1 serS_2 [05:31:47] Fixed 2 duplicate /gene - dppA_1 dppA_2 [05:31:47] Fixed 2 duplicate /gene - arsH_1 arsH_2 [05:31:47] Fixed 2 duplicate /gene - ctb_1 ctb_2 [05:31:47] Fixed 2 duplicate /gene - ppx_1 ppx_2 [05:31:47] Fixed 3 duplicate /gene - ugpB_1 ugpB_2 ugpB_3 [05:31:47] Fixed 4 duplicate /gene - cpsD_1 cpsD_2 cpsD_3 cpsD_4 [05:31:47] Fixed 2 duplicate /gene - betS_1 betS_2 [05:31:47] Fixed 2 duplicate /gene - cysK_1 cysK_2 [05:31:47] Fixed 2 duplicate /gene - malF_1 malF_2 [05:31:47] Fixed 5 duplicate /gene - dppC_1 dppC_2 dppC_3 dppC_4 dppC_5 [05:31:47] Fixed 2 duplicate /gene - metC_1 metC_2 [05:31:47] Fixed 2 duplicate /gene - cheW_1 cheW_2 [05:31:47] Fixed 2 duplicate /gene - pscN_1 pscN_2 [05:31:47] Fixed 37 duplicate /gene - entA_1 entA_2 entA_3 entA_4 entA_5 entA_6 entA_7 entA_8 entA_9 entA_10 entA_11 entA_12 entA_13 entA_14 entA_15 entA_16 entA_17 entA_18 entA_19 entA_20 entA_21 entA_22 entA_23 entA_24 entA_25 entA_26 entA_27 entA_28 entA_29 entA_30 entA_31 entA_32 entA_33 entA_34 entA_35 entA_36 entA_37 [05:31:47] Fixed 3 duplicate /gene - tviC_1 tviC_2 tviC_3 [05:31:47] Fixed 3 duplicate /gene - gst_1 gst_2 gst_3 [05:31:47] Fixed 3 duplicate /gene - proC_1 proC_2 proC_3 [05:31:47] Fixed 2 duplicate /gene - cobW_1 cobW_2 [05:31:47] Fixed 2 duplicate /gene - lpeA_1 lpeA_2 [05:31:47] Fixed 2 duplicate /gene - hutU_1 hutU_2 [05:31:47] Fixed 2 duplicate /gene - dapE_1 dapE_2 [05:31:47] Fixed 3 duplicate /gene - fleR_1 fleR_2 fleR_3 [05:31:47] Fixed 2 duplicate /gene - map_1 map_2 [05:31:47] Fixed 2 duplicate /gene - cpsO_1 cpsO_2 [05:31:47] Fixed 3 duplicate /gene - bfmS_1 bfmS_2 bfmS_3 [05:31:47] Fixed 3 duplicate /gene - repC_1 repC_2 repC_3 [05:31:47] Fixed 2 duplicate /gene - exsI_1 exsI_2 [05:31:47] Fixed 4 duplicate /gene - arsC_1 arsC_2 arsC_3 arsC_4 [05:31:47] Fixed 2 duplicate /gene - hipO_1 hipO_2 [05:31:47] Fixed 3 duplicate /gene - guaB_1 guaB_2 guaB_3 [05:31:47] Fixed 2 duplicate /gene - pcaD_1 pcaD_2 [05:31:47] Fixed 2 duplicate /gene - sdaA_1 sdaA_2 [05:31:47] Fixed 7 duplicate /gene - dapA_1 dapA_2 dapA_3 dapA_4 dapA_5 dapA_6 dapA_7 [05:31:47] Fixed 2 duplicate /gene - bacA_1 bacA_2 [05:31:47] Fixed 5 duplicate /gene - virB11_1 virB11_2 virB11_3 virB11_4 virB11_5 [05:31:47] Fixed 2 duplicate /gene - gapA_1 gapA_2 [05:31:47] Fixed 2 duplicate /gene - enhC_1 enhC_2 [05:31:47] Fixed 2 duplicate /gene - virB4_1 virB4_2 [05:31:47] Fixed 3 duplicate /gene - ugpE_1 ugpE_2 ugpE_3 [05:31:47] Fixed 8 duplicate /gene - exsA_1 exsA_2 exsA_3 exsA_4 exsA_5 exsA_6 exsA_7 exsA_8 [05:31:47] Fixed 2 duplicate /gene - gltX_1 gltX_2 [05:31:47] Fixed 2 duplicate /gene - cobT_1 cobT_2 [05:31:47] Fixed 2 duplicate /gene - algB_1 algB_2 [05:31:47] Fixed 2 duplicate /gene - dacF_1 dacF_2 [05:31:47] Fixed 3 duplicate /gene - rbsB_1 rbsB_2 rbsB_3 [05:31:47] Fixed 2 duplicate /gene - citE_1 citE_2 [05:31:47] Fixed 2 duplicate /gene - gcd_1 gcd_2 [05:31:47] Fixed 3 duplicate /gene - vanHB_1 vanHB_2 vanHB_3 [05:31:47] Fixed 3 duplicate /gene - scpB_1 scpB_2 scpB_3 [05:31:47] Fixed 2 duplicate /gene - cadF_1 cadF_2 [05:31:47] Fixed 2 duplicate /gene - iunH_1 iunH_2 [05:31:47] Fixed 2 duplicate /gene - qacB_1 qacB_2 [05:31:47] Fixed 2 duplicate /gene - abaR_1 abaR_2 [05:31:47] Fixed 3 duplicate /gene - allC_1 allC_2 allC_3 [05:31:47] Fixed 2 duplicate /gene - lexA_1 lexA_2 [05:31:47] Fixed 2 duplicate /gene - mltB_1 mltB_2 [05:31:47] Fixed 2 duplicate /gene - soxR_1 soxR_2 [05:31:47] Fixed 2 duplicate /gene - tet(D)_1 tet(D)_2 [05:31:47] Fixed 2 duplicate /gene - baeR_1 baeR_2 [05:31:47] Fixed 2 duplicate /gene - gyrB_1 gyrB_2 [05:31:47] Fixed 2 duplicate /gene - gshB_1 gshB_2 [05:31:47] Fixed 2 duplicate /gene - tpiA_1 tpiA_2 [05:31:47] Fixed 7 duplicate /gene - novA_1 novA_2 novA_3 novA_4 novA_5 novA_6 novA_7 [05:31:47] Fixed 2 duplicate /gene - fadB_1 fadB_2 [05:31:47] Fixed 2 duplicate /gene - mbtE_1 mbtE_2 [05:31:47] Fixed 2 duplicate /gene - nuoE_1 nuoE_2 [05:31:47] Fixed 3 duplicate /gene - cmlv_1 cmlv_2 cmlv_3 [05:31:47] Fixed 3 duplicate /gene - emrR_1 emrR_2 emrR_3 [05:31:47] Fixed 6 duplicate /gene - pilS_1 pilS_2 pilS_3 pilS_4 pilS_5 pilS_6 [05:31:47] Fixed 2 duplicate /gene - exoI_1 exoI_2 [05:31:47] Fixed 2 duplicate /gene - virB9_1 virB9_2 [05:31:47] Fixed 5 duplicate /gene - algU_1 algU_2 algU_3 algU_4 algU_5 [05:31:47] Fixed 2 duplicate /gene - rnd_1 rnd_2 [05:31:47] Fixed 3 duplicate /gene - traC_1 traC_2 traC_3 [05:31:47] Fixed 2 duplicate /gene - fliC_1 fliC_2 [05:31:47] Fixed 2 duplicate /gene - ropAch1_1 ropAch1_2 [05:31:47] Fixed 3 duplicate /gene - patB_1 patB_2 patB_3 [05:31:47] Fixed 2 duplicate /gene - virB3_1 virB3_2 [05:31:47] Fixed 2 duplicate /gene - wcaJ_1 wcaJ_2 [05:31:47] Fixed 18 duplicate /gene - cdpA_1 cdpA_2 cdpA_3 cdpA_4 cdpA_5 cdpA_6 cdpA_7 cdpA_8 cdpA_9 cdpA_10 cdpA_11 cdpA_12 cdpA_13 cdpA_14 cdpA_15 cdpA_16 cdpA_17 cdpA_18 [05:31:47] Fixed 5 duplicate /gene - chuV_1 chuV_2 chuV_3 chuV_4 chuV_5 [05:31:47] Fixed 2 duplicate /gene - ubiG_1 ubiG_2 [05:31:47] Fixed 2 duplicate /gene - pilH_1 pilH_2 [05:31:47] Fixed 50 duplicate /gene - hitC_1 hitC_2 hitC_3 hitC_4 hitC_5 hitC_6 hitC_7 hitC_8 hitC_9 hitC_10 hitC_11 hitC_12 hitC_13 hitC_14 hitC_15 hitC_16 hitC_17 hitC_18 hitC_19 hitC_20 hitC_21 hitC_22 hitC_23 hitC_24 hitC_25 hitC_26 hitC_27 hitC_28 hitC_29 hitC_30 hitC_31 hitC_32 hitC_33 hitC_34 hitC_35 hitC_36 hitC_37 hitC_38 hitC_39 hitC_40 hitC_41 hitC_42 hitC_43 hitC_44 hitC_45 hitC_46 hitC_47 hitC_48 hitC_49 hitC_50 [05:31:47] Fixed 2 duplicate /gene - virF_1 virF_2 [05:31:47] Fixed 2 duplicate /gene - bcr-1_1 bcr-1_2 [05:31:47] Fixed 4 duplicate /gene - acpP_1 acpP_2 acpP_3 acpP_4 [05:31:47] Fixed 316 colliding /gene names. [05:31:47] Adding /locus_tag identifiers [05:31:47] Assigned 5108 locus_tags to CDS and RNA features. [05:31:47] Writing outputs to /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/ [05:32:15] Generating annotation statistics file [05:32:15] Generating Genbank and Sequin files [05:32:15] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.12 from https://github.com/tseemann/prokka' -Z \/data\/annotations\/Agrobacterium_rhizogenes_ST15\-16\-021\/Agrobacterium_rhizogenes_ST15\-16\-021\.err -i \/data\/annotations\/Agrobacterium_rhizogenes_ST15\-16\-021\/Agrobacterium_rhizogenes_ST15\-16\-021\.fsa 2> /dev/null [05:32:43] Deleting unwanted file: /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/errorsummary.val [05:32:43] Deleting unwanted file: /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.dr [05:32:43] Deleting unwanted file: /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.fixedproducts [05:32:43] Deleting unwanted file: /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.ecn [05:32:43] Deleting unwanted file: /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.val [05:32:43] Repairing broken .GBK output that tbl2asn produces... [05:32:43] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < \/data\/annotations\/Agrobacterium_rhizogenes_ST15\-16\-021\/Agrobacterium_rhizogenes_ST15\-16\-021\.gbf > \/data\/annotations\/Agrobacterium_rhizogenes_ST15\-16\-021\/Agrobacterium_rhizogenes_ST15\-16\-021\.gbk [05:32:45] Deleting unwanted file: /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.gbf [05:32:45] Output files: [05:32:45] /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.err [05:32:45] /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.faa [05:32:45] /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.ffn [05:32:45] /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.fna [05:32:45] /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.fsa [05:32:45] /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.gbk [05:32:45] /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.gff [05:32:45] /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.log [05:32:45] /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.sqn [05:32:45] /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.tbl [05:32:45] /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.tsv [05:32:45] /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.txt [05:32:45] Annotation finished successfully. [05:32:45] Walltime used: 22.32 minutes [05:32:45] If you use this result please cite the Prokka paper: [05:32:45] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9. [05:32:45] Type 'prokka --citation' for more details. [05:32:45] Share and enjoy!

This is the log for the taxonomy analysis for the same genome: `05:10:37.259 [main] INFO asap-taxonomy - SCRIPT: /asap/scripts/asap-taxonomy.groovy 05:10:37.282 [main] INFO asap-taxonomy - USER: null 05:10:37.287 [main] INFO asap-taxonomy - CWD: /data 05:10:37.289 [main] INFO asap-taxonomy - HOSTNAME: 57e97b00685c 05:10:37.289 [main] INFO asap-taxonomy - ASAP_HOME: /asap 05:10:37.290 [main] INFO asap-taxonomy - PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 05:10:37.326 [main] INFO asap-taxonomy - script.name: /asap/bin/groovy 05:10:37.334 [main] INFO asap-taxonomy - groovy.home: /asap/share/groovy-2.4.10 05:10:37.335 [main] INFO asap-taxonomy - file.encoding: ANSI_X3.4-1968 05:10:37.336 [main] INFO asap-taxonomy - genome-id: 6 05:10:37.505 [main] INFO asap-taxonomy - project-path: /data 05:10:37.688 [main] INFO asap-taxonomy - genome-name: Agrobacterium_rhizogenes_ST15-16-021 05:10:37.713 [main] INFO asap-taxonomy - sequence file (scaffolds): /data/scaffolds/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.fasta 05:10:37.800 [main] INFO asap-taxonomy - tmp-folder: /var/scratch/tmp-1566882637714-471 05:10:37.847 [main] INFO asap-taxonomy - start kmer species classification via Kraken 05:10:37.904 [main] INFO asap-taxonomy - exec: [sh, -c, /asap/share/kraken/kraken --fasta-input /data/scaffolds/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.fasta --threads 4 | /asap/share/kraken/kraken-translate > tax.txt] 05:10:37.908 [main] INFO asap-taxonomy - ---------------------------------------------------------------------------------------------- classify: thread count exceeds number of processors 05:11:15.641 [main] INFO asap-taxonomy - ---------------------------------------------------------------------------------------------- 05:11:15.716 [main] INFO asap-taxonomy - start 16S rRNA classification via blastn vs RDP db 05:11:15.740 [main] INFO asap-taxonomy - exec: [/asap/share/infernal/cmsearch, --rfam, --noali, --cpu, 4, --tblout, /var/scratch/tmp-1566882637714-471/cm.out, /asap/db/RF00177.cm, /data/scaffolds/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.fasta] 05:11:15.741 [main] INFO asap-taxonomy - ---------------------------------------------------------------------------------------------- 05:11:21.772 [main] INFO asap-taxonomy - ---------------------------------------------------------------------------------------------- 05:11:21.816 [main] INFO asap-taxonomy - detected 16S rRNA: contig=Arhiz_ST15-16-021_9, start=169687, end=171171, score=1559.2 05:11:22.673 [main] INFO asap-taxonomy - extracted 16S rRNA: contig=Arhiz_ST15-16-021_9, seq=CAACTTGAGAGTTTGATCCTGGCTCAGAACGAACGCTGGCGGCAGGCTTA... 05:11:22.790 [main] INFO asap-taxonomy - exec: [/asap/share/blast/bin/blastn, -query, /var/scratch/tmp-1566882637714-471/16S.fasta, -db, /asap/db/rdp/rdp-bacteria.fasta, -num_threads, 4, -evalue, 1E-10, -outfmt, 6 sseqid slen nident score stitle] 05:11:22.791 [main] INFO asap-taxonomy - ---------------------------------------------------------------------------------------------- 05:11:23.861 [main] ERROR asap-taxonomy - USAGE blastn [-h] [-help] [-import_search_strategy filename] [-export_search_strategy filename] [-task task_name] [-db database_name] [-dbsize num_letters] [-gilist filename] [-seqidlist filename] [-negative_gilist filename] [-negative_seqidlist filename] [-entrez_query entrez_query] [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm] [-subject subject_input_file] [-subject_loc range] [-query input_file] [-out output_file] [-evalue evalue] [-word_size int_value] [-gapopen open_penalty] [-gapextend extend_penalty] [-perc_identity float_value] [-qcov_hsp_perc float_value] [-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value] [-xdrop_gap_final float_value] [-searchsp int_value] [-sum_stats bool_value] [-penalty penalty] [-reward reward] [-no_greedy] [-min_raw_gapped_score int_value] [-template_type type] [-template_length int_value] [-dust DUST_options] [-filtering_db filtering_database] [-window_masker_taxid window_masker_taxid] [-window_masker_db window_masker_db] [-soft_masking soft_masking] [-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value] [-best_hit_score_edge float_value] [-window_size int_value] [-off_diagonal_range int_value] [-use_index boolean] [-index_name string] [-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines] [-outfmt format] [-show_gis] [-num_descriptions int_value] [-num_alignments int_value] [-line_length line_length] [-html] [-max_target_seqs num_sequences] [-num_threads int_value] [-remote] [-version]

DESCRIPTION Nucleotide-Nucleotide BLAST 2.7.1+

Use '-help' to print detailed descriptions of command line arguments

Error: Argument "num_threads". Illegal value, expected (>=1 and =<2): 4' Error: (CArgException::eConstraint) Argument "num_threads". Illegal value, expected (>=1 and =<2):4'

05:11:23.869 [main] ERROR asap-taxonomy - could not exec blastn! `

This is the MLST log for the same genome: 05:10:37.105 [main] INFO asap-mlst - SCRIPT: /asap/scripts/asap-mlst.groovy 05:10:37.171 [main] INFO asap-mlst - USER: null 05:10:37.172 [main] INFO asap-mlst - CWD: /data/mlst 05:10:37.172 [main] INFO asap-mlst - HOSTNAME: 57e97b00685c 05:10:37.173 [main] INFO asap-mlst - ASAP_HOME: /asap 05:10:37.176 [main] INFO asap-mlst - PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 05:10:37.268 [main] INFO asap-mlst - script.name: /asap/bin/groovy 05:10:37.269 [main] INFO asap-mlst - groovy.home: /asap/share/groovy-2.4.10 05:10:37.270 [main] INFO asap-mlst - file.encoding: ANSI_X3.4-1968 05:10:37.271 [main] INFO asap-mlst - genome-id: 6 05:10:37.474 [main] INFO asap-mlst - project-path: /data 05:10:37.671 [main] INFO asap-mlst - genome-name: Agrobacterium_rhizogenes_ST15-16-021 05:10:37.703 [main] INFO asap-mlst - sequence file (scaffolds): /data/scaffolds/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.fasta 05:10:37.799 [main] INFO asap-mlst - exec: [/asap/share/blast/bin/blastn, -query, /data/scaffolds/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.fasta, -db, /asap/db/mlst/mlst, -num_threads, 1, -dust, no, -word_size, 32, -ungapped, -max_target_seqs, 100000, -perc_identity, 99, -outfmt, 6 sseqid slen length nident] 05:10:37.820 [main] INFO asap-mlst - ---------------------------------------------------------------------------------------------- 05:10:43.069 [main] INFO asap-mlst - ----------------------------------------------------------------------------------------------

This is the virulence factor log for the same genome: 05:33:27.391 [main] INFO asap-vf - SCRIPT: /asap/scripts/asap-vf.groovy 05:33:27.406 [main] INFO asap-vf - USER: null 05:33:27.406 [main] INFO asap-vf - CWD: /data 05:33:27.407 [main] INFO asap-vf - HOSTNAME: 57e97b00685c 05:33:27.408 [main] INFO asap-vf - ASAP_HOME: /asap 05:33:27.409 [main] INFO asap-vf - PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 05:33:27.425 [main] INFO asap-vf - script.name: /asap/bin/groovy 05:33:27.426 [main] INFO asap-vf - groovy.home: /asap/share/groovy-2.4.10 05:33:27.427 [main] INFO asap-vf - file.encoding: ANSI_X3.4-1968 05:33:27.428 [main] INFO asap-vf - genome-id: 6 05:33:27.480 [main] INFO asap-vf - project-path: /data 05:33:27.632 [main] INFO asap-vf - genome-name: Agrobacterium_rhizogenes_ST15-16-021 05:33:27.661 [main] INFO asap-vf - tmp-folder: /var/scratch/tmp-1566884007639-687 05:33:27.796 [main] INFO asap-vf - exec: [/asap/share/blast/bin/blastp, -query, /data/annotations/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021.faa, -db, /asap/db/sequences/vfdb, -num_threads, 1, -culling_limit, 2, -outfmt, 6 qseqid sseqid qcovs pident evalue bitscore stitle] 05:33:27.799 [main] INFO asap-vf - ---------------------------------------------------------------------------------------------- 05:35:01.069 [main] INFO asap-vf - ---------------------------------------------------------------------------------------------- 05:35:01.473 [main] DEBUG asap-vf - delete tmp-dir

And this is the phylogeny log: 20:28:17.793 [main] INFO asap-phylogeny - SCRIPT: /asap/scripts/asap-phylogeny.groovy 20:28:17.822 [main] INFO asap-phylogeny - USER: null 20:28:17.832 [main] INFO asap-phylogeny - CWD: /data 20:28:17.832 [main] INFO asap-phylogeny - HOSTNAME: 57e97b00685c 20:28:17.833 [main] INFO asap-phylogeny - ASAP_HOME: /asap 20:28:17.834 [main] INFO asap-phylogeny - PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 20:28:17.880 [main] INFO asap-phylogeny - script.name: /asap/bin/groovy 20:28:17.881 [main] INFO asap-phylogeny - groovy.home: /asap/share/groovy-2.4.10 20:28:17.882 [main] INFO asap-phylogeny - file.encoding: ANSI_X3.4-1968 20:28:18.010 [main] INFO asap-phylogeny - project-path: /data 20:28:18.253 [main] INFO asap-phylogeny - copy ref=NZ_CP019701_2.gbk 20:28:18.265 [main] DEBUG asap-phylogeny - copy content from ref=NZ_CP019701_2.gbk, file=/data/references/NZ_CP019701_2.fasta to consensus file=/data/phylogeny/consensus.fasta 20:28:19.551 [main] INFO asap-phylogeny - copy genome-id=1, genome-name=Agrobacterium_rhizogenes_MAFF210265 20:28:20.487 [main] INFO asap-phylogeny - copy genome-id=2, genome-name=Agrobacterium_rhizogenes_ST07-17-029 20:28:21.105 [main] INFO asap-phylogeny - copy genome-id=3, genome-name=Agrobacterium_rhizogenes_ST07-17-032 20:28:21.766 [main] INFO asap-phylogeny - copy genome-id=4, genome-name=Agrobacterium_rhizogenes_ST15-13-091 20:28:22.907 [main] INFO asap-phylogeny - copy genome-id=5, genome-name=Agrobacterium_rhizogenes_ST15-16-020 20:28:23.324 [main] INFO asap-phylogeny - copy genome-id=6, genome-name=Agrobacterium_rhizogenes_ST15-16-021 20:28:23.834 [main] INFO asap-phylogeny - copy genome-id=7, genome-name=Agrobacterium_rhizogenes_NCPPB4042 20:28:24.298 [main] INFO asap-phylogeny - copy genome-id=8, genome-name=Agrobacterium_rhizogenes_NCPPB4062 20:28:24.774 [main] INFO asap-phylogeny - copy genome-id=9, genome-name=Agrobacterium_rhizogenes_ST04-16-045 20:28:25.247 [main] INFO asap-phylogeny - copy genome-id=10, genome-name=Agrobacterium_rhizogenes_ST-04-16-212 20:28:25.662 [main] INFO asap-phylogeny - copy genome-id=11, genome-name=Agrobacterium_rhizogenes_ST04-17-025 20:28:26.055 [main] INFO asap-phylogeny - copy genome-id=12, genome-name=Agrobacterium_rhizogenes_ST07-17-004 20:28:26.484 [main] INFO asap-phylogeny - copy genome-id=13, genome-name=Agrobacterium_rhizogenes_ST07-17-018 20:28:26.928 [main] INFO asap-phylogeny - copy genome-id=14, genome-name=Agrobacterium_rhizogenes_ST07-17-026 20:28:27.578 [main] INFO asap-phylogeny - copy genome-id=15, genome-name=Agrobacterium_rhizogenes_ST15-13-042 20:28:28.090 [main] INFO asap-phylogeny - copy genome-id=16, genome-name=Agrobacterium_rhizogenes_ST15-13-056 20:28:28.494 [main] INFO asap-phylogeny - copy genome-id=17, genome-name=Agrobacterium_rhizogenes_ST15-13-057 20:28:28.765 [main] INFO asap-phylogeny - exec: [/asap/share/fasttreemp/FastTreeMP, -nt, -boot, 100, -out, /data/phylogeny/tree.nwk, /data/phylogeny/consensus.fasta] 20:28:28.769 [main] INFO asap-phylogeny - ---------------------------------------------------------------------------------------------- FastTree Version 2.1.10 Double precision (No SSE3), OpenMP (2 threads) Alignment: /data/phylogeny/consensus.fasta Nucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 100 Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1 TopHits: 1.00*sqrtN close=default refresh=0.80 ML Model: Jukes-Cantor, CAT approximation with 20 rate categories 2.84 seconds: Checking top hits for 1 of 17 seqs Initial topology in 11.55 seconds Refining topology: 16 rounds ME-NNIs, 2 rounds ME-SPRs, 8 rounds ML-NNIs 11.55 seconds: ME NNI round 1 of 16, 1 of 15 splits 15.06 seconds: SPR round 1 of 2, 1 of 32 nodes 87.89 seconds: ME NNI round 6 of 16, 1 of 15 splits 91.13 seconds: SPR round 2 of 2, 1 of 32 nodes 161.54 seconds: ME NNI round 11 of 16, 1 of 15 splits Total branch-length 0.048 after 169.64 sec 170.39 seconds: ML Lengths 1 of 15 splits 212.69 seconds: ML NNI round 1 of 8, 1 of 15 splits ML-NNI round 1: LogLk = -5456191.492 NNIs 1 max delta 588.30 Time 306.88 309.88 seconds: Site likelihoods with rate category 1 of 20 312.54 seconds: Site likelihoods with rate category 2 of 20 315.15 seconds: Site likelihoods with rate category 3 of 20 317.91 seconds: Site likelihoods with rate category 4 of 20 320.49 seconds: Site likelihoods with rate category 5 of 20 323.07 seconds: Site likelihoods with rate category 6 of 20 326.42 seconds: Site likelihoods with rate category 7 of 20 329.80 seconds: Site likelihoods with rate category 8 of 20 333.38 seconds: Site likelihoods with rate category 9 of 20 336.85 seconds: Site likelihoods with rate category 10 of 20 340.99 seconds: Site likelihoods with rate category 11 of 20 344.25 seconds: Site likelihoods with rate category 12 of 20 347.79 seconds: Site likelihoods with rate category 13 of 20 351.45 seconds: Site likelihoods with rate category 14 of 20 354.90 seconds: Site likelihoods with rate category 15 of 20 358.41 seconds: Site likelihoods with rate category 16 of 20 20:34:35.820 [main] ERROR asap-phylogeny - could not exec fasttreeMP!

Thank you very much in advance for your help!

Cheers, Pablo

oschwengers commented 5 years ago

@pavlo888 , could you please provide some more details regarding your system? I think I have an idea regarding this issue. I assume you have only 2 cores, thus the numbers of cores you have is smaller than 4. In this case, I need to add a dynamic threshold. This kind of bug never occurred before as we always used machines with at least 4 cores for testing.

So thank you very much for this bug report! If you once again provide some information:

I'll start immediately on a bugfix...

pavlo888 commented 5 years ago

Hi @oschwengers,

I have just checked that indeed my laptop got only 2 cores ;(

Here are the details you asked for: OS --> MacOS Mojave 10.14.6 Number of cores --> 2 RAM --> 8 GB

This is the complete asap.log file

2019-08-26 21:53:11.405 INFO [main] bio.comp.jlu.asap.ASAP : version: 1.1.2 2019-08-26 21:53:11.413 INFO [main] bio.comp.jlu.asap.ASAP : project-path: /data 2019-08-26 21:53:11.420 INFO [main] bio.comp.jlu.asap.ASAP : USER: null 2019-08-26 21:53:11.421 INFO [main] bio.comp.jlu.asap.ASAP : CWD: null 2019-08-26 21:53:11.421 INFO [main] bio.comp.jlu.asap.ASAP : HOSTNAME: 57e97b00685c 2019-08-26 21:53:11.423 INFO [main] bio.comp.jlu.asap.ASAP : ASAP_HOME: /asap 2019-08-26 21:53:11.424 INFO [main] bio.comp.jlu.asap.ASAP : PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 2019-08-26 21:53:11.456 INFO [main] bio.comp.jlu.asap.ASAP : file.encoding: ANSI_X3.4-1968 2019-08-26 21:53:12.402 INFO [main] bio.comp.jlu.asap.ASAP : execution mode: local 2019-08-26 21:53:12.403 INFO [main] bio.comp.jlu.asap.ASAP : slot size: 1 2019-08-26 21:53:12.585 DEBUG [main] bio.comp.jlu.asap.ASAP : build project folder structure 2019-08-26 21:53:12.591 DEBUG [main] bio.comp.jlu.asap.ASAP : created folder: /data/sequences 2019-08-26 21:53:12.603 DEBUG [main] bio.comp.jlu.asap.ASAP : created folder: /data/references 2019-08-26 21:53:12.612 DEBUG [main] bio.comp.jlu.asap.ASAP : created folder: /data/reads_raw 2019-08-26 21:53:12.616 DEBUG [main] bio.comp.jlu.asap.ASAP : created folder: /data/reads_qc 2019-08-26 21:53:12.620 DEBUG [main] bio.comp.jlu.asap.ASAP : created folder: /data/assemblies 2019-08-26 21:53:12.624 DEBUG [main] bio.comp.jlu.asap.ASAP : created folder: /data/scaffolds 2019-08-26 21:53:12.628 DEBUG [main] bio.comp.jlu.asap.ASAP : created folder: /data/annotations 2019-08-26 21:53:12.632 DEBUG [main] bio.comp.jlu.asap.ASAP : created folder: /data/taxonomy 2019-08-26 21:53:12.635 DEBUG [main] bio.comp.jlu.asap.ASAP : created folder: /data/mlst 2019-08-26 21:53:12.640 DEBUG [main] bio.comp.jlu.asap.ASAP : created folder: /data/abr 2019-08-26 21:53:12.643 DEBUG [main] bio.comp.jlu.asap.ASAP : created folder: /data/vf 2019-08-26 21:53:12.646 DEBUG [main] bio.comp.jlu.asap.ASAP : created folder: /data/mappings 2019-08-26 21:53:12.652 DEBUG [main] bio.comp.jlu.asap.ASAP : created folder: /data/snps 2019-08-26 21:53:12.831 DEBUG [ConfigWriterThread] b.comp.jlu.asap.ConfigWriterThread : start json writer... 2019-08-26 21:53:13.099 DEBUG [Thread-2] b.c.j.a.steps.ReferenceProcessings : genbank: /data/references/NZ_CP019701_2.gbk, fileName: NZ_CP019701_2, fasta: /data/references/NZ_CP019701_2.fasta 2019-08-26 21:53:13.238 INFO [Thread-2] b.c.j.a.steps.ReferenceProcessings : exec: [/usr/bin/env, python3, -c, from Bio import SeqIO SeqIO.convert( "/data/references/NZ_CP019701_2.gbk", "genbank", "/data/references/NZ_CP019701_2.fasta", "fasta" ) ] 2019-08-26 21:53:13.240 INFO [Thread-2] b.c.j.a.steps.ReferenceProcessings : ---------------------------------------------------------------------------------------------- 2019-08-26 21:53:14.056 INFO [Thread-2] b.c.j.a.steps.ReferenceProcessings : ---------------------------------------------------------------------------------------------- 2019-08-26 21:53:14.551 INFO [Thread-2] b.c.j.a.steps.ReferenceProcessings : exec: [/asap/share/samtools/samtools, faidx, /data/references/NZ_CP019701_2.fasta] 2019-08-26 21:53:14.552 INFO [Thread-2] b.c.j.a.steps.ReferenceProcessings : ---------------------------------------------------------------------------------------------- 2019-08-26 21:53:14.767 INFO [Thread-2] b.c.j.a.steps.ReferenceProcessings : ---------------------------------------------------------------------------------------------- 2019-08-26 21:53:14.771 DEBUG [Thread-2] b.c.j.a.steps.ReferenceProcessings : genbank: /data/references/NZ_CP019702_2.gbk, fileName: NZ_CP019702_2, fasta: /data/references/NZ_CP019702_2.fasta 2019-08-26 21:53:14.772 INFO [Thread-2] b.c.j.a.steps.ReferenceProcessings : exec: [/usr/bin/env, python3, -c, from Bio import SeqIO SeqIO.convert( "/data/references/NZ_CP019702_2.gbk", "genbank", "/data/references/NZ_CP019702_2.fasta", "fasta" ) ] 2019-08-26 21:53:14.773 INFO [Thread-2] b.c.j.a.steps.ReferenceProcessings : ---------------------------------------------------------------------------------------------- 2019-08-26 21:53:15.269 INFO [Thread-2] b.c.j.a.steps.ReferenceProcessings : ---------------------------------------------------------------------------------------------- 2019-08-26 21:53:15.502 INFO [Thread-2] b.c.j.a.steps.ReferenceProcessings : exec: [/asap/share/samtools/samtools, faidx, /data/references/NZ_CP019702_2.fasta] 2019-08-26 21:53:15.505 INFO [Thread-2] b.c.j.a.steps.ReferenceProcessings : ---------------------------------------------------------------------------------------------- 2019-08-26 21:53:15.547 INFO [Thread-2] b.c.j.a.steps.ReferenceProcessings : ---------------------------------------------------------------------------------------------- 2019-08-26 21:53:15.552 DEBUG [Thread-2] b.c.j.a.steps.ReferenceProcessings : genbank: /data/references/NZ_CP019703_3.gbk, fileName: NZ_CP019703_3, fasta: /data/references/NZ_CP019703_3.fasta 2019-08-26 21:53:15.552 INFO [Thread-2] b.c.j.a.steps.ReferenceProcessings : exec: [/usr/bin/env, python3, -c, from Bio import SeqIO SeqIO.convert( "/data/references/NZ_CP019703_3.gbk", "genbank", "/data/references/NZ_CP019703_3.fasta", "fasta" ) ] 2019-08-26 21:53:15.553 INFO [Thread-2] b.c.j.a.steps.ReferenceProcessings : ---------------------------------------------------------------------------------------------- 2019-08-26 21:53:15.828 INFO [Thread-2] b.c.j.a.steps.ReferenceProcessings : ---------------------------------------------------------------------------------------------- 2019-08-26 21:53:15.865 INFO [Thread-2] b.c.j.a.steps.ReferenceProcessings : exec: [/asap/share/samtools/samtools, faidx, /data/references/NZ_CP019703_3.fasta] 2019-08-26 21:53:15.866 INFO [Thread-2] b.c.j.a.steps.ReferenceProcessings : ---------------------------------------------------------------------------------------------- 2019-08-26 21:53:15.893 INFO [Thread-2] b.c.j.a.steps.ReferenceProcessings : ---------------------------------------------------------------------------------------------- 2019-08-26 21:53:23.101 DEBUG [Thread-4] b.c.j.asap.steps.SNPAnnotationSetup : create snpEff ref dir: /data/snps/ref 2019-08-26 21:53:23.103 DEBUG [Thread-3] b.c.jlu.asap.steps.MappingIndices : reference-file: NZ_CP019701_2.gbk, fileName: NZ_CP019701_2, fasta: /data/references/NZ_CP019701_2.fasta 2019-08-26 21:53:23.106 INFO [Thread-3] b.c.jlu.asap.steps.MappingIndices : exec: [/asap/share/bowtie2/bowtie2-build, /data/references/NZ_CP019701_2.fasta, NZ_CP019701_2] 2019-08-26 21:53:23.107 DEBUG [Thread-4] b.c.j.asap.steps.SNPAnnotationSetup : create hard link reference genome->snpEff ref: /data/snps/ref/genes.gbk -> /data/references/NZ_CP019701_2.gbk 2019-08-26 21:53:23.107 INFO [Thread-3] b.c.jlu.asap.steps.MappingIndices : ---------------------------------------------------------------------------------------------- 2019-08-26 21:53:23.659 INFO [Thread-4] b.c.j.asap.steps.SNPAnnotationSetup : build snpEff database: /data/snps/snpEff.config 2019-08-26 21:53:26.947 INFO [Thread-3] b.c.jlu.asap.steps.MappingIndices : ---------------------------------------------------------------------------------------------- 2019-08-26 21:53:26.948 DEBUG [Thread-3] b.c.jlu.asap.steps.MappingIndices : reference-file: NZ_CP019702_2.gbk, fileName: NZ_CP019702_2, fasta: /data/references/NZ_CP019702_2.fasta 2019-08-26 21:53:26.949 INFO [Thread-3] b.c.jlu.asap.steps.MappingIndices : exec: [/asap/share/bowtie2/bowtie2-build, /data/references/NZ_CP019702_2.fasta, NZ_CP019702_2] 2019-08-26 21:53:26.951 INFO [Thread-3] b.c.jlu.asap.steps.MappingIndices : ---------------------------------------------------------------------------------------------- 2019-08-26 21:53:31.518 INFO [Thread-3] b.c.jlu.asap.steps.MappingIndices : ---------------------------------------------------------------------------------------------- 2019-08-26 21:53:31.520 DEBUG [Thread-3] b.c.jlu.asap.steps.MappingIndices : reference-file: NZ_CP019703_3.gbk, fileName: NZ_CP019703_3, fasta: /data/references/NZ_CP019703_3.fasta 2019-08-26 21:53:31.521 INFO [Thread-3] b.c.jlu.asap.steps.MappingIndices : exec: [/asap/share/bowtie2/bowtie2-build, /data/references/NZ_CP019703_3.fasta, NZ_CP019703_3] 2019-08-26 21:53:31.522 INFO [Thread-3] b.c.jlu.asap.steps.MappingIndices : ---------------------------------------------------------------------------------------------- 2019-08-26 21:53:33.087 INFO [Thread-3] b.c.jlu.asap.steps.MappingIndices : ---------------------------------------------------------------------------------------------- 2019-08-26 21:53:34.559 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : genome-id=1: running... 2019-08-26 21:53:34.706 DEBUG [QC-Step-Thread-1] bio.comp.jlu.asap.genomes.QCStep : genome.id=1: found reads: read.type=paired-end 2019-08-26 21:53:34.711 DEBUG [QC-Step-Thread-1] bio.comp.jlu.asap.genomes.QCStep : genome.id=1: dir "/data/reads_qc/Agrobacterium_rhizogenes_MAFF210265" created 2019-08-26 21:53:34.717 DEBUG [QC-Step-Thread-1] bio.comp.jlu.asap.genomes.QCStep : genome.id=1: exec: [/asap/bin/groovy, /asap/scripts/asap-qc.groovy, --project-path, /data, --genome-id, 1] 2019-08-26 22:03:11.002 DEBUG [QC-Step-Thread-1] bio.comp.jlu.asap.genomes.QCStep : genome.id=1: exp backoff=1 s 2019-08-26 22:03:34.287 DEBUG [Assembly-Step-Thread-1] b.c.jlu.asap.genomes.AssemblyStep : genome.id=1: dir "/data/assemblies/Agrobacterium_rhizogenes_MAFF210265" created 2019-08-26 22:03:34.386 DEBUG [Assembly-Step-Thread-1] b.c.jlu.asap.genomes.AssemblyStep : genome.id=1: exec: [/asap/bin/groovy, /asap/scripts/asap-assembly.groovy, --project-path, /data, --genome-id, 1] 2019-08-26 22:03:34.387 DEBUG [Mapping-Step-Thread-1] b.comp.jlu.asap.genomes.MappingStep : genome.id=1: exec: [/asap/bin/groovy, /asap/scripts/asap-mapping.groovy, --project-path, /data, --genome-id, 1] 2019-08-26 22:08:17.515 DEBUG [Mapping-Step-Thread-1] b.comp.jlu.asap.genomes.MappingStep : genome.id=1: exp backoff=1 s 2019-08-26 22:08:33.814 DEBUG [SNPDetection-Step-Thread-1] b.c.j.asap.genomes.SNPDetectionStep : genome.id=1: exec: [/asap/bin/groovy, /asap/scripts/asap-snp.groovy, --project-path, /data, --genome-id, 1] 2019-08-26 22:10:26.979 DEBUG [SNPDetection-Step-Thread-1] b.c.j.asap.genomes.SNPDetectionStep : genome.id=1: exp backoff=1 s 2019-08-26 22:44:07.821 DEBUG [Assembly-Step-Thread-1] b.c.jlu.asap.genomes.AssemblyStep : genome.id=1: exp backoff=1 s 2019-08-26 22:44:31.466 DEBUG [Scaffolding-Step-Thread-1] b.c.j.asap.genomes.ScaffoldingStep : run 1: dir "/data/scaffolds/Agrobacterium_rhizogenes_MAFF210265" created 2019-08-26 22:44:31.473 DEBUG [Scaffolding-Step-Thread-1] b.c.j.asap.genomes.ScaffoldingStep : genome.id=1: exec=[/asap/bin/groovy, /asap/scripts/asap-scaffolding.groovy, --project-path, /data, --genome-id, 1] 2019-08-26 22:46:24.644 DEBUG [Scaffolding-Step-Thread-1] b.c.j.asap.genomes.ScaffoldingStep : genome.id=1: exp backoff=1 s 2019-08-26 22:46:31.329 DEBUG [Annotation-Step-Thread-1] b.c.jlu.asap.genomes.AnnotationStep : genome.id=1: found user provided pseudo genome: path=/data/scaffolds/Agrobacterium_rhizogenes_MAFF210265/Agrobacterium_rhizogenes_MAFF210265-pseudo.fasta 2019-08-26 22:46:31.338 DEBUG [ABRDetection-Step-Thread-1] b.c.j.asap.genomes.ABRDetectionStep : genome.id=1: exec: [/asap/bin/groovy, /asap/scripts/asap-abr.groovy, --project-path, /data, --genome-id, 1] 2019-08-26 22:46:31.341 DEBUG [Taxonomy-Step-Thread-1] b.c.jlu.asap.genomes.TaxonomyStep : genome.id=1: exec: [/asap/bin/groovy, /asap/scripts/asap-taxonomy.groovy, --project-path, /data, --genome-id, 1] 2019-08-26 22:46:31.344 DEBUG [MLST-Step-Thread-1] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=1: exec: [/asap/bin/groovy, /asap/scripts/asap-mlst.groovy, --project-path, /data, --genome-id, 1] 2019-08-26 22:46:31.349 DEBUG [Annotation-Step-Thread-1] b.c.jlu.asap.genomes.AnnotationStep : run 1: dir '/data/annotations/Agrobacterium_rhizogenes_MAFF210265' created 2019-08-26 22:46:31.856 DEBUG [Annotation-Step-Thread-1] b.c.jlu.asap.genomes.AnnotationStep : genome.id=1: exec: [/asap/share/prokka/bin/prokka, --genus, Agrobacterium, --species, rhizogenes, --strain, MAFF210265, --prefix, Agrobacterium_rhizogenes_MAFF210265, --locustag, Arhiz_MAFF210265, --centre, JLU, --cpus, 8, --outdir, /data/annotations/Agrobacterium_rhizogenes_MAFF210265, --proteins, /asap/db/sequences/asap-proteins.faa, --usegenus, --force, --addgenes, --rfam, --rawproduct, /data/scaffolds/Agrobacterium_rhizogenes_MAFF210265/Agrobacterium_rhizogenes_MAFF210265-pseudo.fasta] 2019-08-26 22:46:49.374 DEBUG [MLST-Step-Thread-1] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=1: exp backoff=1 s 2019-08-26 22:47:29.098 ERROR [Taxonomy-Step-Thread-1] b.comp.jlu.asap.genomes.GenomeStep : taxonomy genome step for genome id=1 aborted! java.lang.IllegalStateException: abnormal taxonomy exit code! exitCode=1 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:60) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:235) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.genomes.TaxonomyStep.runStep(TaxonomyStep.groovy:146) at bio.comp.jlu.asap.genomes.TaxonomyStep$runStep$2.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at bio.comp.jlu.asap.genomes.ScaffoldingStep$runStep$2.callCurrent(Unknown Source) at bio.comp.jlu.asap.genomes.GenomeStep.run(GenomeStep.groovy:86) 2019-08-26 22:55:46.972 DEBUG [ABRDetection-Step-Thread-1] b.c.j.asap.genomes.ABRDetectionStep : genome.id=1: exp backoff=1 s 2019-08-26 23:09:29.821 DEBUG [VFDetection-Step-Thread-1] b.c.j.asap.genomes.VFDetectionStep : genome.id=1: exec: [/asap/bin/groovy, /asap/scripts/asap-vf.groovy, --project-path, /data, --genome-id, 1] 2019-08-26 23:11:20.000 DEBUG [VFDetection-Step-Thread-1] b.c.j.asap.genomes.VFDetectionStep : genome.id=1: exp backoff=1 s 2019-08-26 23:11:20.085 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : genome-id=2: running... 2019-08-26 23:11:20.100 DEBUG [QC-Step-Thread-2] bio.comp.jlu.asap.genomes.QCStep : genome.id=2: found reads: read.type=paired-end 2019-08-26 23:11:20.117 DEBUG [QC-Step-Thread-2] bio.comp.jlu.asap.genomes.QCStep : genome.id=2: dir "/data/reads_qc/Agrobacterium_rhizogenes_ST07-17-029" created 2019-08-26 23:11:20.118 DEBUG [QC-Step-Thread-2] bio.comp.jlu.asap.genomes.QCStep : genome.id=2: exec: [/asap/bin/groovy, /asap/scripts/asap-qc.groovy, --project-path, /data, --genome-id, 2] 2019-08-26 23:22:34.524 DEBUG [QC-Step-Thread-2] bio.comp.jlu.asap.genomes.QCStep : genome.id=2: exp backoff=1 s 2019-08-26 23:23:23.931 DEBUG [Mapping-Step-Thread-2] b.comp.jlu.asap.genomes.MappingStep : genome.id=2: exec: [/asap/bin/groovy, /asap/scripts/asap-mapping.groovy, --project-path, /data, --genome-id, 2] 2019-08-26 23:23:23.982 DEBUG [Assembly-Step-Thread-2] b.c.jlu.asap.genomes.AssemblyStep : genome.id=2: dir "/data/assemblies/Agrobacterium_rhizogenes_ST07-17-029" created 2019-08-26 23:23:23.987 DEBUG [Assembly-Step-Thread-2] b.c.jlu.asap.genomes.AssemblyStep : genome.id=2: exec: [/asap/bin/groovy, /asap/scripts/asap-assembly.groovy, --project-path, /data, --genome-id, 2] 2019-08-26 23:29:40.912 DEBUG [Mapping-Step-Thread-2] b.comp.jlu.asap.genomes.MappingStep : genome.id=2: exp backoff=1 s 2019-08-26 23:30:22.214 DEBUG [SNPDetection-Step-Thread-2] b.c.j.asap.genomes.SNPDetectionStep : genome.id=2: exec: [/asap/bin/groovy, /asap/scripts/asap-snp.groovy, --project-path, /data, --genome-id, 2] 2019-08-26 23:32:48.652 DEBUG [SNPDetection-Step-Thread-2] b.c.j.asap.genomes.SNPDetectionStep : genome.id=2: exp backoff=1 s 2019-08-27 00:09:18.551 DEBUG [Assembly-Step-Thread-2] b.c.jlu.asap.genomes.AssemblyStep : genome.id=2: exp backoff=1 s 2019-08-27 00:09:20.939 DEBUG [Scaffolding-Step-Thread-2] b.c.j.asap.genomes.ScaffoldingStep : run 2: dir "/data/scaffolds/Agrobacterium_rhizogenes_ST07-17-029" created 2019-08-27 00:09:20.946 DEBUG [Scaffolding-Step-Thread-2] b.c.j.asap.genomes.ScaffoldingStep : genome.id=2: exec=[/asap/bin/groovy, /asap/scripts/asap-scaffolding.groovy, --project-path, /data, --genome-id, 2] 2019-08-27 00:10:55.973 DEBUG [Scaffolding-Step-Thread-2] b.c.j.asap.genomes.ScaffoldingStep : genome.id=2: exp backoff=1 s 2019-08-27 00:11:19.888 DEBUG [MLST-Step-Thread-2] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=2: exec: [/asap/bin/groovy, /asap/scripts/asap-mlst.groovy, --project-path, /data, --genome-id, 2] 2019-08-27 00:11:20.787 DEBUG [Taxonomy-Step-Thread-2] b.c.jlu.asap.genomes.TaxonomyStep : genome.id=2: exec: [/asap/bin/groovy, /asap/scripts/asap-taxonomy.groovy, --project-path, /data, --genome-id, 2] 2019-08-27 00:11:20.794 DEBUG [ABRDetection-Step-Thread-2] b.c.j.asap.genomes.ABRDetectionStep : genome.id=2: exec: [/asap/bin/groovy, /asap/scripts/asap-abr.groovy, --project-path, /data, --genome-id, 2] 2019-08-27 00:11:20.796 DEBUG [Annotation-Step-Thread-2] b.c.jlu.asap.genomes.AnnotationStep : genome.id=2: found user provided pseudo genome: path=/data/scaffolds/Agrobacterium_rhizogenes_ST07-17-029/Agrobacterium_rhizogenes_ST07-17-029-pseudo.fasta 2019-08-27 00:11:20.808 DEBUG [Annotation-Step-Thread-2] b.c.jlu.asap.genomes.AnnotationStep : run 2: dir '/data/annotations/Agrobacterium_rhizogenes_ST07-17-029' created 2019-08-27 00:11:20.841 DEBUG [Annotation-Step-Thread-2] b.c.jlu.asap.genomes.AnnotationStep : genome.id=2: exec: [/asap/share/prokka/bin/prokka, --genus, Agrobacterium, --species, rhizogenes, --strain, ST07-17-029, --prefix, Agrobacterium_rhizogenes_ST07-17-029, --locustag, Arhiz_ST07-17-029, --centre, JLU, --cpus, 8, --outdir, /data/annotations/Agrobacterium_rhizogenes_ST07-17-029, --proteins, /asap/db/sequences/asap-proteins.faa, --usegenus, --force, --addgenes, --rfam, --rawproduct, /data/scaffolds/Agrobacterium_rhizogenes_ST07-17-029/Agrobacterium_rhizogenes_ST07-17-029-pseudo.fasta] 2019-08-27 00:11:36.708 DEBUG [MLST-Step-Thread-2] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=2: exp backoff=1 s 2019-08-27 00:12:17.229 ERROR [Taxonomy-Step-Thread-2] b.comp.jlu.asap.genomes.GenomeStep : taxonomy genome step for genome id=2 aborted! java.lang.IllegalStateException: abnormal taxonomy exit code! exitCode=1 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.genomes.TaxonomyStep.runStep(TaxonomyStep.groovy:146) at bio.comp.jlu.asap.genomes.TaxonomyStep$runStep$2.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at bio.comp.jlu.asap.genomes.MLSTStep$runStep$2.callCurrent(Unknown Source) at bio.comp.jlu.asap.genomes.GenomeStep.run(GenomeStep.groovy:86) 2019-08-27 00:21:14.521 DEBUG [ABRDetection-Step-Thread-2] b.c.j.asap.genomes.ABRDetectionStep : genome.id=2: exp backoff=1 s 2019-08-27 00:35:19.289 DEBUG [VFDetection-Step-Thread-2] b.c.j.asap.genomes.VFDetectionStep : genome.id=2: exec: [/asap/bin/groovy, /asap/scripts/asap-vf.groovy, --project-path, /data, --genome-id, 2] 2019-08-27 00:37:06.264 DEBUG [VFDetection-Step-Thread-2] b.c.j.asap.genomes.VFDetectionStep : genome.id=2: exp backoff=1 s 2019-08-27 00:37:06.305 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : genome-id=3: running... 2019-08-27 00:37:06.339 DEBUG [QC-Step-Thread-3] bio.comp.jlu.asap.genomes.QCStep : genome.id=3: found reads: read.type=paired-end 2019-08-27 00:37:06.494 DEBUG [QC-Step-Thread-3] bio.comp.jlu.asap.genomes.QCStep : genome.id=3: dir "/data/reads_qc/Agrobacterium_rhizogenes_ST07-17-032" created 2019-08-27 00:37:06.497 DEBUG [QC-Step-Thread-3] bio.comp.jlu.asap.genomes.QCStep : genome.id=3: exec: [/asap/bin/groovy, /asap/scripts/asap-qc.groovy, --project-path, /data, --genome-id, 3] 2019-08-27 00:47:03.837 DEBUG [QC-Step-Thread-3] bio.comp.jlu.asap.genomes.QCStep : genome.id=3: exp backoff=1 s 2019-08-27 00:47:05.717 DEBUG [Mapping-Step-Thread-3] b.comp.jlu.asap.genomes.MappingStep : genome.id=3: exec: [/asap/bin/groovy, /asap/scripts/asap-mapping.groovy, --project-path, /data, --genome-id, 3] 2019-08-27 00:47:05.720 DEBUG [Assembly-Step-Thread-3] b.c.jlu.asap.genomes.AssemblyStep : genome.id=3: dir "/data/assemblies/Agrobacterium_rhizogenes_ST07-17-032" created 2019-08-27 00:47:05.723 DEBUG [Assembly-Step-Thread-3] b.c.jlu.asap.genomes.AssemblyStep : genome.id=3: exec: [/asap/bin/groovy, /asap/scripts/asap-assembly.groovy, --project-path, /data, --genome-id, 3] 2019-08-27 00:51:47.731 DEBUG [Mapping-Step-Thread-3] b.comp.jlu.asap.genomes.MappingStep : genome.id=3: exp backoff=1 s 2019-08-27 00:52:05.374 DEBUG [SNPDetection-Step-Thread-3] b.c.j.asap.genomes.SNPDetectionStep : genome.id=3: exec: [/asap/bin/groovy, /asap/scripts/asap-snp.groovy, --project-path, /data, --genome-id, 3] 2019-08-27 00:53:43.373 DEBUG [SNPDetection-Step-Thread-3] b.c.j.asap.genomes.SNPDetectionStep : genome.id=3: exp backoff=1 s 2019-08-27 01:32:20.316 DEBUG [Assembly-Step-Thread-3] b.c.jlu.asap.genomes.AssemblyStep : genome.id=3: exp backoff=1 s 2019-08-27 01:33:02.805 DEBUG [Scaffolding-Step-Thread-3] b.c.j.asap.genomes.ScaffoldingStep : run 3: dir "/data/scaffolds/Agrobacterium_rhizogenes_ST07-17-032" created 2019-08-27 01:33:02.808 DEBUG [Scaffolding-Step-Thread-3] b.c.j.asap.genomes.ScaffoldingStep : genome.id=3: exec=[/asap/bin/groovy, /asap/scripts/asap-scaffolding.groovy, --project-path, /data, --genome-id, 3] 2019-08-27 01:34:58.830 DEBUG [Scaffolding-Step-Thread-3] b.c.j.asap.genomes.ScaffoldingStep : genome.id=3: exp backoff=1 s 2019-08-27 01:35:02.566 DEBUG [Taxonomy-Step-Thread-3] b.c.jlu.asap.genomes.TaxonomyStep : genome.id=3: exec: [/asap/bin/groovy, /asap/scripts/asap-taxonomy.groovy, --project-path, /data, --genome-id, 3] 2019-08-27 01:35:02.567 DEBUG [ABRDetection-Step-Thread-3] b.c.j.asap.genomes.ABRDetectionStep : genome.id=3: exec: [/asap/bin/groovy, /asap/scripts/asap-abr.groovy, --project-path, /data, --genome-id, 3] 2019-08-27 01:35:02.570 DEBUG [MLST-Step-Thread-3] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=3: exec: [/asap/bin/groovy, /asap/scripts/asap-mlst.groovy, --project-path, /data, --genome-id, 3] 2019-08-27 01:35:02.575 DEBUG [Annotation-Step-Thread-3] b.c.jlu.asap.genomes.AnnotationStep : genome.id=3: found user provided pseudo genome: path=/data/scaffolds/Agrobacterium_rhizogenes_ST07-17-032/Agrobacterium_rhizogenes_ST07-17-032-pseudo.fasta 2019-08-27 01:35:02.990 DEBUG [Annotation-Step-Thread-3] b.c.jlu.asap.genomes.AnnotationStep : run 3: dir '/data/annotations/Agrobacterium_rhizogenes_ST07-17-032' created 2019-08-27 01:35:02.997 DEBUG [Annotation-Step-Thread-3] b.c.jlu.asap.genomes.AnnotationStep : genome.id=3: exec: [/asap/share/prokka/bin/prokka, --genus, Agrobacterium, --species, rhizogenes, --strain, ST07-17-032, --prefix, Agrobacterium_rhizogenes_ST07-17-032, --locustag, Arhiz_ST07-17-032, --centre, JLU, --cpus, 8, --outdir, /data/annotations/Agrobacterium_rhizogenes_ST07-17-032, --proteins, /asap/db/sequences/asap-proteins.faa, --usegenus, --force, --addgenes, --rfam, --rawproduct, /data/scaffolds/Agrobacterium_rhizogenes_ST07-17-032/Agrobacterium_rhizogenes_ST07-17-032-pseudo.fasta] 2019-08-27 01:35:21.863 DEBUG [MLST-Step-Thread-3] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=3: exp backoff=1 s 2019-08-27 01:35:59.996 ERROR [Taxonomy-Step-Thread-3] b.comp.jlu.asap.genomes.GenomeStep : taxonomy genome step for genome id=3 aborted! java.lang.IllegalStateException: abnormal taxonomy exit code! exitCode=1 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.genomes.TaxonomyStep.runStep(TaxonomyStep.groovy:146) at bio.comp.jlu.asap.genomes.TaxonomyStep$runStep$2.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at bio.comp.jlu.asap.genomes.ScaffoldingStep$runStep$2.callCurrent(Unknown Source) at bio.comp.jlu.asap.genomes.GenomeStep.run(GenomeStep.groovy:86) 2019-08-27 01:46:31.866 DEBUG [ABRDetection-Step-Thread-3] b.c.j.asap.genomes.ABRDetectionStep : genome.id=3: exp backoff=1 s 2019-08-27 02:09:00.322 DEBUG [VFDetection-Step-Thread-3] b.c.j.asap.genomes.VFDetectionStep : genome.id=3: exec: [/asap/bin/groovy, /asap/scripts/asap-vf.groovy, --project-path, /data, --genome-id, 3] 2019-08-27 02:11:19.221 DEBUG [VFDetection-Step-Thread-3] b.c.j.asap.genomes.VFDetectionStep : genome.id=3: exp backoff=1 s 2019-08-27 02:11:19.387 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : genome-id=4: running... 2019-08-27 02:11:19.405 DEBUG [QC-Step-Thread-4] bio.comp.jlu.asap.genomes.QCStep : genome.id=4: found reads: read.type=paired-end 2019-08-27 02:11:19.412 DEBUG [QC-Step-Thread-4] bio.comp.jlu.asap.genomes.QCStep : genome.id=4: dir "/data/reads_qc/Agrobacterium_rhizogenes_ST15-13-091" created 2019-08-27 02:11:19.415 DEBUG [QC-Step-Thread-4] bio.comp.jlu.asap.genomes.QCStep : genome.id=4: exec: [/asap/bin/groovy, /asap/scripts/asap-qc.groovy, --project-path, /data, --genome-id, 4] 2019-08-27 02:20:25.044 DEBUG [QC-Step-Thread-4] bio.comp.jlu.asap.genomes.QCStep : genome.id=4: exp backoff=1 s 2019-08-27 02:21:18.745 DEBUG [Mapping-Step-Thread-4] b.comp.jlu.asap.genomes.MappingStep : genome.id=4: exec: [/asap/bin/groovy, /asap/scripts/asap-mapping.groovy, --project-path, /data, --genome-id, 4] 2019-08-27 02:21:18.770 DEBUG [Assembly-Step-Thread-4] b.c.jlu.asap.genomes.AssemblyStep : genome.id=4: dir "/data/assemblies/Agrobacterium_rhizogenes_ST15-13-091" created 2019-08-27 02:21:18.772 DEBUG [Assembly-Step-Thread-4] b.c.jlu.asap.genomes.AssemblyStep : genome.id=4: exec: [/asap/bin/groovy, /asap/scripts/asap-assembly.groovy, --project-path, /data, --genome-id, 4] 2019-08-27 02:25:55.709 DEBUG [Mapping-Step-Thread-4] b.comp.jlu.asap.genomes.MappingStep : genome.id=4: exp backoff=1 s 2019-08-27 02:26:18.416 DEBUG [SNPDetection-Step-Thread-4] b.c.j.asap.genomes.SNPDetectionStep : genome.id=4: exec: [/asap/bin/groovy, /asap/scripts/asap-snp.groovy, --project-path, /data, --genome-id, 4] 2019-08-27 02:28:09.424 DEBUG [SNPDetection-Step-Thread-4] b.c.j.asap.genomes.SNPDetectionStep : genome.id=4: exp backoff=1 s 2019-08-27 03:00:30.670 DEBUG [Assembly-Step-Thread-4] b.c.jlu.asap.genomes.AssemblyStep : genome.id=4: exp backoff=1 s 2019-08-27 03:01:16.175 DEBUG [Scaffolding-Step-Thread-4] b.c.j.asap.genomes.ScaffoldingStep : run 4: dir "/data/scaffolds/Agrobacterium_rhizogenes_ST15-13-091" created 2019-08-27 03:01:16.181 DEBUG [Scaffolding-Step-Thread-4] b.c.j.asap.genomes.ScaffoldingStep : genome.id=4: exec=[/asap/bin/groovy, /asap/scripts/asap-scaffolding.groovy, --project-path, /data, --genome-id, 4] 2019-08-27 03:03:08.984 DEBUG [Scaffolding-Step-Thread-4] b.c.j.asap.genomes.ScaffoldingStep : genome.id=4: exp backoff=1 s 2019-08-27 03:03:16.022 DEBUG [Annotation-Step-Thread-4] b.c.jlu.asap.genomes.AnnotationStep : genome.id=4: found user provided pseudo genome: path=/data/scaffolds/Agrobacterium_rhizogenes_ST15-13-091/Agrobacterium_rhizogenes_ST15-13-091-pseudo.fasta 2019-08-27 03:03:16.025 DEBUG [ABRDetection-Step-Thread-4] b.c.j.asap.genomes.ABRDetectionStep : genome.id=4: exec: [/asap/bin/groovy, /asap/scripts/asap-abr.groovy, --project-path, /data, --genome-id, 4] 2019-08-27 03:03:16.027 DEBUG [MLST-Step-Thread-4] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=4: exec: [/asap/bin/groovy, /asap/scripts/asap-mlst.groovy, --project-path, /data, --genome-id, 4] 2019-08-27 03:03:16.027 DEBUG [Taxonomy-Step-Thread-4] b.c.jlu.asap.genomes.TaxonomyStep : genome.id=4: exec: [/asap/bin/groovy, /asap/scripts/asap-taxonomy.groovy, --project-path, /data, --genome-id, 4] 2019-08-27 03:03:16.090 DEBUG [Annotation-Step-Thread-4] b.c.jlu.asap.genomes.AnnotationStep : run 4: dir '/data/annotations/Agrobacterium_rhizogenes_ST15-13-091' created 2019-08-27 03:03:16.128 DEBUG [Annotation-Step-Thread-4] b.c.jlu.asap.genomes.AnnotationStep : genome.id=4: exec: [/asap/share/prokka/bin/prokka, --genus, Agrobacterium, --species, rhizogenes, --strain, ST15-13-091, --prefix, Agrobacterium_rhizogenes_ST15-13-091, --locustag, Arhiz_ST15-13-091, --centre, JLU, --cpus, 8, --outdir, /data/annotations/Agrobacterium_rhizogenes_ST15-13-091, --proteins, /asap/db/sequences/asap-proteins.faa, --usegenus, --force, --addgenes, --rfam, --rawproduct, /data/scaffolds/Agrobacterium_rhizogenes_ST15-13-091/Agrobacterium_rhizogenes_ST15-13-091-pseudo.fasta] 2019-08-27 03:03:33.823 DEBUG [MLST-Step-Thread-4] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=4: exp backoff=1 s 2019-08-27 03:04:14.399 ERROR [Taxonomy-Step-Thread-4] b.comp.jlu.asap.genomes.GenomeStep : taxonomy genome step for genome id=4 aborted! java.lang.IllegalStateException: abnormal taxonomy exit code! exitCode=1 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.genomes.TaxonomyStep.runStep(TaxonomyStep.groovy:146) at bio.comp.jlu.asap.genomes.TaxonomyStep$runStep$2.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at bio.comp.jlu.asap.genomes.ABRDetectionStep$runStep$2.callCurrent(Unknown Source) at bio.comp.jlu.asap.genomes.GenomeStep.run(GenomeStep.groovy:86) 2019-08-27 03:12:18.083 DEBUG [ABRDetection-Step-Thread-4] b.c.j.asap.genomes.ABRDetectionStep : genome.id=4: exp backoff=1 s 2019-08-27 03:26:14.515 DEBUG [VFDetection-Step-Thread-4] b.c.j.asap.genomes.VFDetectionStep : genome.id=4: exec: [/asap/bin/groovy, /asap/scripts/asap-vf.groovy, --project-path, /data, --genome-id, 4] 2019-08-27 03:27:54.137 DEBUG [VFDetection-Step-Thread-4] b.c.j.asap.genomes.VFDetectionStep : genome.id=4: exp backoff=1 s 2019-08-27 03:27:54.187 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : genome-id=5: running... 2019-08-27 03:27:54.223 DEBUG [QC-Step-Thread-5] bio.comp.jlu.asap.genomes.QCStep : genome.id=5: found reads: read.type=paired-end 2019-08-27 03:27:54.230 DEBUG [QC-Step-Thread-5] bio.comp.jlu.asap.genomes.QCStep : genome.id=5: dir "/data/reads_qc/Agrobacterium_rhizogenes_ST15-16-020" created 2019-08-27 03:27:54.231 DEBUG [QC-Step-Thread-5] bio.comp.jlu.asap.genomes.QCStep : genome.id=5: exec: [/asap/bin/groovy, /asap/scripts/asap-qc.groovy, --project-path, /data, --genome-id, 5] 2019-08-27 03:34:46.848 DEBUG [QC-Step-Thread-5] bio.comp.jlu.asap.genomes.QCStep : genome.id=5: exp backoff=1 s 2019-08-27 03:34:53.768 DEBUG [Mapping-Step-Thread-5] b.comp.jlu.asap.genomes.MappingStep : genome.id=5: exec: [/asap/bin/groovy, /asap/scripts/asap-mapping.groovy, --project-path, /data, --genome-id, 5] 2019-08-27 03:34:53.780 DEBUG [Assembly-Step-Thread-5] b.c.jlu.asap.genomes.AssemblyStep : genome.id=5: dir "/data/assemblies/Agrobacterium_rhizogenes_ST15-16-020" created 2019-08-27 03:34:53.869 DEBUG [Assembly-Step-Thread-5] b.c.jlu.asap.genomes.AssemblyStep : genome.id=5: exec: [/asap/bin/groovy, /asap/scripts/asap-assembly.groovy, --project-path, /data, --genome-id, 5] 2019-08-27 03:38:32.579 DEBUG [Mapping-Step-Thread-5] b.comp.jlu.asap.genomes.MappingStep : genome.id=5: exp backoff=1 s 2019-08-27 03:38:53.500 DEBUG [SNPDetection-Step-Thread-5] b.c.j.asap.genomes.SNPDetectionStep : genome.id=5: exec: [/asap/bin/groovy, /asap/scripts/asap-snp.groovy, --project-path, /data, --genome-id, 5] 2019-08-27 03:40:45.646 DEBUG [SNPDetection-Step-Thread-5] b.c.j.asap.genomes.SNPDetectionStep : genome.id=5: exp backoff=1 s 2019-08-27 04:04:23.980 DEBUG [Assembly-Step-Thread-5] b.c.jlu.asap.genomes.AssemblyStep : genome.id=5: exp backoff=1 s 2019-08-27 04:04:51.822 DEBUG [Scaffolding-Step-Thread-5] b.c.j.asap.genomes.ScaffoldingStep : run 5: dir "/data/scaffolds/Agrobacterium_rhizogenes_ST15-16-020" created 2019-08-27 04:04:51.828 DEBUG [Scaffolding-Step-Thread-5] b.c.j.asap.genomes.ScaffoldingStep : genome.id=5: exec=[/asap/bin/groovy, /asap/scripts/asap-scaffolding.groovy, --project-path, /data, --genome-id, 5] 2019-08-27 04:06:27.866 DEBUG [Scaffolding-Step-Thread-5] b.c.j.asap.genomes.ScaffoldingStep : genome.id=5: exp backoff=1 s 2019-08-27 04:06:51.785 DEBUG [Taxonomy-Step-Thread-5] b.c.jlu.asap.genomes.TaxonomyStep : genome.id=5: exec: [/asap/bin/groovy, /asap/scripts/asap-taxonomy.groovy, --project-path, /data, --genome-id, 5] 2019-08-27 04:06:51.790 DEBUG [ABRDetection-Step-Thread-5] b.c.j.asap.genomes.ABRDetectionStep : genome.id=5: exec: [/asap/bin/groovy, /asap/scripts/asap-abr.groovy, --project-path, /data, --genome-id, 5] 2019-08-27 04:06:51.812 DEBUG [Annotation-Step-Thread-5] b.c.jlu.asap.genomes.AnnotationStep : genome.id=5: found user provided pseudo genome: path=/data/scaffolds/Agrobacterium_rhizogenes_ST15-16-020/Agrobacterium_rhizogenes_ST15-16-020-pseudo.fasta 2019-08-27 04:06:51.825 DEBUG [MLST-Step-Thread-5] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=5: exec: [/asap/bin/groovy, /asap/scripts/asap-mlst.groovy, --project-path, /data, --genome-id, 5] 2019-08-27 04:06:51.883 DEBUG [Annotation-Step-Thread-5] b.c.jlu.asap.genomes.AnnotationStep : run 5: dir '/data/annotations/Agrobacterium_rhizogenes_ST15-16-020' created 2019-08-27 04:06:51.891 DEBUG [Annotation-Step-Thread-5] b.c.jlu.asap.genomes.AnnotationStep : genome.id=5: exec: [/asap/share/prokka/bin/prokka, --genus, Agrobacterium, --species, rhizogenes, --strain, ST15-16-020, --prefix, Agrobacterium_rhizogenes_ST15-16-020, --locustag, Arhiz_ST15-16-020, --centre, JLU, --cpus, 8, --outdir, /data/annotations/Agrobacterium_rhizogenes_ST15-16-020, --proteins, /asap/db/sequences/asap-proteins.faa, --usegenus, --force, --addgenes, --rfam, --rawproduct, /data/scaffolds/Agrobacterium_rhizogenes_ST15-16-020/Agrobacterium_rhizogenes_ST15-16-020-pseudo.fasta] 2019-08-27 04:07:09.694 DEBUG [MLST-Step-Thread-5] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=5: exp backoff=1 s 2019-08-27 04:07:50.769 ERROR [Taxonomy-Step-Thread-5] b.comp.jlu.asap.genomes.GenomeStep : taxonomy genome step for genome id=5 aborted! java.lang.IllegalStateException: abnormal taxonomy exit code! exitCode=1 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.genomes.TaxonomyStep.runStep(TaxonomyStep.groovy:146) at bio.comp.jlu.asap.genomes.TaxonomyStep$runStep$2.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at bio.comp.jlu.asap.genomes.ScaffoldingStep$runStep$2.callCurrent(Unknown Source) at bio.comp.jlu.asap.genomes.GenomeStep.run(GenomeStep.groovy:86) 2019-08-27 04:15:57.000 DEBUG [ABRDetection-Step-Thread-5] b.c.j.asap.genomes.ABRDetectionStep : genome.id=5: exp backoff=1 s 2019-08-27 04:28:50.266 DEBUG [VFDetection-Step-Thread-5] b.c.j.asap.genomes.VFDetectionStep : genome.id=5: exec: [/asap/bin/groovy, /asap/scripts/asap-vf.groovy, --project-path, /data, --genome-id, 5] 2019-08-27 04:30:27.363 DEBUG [VFDetection-Step-Thread-5] b.c.j.asap.genomes.VFDetectionStep : genome.id=5: exp backoff=1 s 2019-08-27 04:30:27.425 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : genome-id=6: running... 2019-08-27 04:30:27.437 DEBUG [QC-Step-Thread-6] bio.comp.jlu.asap.genomes.QCStep : genome.id=6: found reads: read.type=paired-end 2019-08-27 04:30:27.441 DEBUG [QC-Step-Thread-6] bio.comp.jlu.asap.genomes.QCStep : genome.id=6: dir "/data/reads_qc/Agrobacterium_rhizogenes_ST15-16-021" created 2019-08-27 04:30:27.442 DEBUG [QC-Step-Thread-6] bio.comp.jlu.asap.genomes.QCStep : genome.id=6: exec: [/asap/bin/groovy, /asap/scripts/asap-qc.groovy, --project-path, /data, --genome-id, 6] 2019-08-27 04:37:28.360 DEBUG [QC-Step-Thread-6] bio.comp.jlu.asap.genomes.QCStep : genome.id=6: exp backoff=1 s 2019-08-27 04:38:26.980 DEBUG [Mapping-Step-Thread-6] b.comp.jlu.asap.genomes.MappingStep : genome.id=6: exec: [/asap/bin/groovy, /asap/scripts/asap-mapping.groovy, --project-path, /data, --genome-id, 6] 2019-08-27 04:38:27.077 DEBUG [Assembly-Step-Thread-6] b.c.jlu.asap.genomes.AssemblyStep : genome.id=6: dir "/data/assemblies/Agrobacterium_rhizogenes_ST15-16-021" created 2019-08-27 04:38:27.090 DEBUG [Assembly-Step-Thread-6] b.c.jlu.asap.genomes.AssemblyStep : genome.id=6: exec: [/asap/bin/groovy, /asap/scripts/asap-assembly.groovy, --project-path, /data, --genome-id, 6] 2019-08-27 04:41:42.204 DEBUG [Mapping-Step-Thread-6] b.comp.jlu.asap.genomes.MappingStep : genome.id=6: exp backoff=1 s 2019-08-27 04:42:26.682 DEBUG [SNPDetection-Step-Thread-6] b.c.j.asap.genomes.SNPDetectionStep : genome.id=6: exec: [/asap/bin/groovy, /asap/scripts/asap-snp.groovy, --project-path, /data, --genome-id, 6] 2019-08-27 04:43:50.746 DEBUG [SNPDetection-Step-Thread-6] b.c.j.asap.genomes.SNPDetectionStep : genome.id=6: exp backoff=1 s 2019-08-27 05:07:31.278 DEBUG [Assembly-Step-Thread-6] b.c.jlu.asap.genomes.AssemblyStep : genome.id=6: exp backoff=1 s 2019-08-27 05:08:25.005 DEBUG [Scaffolding-Step-Thread-6] b.c.j.asap.genomes.ScaffoldingStep : run 6: dir "/data/scaffolds/Agrobacterium_rhizogenes_ST15-16-021" created 2019-08-27 05:08:25.008 DEBUG [Scaffolding-Step-Thread-6] b.c.j.asap.genomes.ScaffoldingStep : genome.id=6: exec=[/asap/bin/groovy, /asap/scripts/asap-scaffolding.groovy, --project-path, /data, --genome-id, 6] 2019-08-27 05:10:14.989 DEBUG [Scaffolding-Step-Thread-6] b.c.j.asap.genomes.ScaffoldingStep : genome.id=6: exp backoff=1 s 2019-08-27 05:10:24.872 DEBUG [ABRDetection-Step-Thread-6] b.c.j.asap.genomes.ABRDetectionStep : genome.id=6: exec: [/asap/bin/groovy, /asap/scripts/asap-abr.groovy, --project-path, /data, --genome-id, 6] 2019-08-27 05:10:24.872 DEBUG [Taxonomy-Step-Thread-6] b.c.jlu.asap.genomes.TaxonomyStep : genome.id=6: exec: [/asap/bin/groovy, /asap/scripts/asap-taxonomy.groovy, --project-path, /data, --genome-id, 6] 2019-08-27 05:10:24.873 DEBUG [Annotation-Step-Thread-6] b.c.jlu.asap.genomes.AnnotationStep : genome.id=6: found user provided pseudo genome: path=/data/scaffolds/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021-pseudo.fasta 2019-08-27 05:10:24.878 DEBUG [MLST-Step-Thread-6] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=6: exec: [/asap/bin/groovy, /asap/scripts/asap-mlst.groovy, --project-path, /data, --genome-id, 6] 2019-08-27 05:10:24.980 DEBUG [Annotation-Step-Thread-6] b.c.jlu.asap.genomes.AnnotationStep : run 6: dir '/data/annotations/Agrobacterium_rhizogenes_ST15-16-021' created 2019-08-27 05:10:25.003 DEBUG [Annotation-Step-Thread-6] b.c.jlu.asap.genomes.AnnotationStep : genome.id=6: exec: [/asap/share/prokka/bin/prokka, --genus, Agrobacterium, --species, rhizogenes, --strain, ST15-16-021, --prefix, Agrobacterium_rhizogenes_ST15-16-021, --locustag, Arhiz_ST15-16-021, --centre, JLU, --cpus, 8, --outdir, /data/annotations/Agrobacterium_rhizogenes_ST15-16-021, --proteins, /asap/db/sequences/asap-proteins.faa, --usegenus, --force, --addgenes, --rfam, --rawproduct, /data/scaffolds/Agrobacterium_rhizogenes_ST15-16-021/Agrobacterium_rhizogenes_ST15-16-021-pseudo.fasta] 2019-08-27 05:10:44.566 DEBUG [MLST-Step-Thread-6] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=6: exp backoff=1 s 2019-08-27 05:11:24.023 ERROR [Taxonomy-Step-Thread-6] b.comp.jlu.asap.genomes.GenomeStep : taxonomy genome step for genome id=6 aborted! java.lang.IllegalStateException: abnormal taxonomy exit code! exitCode=1 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.genomes.TaxonomyStep.runStep(TaxonomyStep.groovy:146) at bio.comp.jlu.asap.genomes.TaxonomyStep$runStep$2.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at bio.comp.jlu.asap.genomes.ABRDetectionStep$runStep$2.callCurrent(Unknown Source) at bio.comp.jlu.asap.genomes.GenomeStep.run(GenomeStep.groovy:86) 2019-08-27 05:19:43.677 DEBUG [ABRDetection-Step-Thread-6] b.c.j.asap.genomes.ABRDetectionStep : genome.id=6: exp backoff=1 s 2019-08-27 05:33:23.369 DEBUG [VFDetection-Step-Thread-6] b.c.j.asap.genomes.VFDetectionStep : genome.id=6: exec: [/asap/bin/groovy, /asap/scripts/asap-vf.groovy, --project-path, /data, --genome-id, 6] 2019-08-27 05:35:02.611 DEBUG [VFDetection-Step-Thread-6] b.c.j.asap.genomes.VFDetectionStep : genome.id=6: exp backoff=1 s 2019-08-27 05:35:02.672 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : genome-id=7: running... 2019-08-27 05:35:02.704 DEBUG [QC-Step-Thread-7] bio.comp.jlu.asap.genomes.QCStep : genome.id=7: found reads: read.type=paired-end 2019-08-27 05:35:02.709 DEBUG [QC-Step-Thread-7] bio.comp.jlu.asap.genomes.QCStep : genome.id=7: dir "/data/reads_qc/Agrobacterium_rhizogenes_NCPPB4042" created 2019-08-27 05:35:02.710 DEBUG [QC-Step-Thread-7] bio.comp.jlu.asap.genomes.QCStep : genome.id=7: exec: [/asap/bin/groovy, /asap/scripts/asap-qc.groovy, --project-path, /data, --genome-id, 7] 2019-08-27 05:43:35.867 DEBUG [QC-Step-Thread-7] bio.comp.jlu.asap.genomes.QCStep : genome.id=7: exp backoff=1 s 2019-08-27 05:44:02.129 DEBUG [Mapping-Step-Thread-7] b.comp.jlu.asap.genomes.MappingStep : genome.id=7: exec: [/asap/bin/groovy, /asap/scripts/asap-mapping.groovy, --project-path, /data, --genome-id, 7] 2019-08-27 05:44:02.143 DEBUG [Assembly-Step-Thread-7] b.c.jlu.asap.genomes.AssemblyStep : genome.id=7: dir "/data/assemblies/Agrobacterium_rhizogenes_NCPPB4042" created 2019-08-27 05:44:02.145 DEBUG [Assembly-Step-Thread-7] b.c.jlu.asap.genomes.AssemblyStep : genome.id=7: exec: [/asap/bin/groovy, /asap/scripts/asap-assembly.groovy, --project-path, /data, --genome-id, 7] 2019-08-27 05:48:25.440 DEBUG [Mapping-Step-Thread-7] b.comp.jlu.asap.genomes.MappingStep : genome.id=7: exp backoff=1 s 2019-08-27 05:49:01.798 DEBUG [SNPDetection-Step-Thread-7] b.c.j.asap.genomes.SNPDetectionStep : genome.id=7: exec: [/asap/bin/groovy, /asap/scripts/asap-snp.groovy, --project-path, /data, --genome-id, 7] 2019-08-27 05:50:59.641 DEBUG [SNPDetection-Step-Thread-7] b.c.j.asap.genomes.SNPDetectionStep : genome.id=7: exp backoff=1 s 2019-08-27 06:21:28.465 DEBUG [Assembly-Step-Thread-7] b.c.jlu.asap.genomes.AssemblyStep : genome.id=7: exp backoff=1 s 2019-08-27 06:21:59.677 DEBUG [Scaffolding-Step-Thread-7] b.c.j.asap.genomes.ScaffoldingStep : run 7: dir "/data/scaffolds/Agrobacterium_rhizogenes_NCPPB4042" created 2019-08-27 06:21:59.680 DEBUG [Scaffolding-Step-Thread-7] b.c.j.asap.genomes.ScaffoldingStep : genome.id=7: exec=[/asap/bin/groovy, /asap/scripts/asap-scaffolding.groovy, --project-path, /data, --genome-id, 7] 2019-08-27 06:23:56.584 DEBUG [Scaffolding-Step-Thread-7] b.c.j.asap.genomes.ScaffoldingStep : genome.id=7: exp backoff=1 s 2019-08-27 06:23:59.514 DEBUG [Taxonomy-Step-Thread-7] b.c.jlu.asap.genomes.TaxonomyStep : genome.id=7: exec: [/asap/bin/groovy, /asap/scripts/asap-taxonomy.groovy, --project-path, /data, --genome-id, 7] 2019-08-27 06:23:59.517 DEBUG [MLST-Step-Thread-7] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=7: exec: [/asap/bin/groovy, /asap/scripts/asap-mlst.groovy, --project-path, /data, --genome-id, 7] 2019-08-27 06:23:59.525 DEBUG [Annotation-Step-Thread-7] b.c.jlu.asap.genomes.AnnotationStep : genome.id=7: found user provided pseudo genome: path=/data/scaffolds/Agrobacterium_rhizogenes_NCPPB4042/Agrobacterium_rhizogenes_NCPPB4042-pseudo.fasta 2019-08-27 06:23:59.533 DEBUG [Annotation-Step-Thread-7] b.c.jlu.asap.genomes.AnnotationStep : run 7: dir '/data/annotations/Agrobacterium_rhizogenes_NCPPB4042' created 2019-08-27 06:23:59.547 DEBUG [Annotation-Step-Thread-7] b.c.jlu.asap.genomes.AnnotationStep : genome.id=7: exec: [/asap/share/prokka/bin/prokka, --genus, Agrobacterium, --species, rhizogenes, --strain, NCPPB4042, --prefix, Agrobacterium_rhizogenes_NCPPB4042, --locustag, Arhiz_NCPPB4042, --centre, JLU, --cpus, 8, --outdir, /data/annotations/Agrobacterium_rhizogenes_NCPPB4042, --proteins, /asap/db/sequences/asap-proteins.faa, --usegenus, --force, --addgenes, --rfam, --rawproduct, /data/scaffolds/Agrobacterium_rhizogenes_NCPPB4042/Agrobacterium_rhizogenes_NCPPB4042-pseudo.fasta] 2019-08-27 06:23:59.661 DEBUG [ABRDetection-Step-Thread-7] b.c.j.asap.genomes.ABRDetectionStep : genome.id=7: exec: [/asap/bin/groovy, /asap/scripts/asap-abr.groovy, --project-path, /data, --genome-id, 7] 2019-08-27 06:24:21.453 DEBUG [MLST-Step-Thread-7] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=7: exp backoff=1 s 2019-08-27 06:25:32.441 ERROR [Taxonomy-Step-Thread-7] b.comp.jlu.asap.genomes.GenomeStep : taxonomy genome step for genome id=7 aborted! java.lang.IllegalStateException: abnormal taxonomy exit code! exitCode=1 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.genomes.TaxonomyStep.runStep(TaxonomyStep.groovy:146) at bio.comp.jlu.asap.genomes.TaxonomyStep$runStep$2.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at bio.comp.jlu.asap.genomes.ScaffoldingStep$runStep$2.callCurrent(Unknown Source) at bio.comp.jlu.asap.genomes.GenomeStep.run(GenomeStep.groovy:86) 2019-08-27 06:33:58.671 DEBUG [ABRDetection-Step-Thread-7] b.c.j.asap.genomes.ABRDetectionStep : genome.id=7: exp backoff=1 s 2019-08-27 06:48:57.898 DEBUG [VFDetection-Step-Thread-7] b.c.j.asap.genomes.VFDetectionStep : genome.id=7: exec: [/asap/bin/groovy, /asap/scripts/asap-vf.groovy, --project-path, /data, --genome-id, 7] 2019-08-27 06:50:39.522 DEBUG [VFDetection-Step-Thread-7] b.c.j.asap.genomes.VFDetectionStep : genome.id=7: exp backoff=1 s 2019-08-27 06:50:39.591 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : genome-id=8: running... 2019-08-27 06:50:39.843 DEBUG [QC-Step-Thread-8] bio.comp.jlu.asap.genomes.QCStep : genome.id=8: found reads: read.type=paired-end 2019-08-27 06:50:39.846 DEBUG [QC-Step-Thread-8] bio.comp.jlu.asap.genomes.QCStep : genome.id=8: dir "/data/reads_qc/Agrobacterium_rhizogenes_NCPPB4062" created 2019-08-27 06:50:39.848 DEBUG [QC-Step-Thread-8] bio.comp.jlu.asap.genomes.QCStep : genome.id=8: exec: [/asap/bin/groovy, /asap/scripts/asap-qc.groovy, --project-path, /data, --genome-id, 8] 2019-08-27 06:58:03.499 DEBUG [QC-Step-Thread-8] bio.comp.jlu.asap.genomes.QCStep : genome.id=8: exp backoff=1 s 2019-08-27 06:58:39.336 DEBUG [Mapping-Step-Thread-8] b.comp.jlu.asap.genomes.MappingStep : genome.id=8: exec: [/asap/bin/groovy, /asap/scripts/asap-mapping.groovy, --project-path, /data, --genome-id, 8] 2019-08-27 06:58:39.340 DEBUG [Assembly-Step-Thread-8] b.c.jlu.asap.genomes.AssemblyStep : genome.id=8: dir "/data/assemblies/Agrobacterium_rhizogenes_NCPPB4062" created 2019-08-27 06:58:39.432 DEBUG [Assembly-Step-Thread-8] b.c.jlu.asap.genomes.AssemblyStep : genome.id=8: exec: [/asap/bin/groovy, /asap/scripts/asap-assembly.groovy, --project-path, /data, --genome-id, 8] 2019-08-27 07:02:32.436 DEBUG [Mapping-Step-Thread-8] b.comp.jlu.asap.genomes.MappingStep : genome.id=8: exp backoff=1 s 2019-08-27 07:02:39.080 DEBUG [SNPDetection-Step-Thread-8] b.c.j.asap.genomes.SNPDetectionStep : genome.id=8: exec: [/asap/bin/groovy, /asap/scripts/asap-snp.groovy, --project-path, /data, --genome-id, 8] 2019-08-27 07:04:20.254 DEBUG [SNPDetection-Step-Thread-8] b.c.j.asap.genomes.SNPDetectionStep : genome.id=8: exp backoff=1 s 2019-08-27 07:31:36.494 DEBUG [Assembly-Step-Thread-8] b.c.jlu.asap.genomes.AssemblyStep : genome.id=8: exp backoff=1 s 2019-08-27 07:31:37.186 DEBUG [Scaffolding-Step-Thread-8] b.c.j.asap.genomes.ScaffoldingStep : run 8: dir "/data/scaffolds/Agrobacterium_rhizogenes_NCPPB4062" created 2019-08-27 07:31:37.190 DEBUG [Scaffolding-Step-Thread-8] b.c.j.asap.genomes.ScaffoldingStep : genome.id=8: exec=[/asap/bin/groovy, /asap/scripts/asap-scaffolding.groovy, --project-path, /data, --genome-id, 8] 2019-08-27 07:33:26.255 DEBUG [Scaffolding-Step-Thread-8] b.c.j.asap.genomes.ScaffoldingStep : genome.id=8: exp backoff=1 s 2019-08-27 07:33:37.052 DEBUG [ABRDetection-Step-Thread-8] b.c.j.asap.genomes.ABRDetectionStep : genome.id=8: exec: [/asap/bin/groovy, /asap/scripts/asap-abr.groovy, --project-path, /data, --genome-id, 8] 2019-08-27 07:33:37.052 DEBUG [Taxonomy-Step-Thread-8] b.c.jlu.asap.genomes.TaxonomyStep : genome.id=8: exec: [/asap/bin/groovy, /asap/scripts/asap-taxonomy.groovy, --project-path, /data, --genome-id, 8] 2019-08-27 07:33:37.053 DEBUG [MLST-Step-Thread-8] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=8: exec: [/asap/bin/groovy, /asap/scripts/asap-mlst.groovy, --project-path, /data, --genome-id, 8] 2019-08-27 07:33:37.059 DEBUG [Annotation-Step-Thread-8] b.c.jlu.asap.genomes.AnnotationStep : genome.id=8: found user provided pseudo genome: path=/data/scaffolds/Agrobacterium_rhizogenes_NCPPB4062/Agrobacterium_rhizogenes_NCPPB4062-pseudo.fasta 2019-08-27 07:33:37.148 DEBUG [Annotation-Step-Thread-8] b.c.jlu.asap.genomes.AnnotationStep : run 8: dir '/data/annotations/Agrobacterium_rhizogenes_NCPPB4062' created 2019-08-27 07:33:37.157 DEBUG [Annotation-Step-Thread-8] b.c.jlu.asap.genomes.AnnotationStep : genome.id=8: exec: [/asap/share/prokka/bin/prokka, --genus, Agrobacterium, --species, rhizogenes, --strain, NCPPB4062, --prefix, Agrobacterium_rhizogenes_NCPPB4062, --locustag, Arhiz_NCPPB4062, --centre, JLU, --cpus, 8, --outdir, /data/annotations/Agrobacterium_rhizogenes_NCPPB4062, --proteins, /asap/db/sequences/asap-proteins.faa, --usegenus, --force, --addgenes, --rfam, --rawproduct, /data/scaffolds/Agrobacterium_rhizogenes_NCPPB4062/Agrobacterium_rhizogenes_NCPPB4062-pseudo.fasta] 2019-08-27 07:33:55.437 DEBUG [MLST-Step-Thread-8] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=8: exp backoff=1 s 2019-08-27 07:34:35.783 ERROR [Taxonomy-Step-Thread-8] b.comp.jlu.asap.genomes.GenomeStep : taxonomy genome step for genome id=8 aborted! java.lang.IllegalStateException: abnormal taxonomy exit code! exitCode=1 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.genomes.TaxonomyStep.runStep(TaxonomyStep.groovy:146) at bio.comp.jlu.asap.genomes.TaxonomyStep$runStep$2.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at bio.comp.jlu.asap.genomes.ABRDetectionStep$runStep$2.callCurrent(Unknown Source) at bio.comp.jlu.asap.genomes.GenomeStep.run(GenomeStep.groovy:86) 2019-08-27 07:43:11.349 DEBUG [ABRDetection-Step-Thread-8] b.c.j.asap.genomes.ABRDetectionStep : genome.id=8: exp backoff=1 s 2019-08-27 07:58:35.435 DEBUG [VFDetection-Step-Thread-8] b.c.j.asap.genomes.VFDetectionStep : genome.id=8: exec: [/asap/bin/groovy, /asap/scripts/asap-vf.groovy, --project-path, /data, --genome-id, 8] 2019-08-27 08:00:20.018 DEBUG [VFDetection-Step-Thread-8] b.c.j.asap.genomes.VFDetectionStep : genome.id=8: exp backoff=1 s 2019-08-27 08:00:20.098 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : genome-id=9: running... 2019-08-27 08:00:20.117 DEBUG [QC-Step-Thread-9] bio.comp.jlu.asap.genomes.QCStep : genome.id=9: found reads: read.type=paired-end 2019-08-27 08:00:20.129 DEBUG [QC-Step-Thread-9] bio.comp.jlu.asap.genomes.QCStep : genome.id=9: dir "/data/reads_qc/Agrobacterium_rhizogenes_ST04-16-045" created 2019-08-27 08:00:20.131 DEBUG [QC-Step-Thread-9] bio.comp.jlu.asap.genomes.QCStep : genome.id=9: exec: [/asap/bin/groovy, /asap/scripts/asap-qc.groovy, --project-path, /data, --genome-id, 9] 2019-08-27 08:08:50.830 DEBUG [QC-Step-Thread-9] bio.comp.jlu.asap.genomes.QCStep : genome.id=9: exp backoff=1 s 2019-08-27 08:09:20.601 DEBUG [Mapping-Step-Thread-9] b.comp.jlu.asap.genomes.MappingStep : genome.id=9: exec: [/asap/bin/groovy, /asap/scripts/asap-mapping.groovy, --project-path, /data, --genome-id, 9] 2019-08-27 08:09:20.789 DEBUG [Assembly-Step-Thread-9] b.c.jlu.asap.genomes.AssemblyStep : genome.id=9: dir "/data/assemblies/Agrobacterium_rhizogenes_ST04-16-045" created 2019-08-27 08:09:20.802 DEBUG [Assembly-Step-Thread-9] b.c.jlu.asap.genomes.AssemblyStep : genome.id=9: exec: [/asap/bin/groovy, /asap/scripts/asap-assembly.groovy, --project-path, /data, --genome-id, 9] 2019-08-27 08:14:06.319 DEBUG [Mapping-Step-Thread-9] b.comp.jlu.asap.genomes.MappingStep : genome.id=9: exp backoff=1 s 2019-08-27 08:14:20.275 DEBUG [SNPDetection-Step-Thread-9] b.c.j.asap.genomes.SNPDetectionStep : genome.id=9: exec: [/asap/bin/groovy, /asap/scripts/asap-snp.groovy, --project-path, /data, --genome-id, 9] 2019-08-27 08:16:40.941 DEBUG [SNPDetection-Step-Thread-9] b.c.j.asap.genomes.SNPDetectionStep : genome.id=9: exp backoff=1 s 2019-08-27 08:46:08.932 DEBUG [Assembly-Step-Thread-9] b.c.jlu.asap.genomes.AssemblyStep : genome.id=9: exp backoff=1 s 2019-08-27 08:46:18.211 DEBUG [Scaffolding-Step-Thread-9] b.c.j.asap.genomes.ScaffoldingStep : run 9: dir "/data/scaffolds/Agrobacterium_rhizogenes_ST04-16-045" created 2019-08-27 08:46:18.213 DEBUG [Scaffolding-Step-Thread-9] b.c.j.asap.genomes.ScaffoldingStep : genome.id=9: exec=[/asap/bin/groovy, /asap/scripts/asap-scaffolding.groovy, --project-path, /data, --genome-id, 9] 2019-08-27 08:47:56.336 DEBUG [Scaffolding-Step-Thread-9] b.c.j.asap.genomes.ScaffoldingStep : genome.id=9: exp backoff=1 s 2019-08-27 08:48:18.074 DEBUG [Annotation-Step-Thread-9] b.c.jlu.asap.genomes.AnnotationStep : genome.id=9: found user provided pseudo genome: path=/data/scaffolds/Agrobacterium_rhizogenes_ST04-16-045/Agrobacterium_rhizogenes_ST04-16-045-pseudo.fasta 2019-08-27 08:48:18.075 DEBUG [Taxonomy-Step-Thread-9] b.c.jlu.asap.genomes.TaxonomyStep : genome.id=9: exec: [/asap/bin/groovy, /asap/scripts/asap-taxonomy.groovy, --project-path, /data, --genome-id, 9] 2019-08-27 08:48:18.078 DEBUG [MLST-Step-Thread-9] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=9: exec: [/asap/bin/groovy, /asap/scripts/asap-mlst.groovy, --project-path, /data, --genome-id, 9] 2019-08-27 08:48:18.080 DEBUG [ABRDetection-Step-Thread-9] b.c.j.asap.genomes.ABRDetectionStep : genome.id=9: exec: [/asap/bin/groovy, /asap/scripts/asap-abr.groovy, --project-path, /data, --genome-id, 9] 2019-08-27 08:48:18.182 DEBUG [Annotation-Step-Thread-9] b.c.jlu.asap.genomes.AnnotationStep : run 9: dir '/data/annotations/Agrobacterium_rhizogenes_ST04-16-045' created 2019-08-27 08:48:18.204 DEBUG [Annotation-Step-Thread-9] b.c.jlu.asap.genomes.AnnotationStep : genome.id=9: exec: [/asap/share/prokka/bin/prokka, --genus, Agrobacterium, --species, rhizogenes, --strain, ST04-16-045, --prefix, Agrobacterium_rhizogenes_ST04-16-045, --locustag, Arhiz_ST04-16-045, --centre, JLU, --cpus, 8, --outdir, /data/annotations/Agrobacterium_rhizogenes_ST04-16-045, --proteins, /asap/db/sequences/asap-proteins.faa, --usegenus, --force, --addgenes, --rfam, --rawproduct, /data/scaffolds/Agrobacterium_rhizogenes_ST04-16-045/Agrobacterium_rhizogenes_ST04-16-045-pseudo.fasta] 2019-08-27 08:48:37.310 DEBUG [MLST-Step-Thread-9] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=9: exp backoff=1 s 2019-08-27 08:49:17.928 ERROR [Taxonomy-Step-Thread-9] b.comp.jlu.asap.genomes.GenomeStep : taxonomy genome step for genome id=9 aborted! java.lang.IllegalStateException: abnormal taxonomy exit code! exitCode=1 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.genomes.TaxonomyStep.runStep(TaxonomyStep.groovy:146) at bio.comp.jlu.asap.genomes.TaxonomyStep$runStep$2.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at bio.comp.jlu.asap.genomes.ScaffoldingStep$runStep$2.callCurrent(Unknown Source) at bio.comp.jlu.asap.genomes.GenomeStep.run(GenomeStep.groovy:86) 2019-08-27 08:58:04.314 DEBUG [ABRDetection-Step-Thread-9] b.c.j.asap.genomes.ABRDetectionStep : genome.id=9: exp backoff=1 s 2019-08-27 09:12:16.492 DEBUG [VFDetection-Step-Thread-9] b.c.j.asap.genomes.VFDetectionStep : genome.id=9: exec: [/asap/bin/groovy, /asap/scripts/asap-vf.groovy, --project-path, /data, --genome-id, 9] 2019-08-27 09:13:59.772 DEBUG [VFDetection-Step-Thread-9] b.c.j.asap.genomes.VFDetectionStep : genome.id=9: exp backoff=1 s 2019-08-27 09:13:59.948 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : genome-id=10: running... 2019-08-27 09:13:59.967 DEBUG [QC-Step-Thread-10] bio.comp.jlu.asap.genomes.QCStep : genome.id=10: found reads: read.type=paired-end 2019-08-27 09:13:59.972 DEBUG [QC-Step-Thread-10] bio.comp.jlu.asap.genomes.QCStep : genome.id=10: dir "/data/reads_qc/Agrobacterium_rhizogenes_ST-04-16-212" created 2019-08-27 09:13:59.973 DEBUG [QC-Step-Thread-10] bio.comp.jlu.asap.genomes.QCStep : genome.id=10: exec: [/asap/bin/groovy, /asap/scripts/asap-qc.groovy, --project-path, /data, --genome-id, 10] 2019-08-27 09:22:03.094 DEBUG [QC-Step-Thread-10] bio.comp.jlu.asap.genomes.QCStep : genome.id=10: exp backoff=1 s 2019-08-27 09:22:59.363 DEBUG [Mapping-Step-Thread-10] b.comp.jlu.asap.genomes.MappingStep : genome.id=10: exec: [/asap/bin/groovy, /asap/scripts/asap-mapping.groovy, --project-path, /data, --genome-id, 10] 2019-08-27 09:22:59.526 DEBUG [Assembly-Step-Thread-10] b.c.jlu.asap.genomes.AssemblyStep : genome.id=10: dir "/data/assemblies/Agrobacterium_rhizogenes_ST-04-16-212" created 2019-08-27 09:22:59.528 DEBUG [Assembly-Step-Thread-10] b.c.jlu.asap.genomes.AssemblyStep : genome.id=10: exec: [/asap/bin/groovy, /asap/scripts/asap-assembly.groovy, --project-path, /data, --genome-id, 10] 2019-08-27 09:26:41.240 DEBUG [Mapping-Step-Thread-10] b.comp.jlu.asap.genomes.MappingStep : genome.id=10: exp backoff=1 s 2019-08-27 09:26:59.099 DEBUG [SNPDetection-Step-Thread-10] b.c.j.asap.genomes.SNPDetectionStep : genome.id=10: exec: [/asap/bin/groovy, /asap/scripts/asap-snp.groovy, --project-path, /data, --genome-id, 10] 2019-08-27 09:28:37.230 DEBUG [SNPDetection-Step-Thread-10] b.c.j.asap.genomes.SNPDetectionStep : genome.id=10: exp backoff=1 s 2019-08-27 09:54:58.749 DEBUG [Assembly-Step-Thread-10] b.c.jlu.asap.genomes.AssemblyStep : genome.id=10: exp backoff=1 s 2019-08-27 09:55:57.209 DEBUG [Scaffolding-Step-Thread-10] b.c.j.asap.genomes.ScaffoldingStep : run 10: dir "/data/scaffolds/Agrobacterium_rhizogenes_ST-04-16-212" created 2019-08-27 09:55:57.216 DEBUG [Scaffolding-Step-Thread-10] b.c.j.asap.genomes.ScaffoldingStep : genome.id=10: exec=[/asap/bin/groovy, /asap/scripts/asap-scaffolding.groovy, --project-path, /data, --genome-id, 10] 2019-08-27 09:57:45.321 DEBUG [Scaffolding-Step-Thread-10] b.c.j.asap.genomes.ScaffoldingStep : genome.id=10: exp backoff=1 s 2019-08-27 09:57:57.080 DEBUG [MLST-Step-Thread-10] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=10: exec: [/asap/bin/groovy, /asap/scripts/asap-mlst.groovy, --project-path, /data, --genome-id, 10] 2019-08-27 09:57:57.087 DEBUG [Taxonomy-Step-Thread-10] b.c.jlu.asap.genomes.TaxonomyStep : genome.id=10: exec: [/asap/bin/groovy, /asap/scripts/asap-taxonomy.groovy, --project-path, /data, --genome-id, 10] 2019-08-27 09:57:57.091 DEBUG [Annotation-Step-Thread-10] b.c.jlu.asap.genomes.AnnotationStep : genome.id=10: found user provided pseudo genome: path=/data/scaffolds/Agrobacterium_rhizogenes_ST-04-16-212/Agrobacterium_rhizogenes_ST-04-16-212-pseudo.fasta 2019-08-27 09:57:57.190 DEBUG [Annotation-Step-Thread-10] b.c.jlu.asap.genomes.AnnotationStep : run 10: dir '/data/annotations/Agrobacterium_rhizogenes_ST-04-16-212' created 2019-08-27 09:57:57.197 DEBUG [Annotation-Step-Thread-10] b.c.jlu.asap.genomes.AnnotationStep : genome.id=10: exec: [/asap/share/prokka/bin/prokka, --genus, Agrobacterium, --species, rhizogenes, --strain, ST-04-16-212, --prefix, Agrobacterium_rhizogenes_ST-04-16-212, --locustag, Arhiz_ST-04-16-212, --centre, JLU, --cpus, 8, --outdir, /data/annotations/Agrobacterium_rhizogenes_ST-04-16-212, --proteins, /asap/db/sequences/asap-proteins.faa, --usegenus, --force, --addgenes, --rfam, --rawproduct, /data/scaffolds/Agrobacterium_rhizogenes_ST-04-16-212/Agrobacterium_rhizogenes_ST-04-16-212-pseudo.fasta] 2019-08-27 09:57:57.526 DEBUG [ABRDetection-Step-Thread-10] b.c.j.asap.genomes.ABRDetectionStep : genome.id=10: exec: [/asap/bin/groovy, /asap/scripts/asap-abr.groovy, --project-path, /data, --genome-id, 10] 2019-08-27 09:58:14.975 DEBUG [MLST-Step-Thread-10] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=10: exp backoff=1 s 2019-08-27 09:58:57.008 ERROR [Taxonomy-Step-Thread-10] b.comp.jlu.asap.genomes.GenomeStep : taxonomy genome step for genome id=10 aborted! java.lang.IllegalStateException: abnormal taxonomy exit code! exitCode=1 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.genomes.TaxonomyStep.runStep(TaxonomyStep.groovy:146) at bio.comp.jlu.asap.genomes.TaxonomyStep$runStep$2.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at bio.comp.jlu.asap.genomes.MLSTStep$runStep$2.callCurrent(Unknown Source) at bio.comp.jlu.asap.genomes.GenomeStep.run(GenomeStep.groovy:86) 2019-08-27 10:06:55.746 DEBUG [ABRDetection-Step-Thread-10] b.c.j.asap.genomes.ABRDetectionStep : genome.id=10: exp backoff=1 s 2019-08-27 10:20:55.554 DEBUG [VFDetection-Step-Thread-10] b.c.j.asap.genomes.VFDetectionStep : genome.id=10: exec: [/asap/bin/groovy, /asap/scripts/asap-vf.groovy, --project-path, /data, --genome-id, 10] 2019-08-27 10:22:42.507 DEBUG [VFDetection-Step-Thread-10] b.c.j.asap.genomes.VFDetectionStep : genome.id=10: exp backoff=1 s 2019-08-27 10:22:42.591 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : genome-id=11: running... 2019-08-27 10:22:42.621 DEBUG [QC-Step-Thread-11] bio.comp.jlu.asap.genomes.QCStep : genome.id=11: found reads: read.type=paired-end 2019-08-27 10:22:42.626 DEBUG [QC-Step-Thread-11] bio.comp.jlu.asap.genomes.QCStep : genome.id=11: dir "/data/reads_qc/Agrobacterium_rhizogenes_ST04-17-025" created 2019-08-27 10:22:42.627 DEBUG [QC-Step-Thread-11] bio.comp.jlu.asap.genomes.QCStep : genome.id=11: exec: [/asap/bin/groovy, /asap/scripts/asap-qc.groovy, --project-path, /data, --genome-id, 11] 2019-08-27 10:31:49.902 DEBUG [QC-Step-Thread-11] bio.comp.jlu.asap.genomes.QCStep : genome.id=11: exp backoff=1 s 2019-08-27 10:32:41.966 DEBUG [Mapping-Step-Thread-11] b.comp.jlu.asap.genomes.MappingStep : genome.id=11: exec: [/asap/bin/groovy, /asap/scripts/asap-mapping.groovy, --project-path, /data, --genome-id, 11] 2019-08-27 10:32:42.011 DEBUG [Assembly-Step-Thread-11] b.c.jlu.asap.genomes.AssemblyStep : genome.id=11: dir "/data/assemblies/Agrobacterium_rhizogenes_ST04-17-025" created 2019-08-27 10:32:42.012 DEBUG [Assembly-Step-Thread-11] b.c.jlu.asap.genomes.AssemblyStep : genome.id=11: exec: [/asap/bin/groovy, /asap/scripts/asap-assembly.groovy, --project-path, /data, --genome-id, 11] 2019-08-27 10:37:23.334 DEBUG [Mapping-Step-Thread-11] b.comp.jlu.asap.genomes.MappingStep : genome.id=11: exp backoff=1 s 2019-08-27 10:37:41.624 DEBUG [SNPDetection-Step-Thread-11] b.c.j.asap.genomes.SNPDetectionStep : genome.id=11: exec: [/asap/bin/groovy, /asap/scripts/asap-snp.groovy, --project-path, /data, --genome-id, 11] 2019-08-27 10:39:40.468 DEBUG [SNPDetection-Step-Thread-11] b.c.j.asap.genomes.SNPDetectionStep : genome.id=11: exp backoff=1 s 2019-08-27 11:10:04.381 DEBUG [Assembly-Step-Thread-11] b.c.jlu.asap.genomes.AssemblyStep : genome.id=11: exp backoff=1 s 2019-08-27 11:10:39.568 DEBUG [Scaffolding-Step-Thread-11] b.c.j.asap.genomes.ScaffoldingStep : run 11: dir "/data/scaffolds/Agrobacterium_rhizogenes_ST04-17-025" created 2019-08-27 11:10:39.570 DEBUG [Scaffolding-Step-Thread-11] b.c.j.asap.genomes.ScaffoldingStep : genome.id=11: exec=[/asap/bin/groovy, /asap/scripts/asap-scaffolding.groovy, --project-path, /data, --genome-id, 11] 2019-08-27 11:12:32.095 DEBUG [Scaffolding-Step-Thread-11] b.c.j.asap.genomes.ScaffoldingStep : genome.id=11: exp backoff=1 s 2019-08-27 11:12:39.440 DEBUG [ABRDetection-Step-Thread-11] b.c.j.asap.genomes.ABRDetectionStep : genome.id=11: exec: [/asap/bin/groovy, /asap/scripts/asap-abr.groovy, --project-path, /data, --genome-id, 11] 2019-08-27 11:12:39.441 DEBUG [MLST-Step-Thread-11] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=11: exec: [/asap/bin/groovy, /asap/scripts/asap-mlst.groovy, --project-path, /data, --genome-id, 11] 2019-08-27 11:12:39.440 DEBUG [Taxonomy-Step-Thread-11] b.c.jlu.asap.genomes.TaxonomyStep : genome.id=11: exec: [/asap/bin/groovy, /asap/scripts/asap-taxonomy.groovy, --project-path, /data, --genome-id, 11] 2019-08-27 11:12:39.446 DEBUG [Annotation-Step-Thread-11] b.c.jlu.asap.genomes.AnnotationStep : genome.id=11: found user provided pseudo genome: path=/data/scaffolds/Agrobacterium_rhizogenes_ST04-17-025/Agrobacterium_rhizogenes_ST04-17-025-pseudo.fasta 2019-08-27 11:12:39.546 DEBUG [Annotation-Step-Thread-11] b.c.jlu.asap.genomes.AnnotationStep : run 11: dir '/data/annotations/Agrobacterium_rhizogenes_ST04-17-025' created 2019-08-27 11:12:39.561 DEBUG [Annotation-Step-Thread-11] b.c.jlu.asap.genomes.AnnotationStep : genome.id=11: exec: [/asap/share/prokka/bin/prokka, --genus, Agrobacterium, --species, rhizogenes, --strain, ST04-17-025, --prefix, Agrobacterium_rhizogenes_ST04-17-025, --locustag, Arhiz_ST04-17-025, --centre, JLU, --cpus, 8, --outdir, /data/annotations/Agrobacterium_rhizogenes_ST04-17-025, --proteins, /asap/db/sequences/asap-proteins.faa, --usegenus, --force, --addgenes, --rfam, --rawproduct, /data/scaffolds/Agrobacterium_rhizogenes_ST04-17-025/Agrobacterium_rhizogenes_ST04-17-025-pseudo.fasta] 2019-08-27 11:12:57.434 DEBUG [MLST-Step-Thread-11] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=11: exp backoff=1 s 2019-08-27 11:13:37.810 ERROR [Taxonomy-Step-Thread-11] b.comp.jlu.asap.genomes.GenomeStep : taxonomy genome step for genome id=11 aborted! java.lang.IllegalStateException: abnormal taxonomy exit code! exitCode=1 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.genomes.TaxonomyStep.runStep(TaxonomyStep.groovy:146) at bio.comp.jlu.asap.genomes.TaxonomyStep$runStep$2.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at bio.comp.jlu.asap.genomes.ABRDetectionStep$runStep$2.callCurrent(Unknown Source) at bio.comp.jlu.asap.genomes.GenomeStep.run(GenomeStep.groovy:86) 2019-08-27 11:22:34.431 DEBUG [ABRDetection-Step-Thread-11] b.c.j.asap.genomes.ABRDetectionStep : genome.id=11: exp backoff=1 s 2019-08-27 11:37:37.784 DEBUG [VFDetection-Step-Thread-11] b.c.j.asap.genomes.VFDetectionStep : genome.id=11: exec: [/asap/bin/groovy, /asap/scripts/asap-vf.groovy, --project-path, /data, --genome-id, 11] 2019-08-27 11:39:24.416 DEBUG [VFDetection-Step-Thread-11] b.c.j.asap.genomes.VFDetectionStep : genome.id=11: exp backoff=1 s 2019-08-27 11:39:24.507 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : genome-id=12: running... 2019-08-27 11:39:24.535 DEBUG [QC-Step-Thread-12] bio.comp.jlu.asap.genomes.QCStep : genome.id=12: found reads: read.type=paired-end 2019-08-27 11:39:24.540 DEBUG [QC-Step-Thread-12] bio.comp.jlu.asap.genomes.QCStep : genome.id=12: dir "/data/reads_qc/Agrobacterium_rhizogenes_ST07-17-004" created 2019-08-27 11:39:24.541 DEBUG [QC-Step-Thread-12] bio.comp.jlu.asap.genomes.QCStep : genome.id=12: exec: [/asap/bin/groovy, /asap/scripts/asap-qc.groovy, --project-path, /data, --genome-id, 12] 2019-08-27 11:47:56.762 DEBUG [QC-Step-Thread-12] bio.comp.jlu.asap.genomes.QCStep : genome.id=12: exp backoff=1 s 2019-08-27 11:48:23.953 DEBUG [Mapping-Step-Thread-12] b.comp.jlu.asap.genomes.MappingStep : genome.id=12: exec: [/asap/bin/groovy, /asap/scripts/asap-mapping.groovy, --project-path, /data, --genome-id, 12] 2019-08-27 11:48:24.077 DEBUG [Assembly-Step-Thread-12] b.c.jlu.asap.genomes.AssemblyStep : genome.id=12: dir "/data/assemblies/Agrobacterium_rhizogenes_ST07-17-004" created 2019-08-27 11:48:24.081 DEBUG [Assembly-Step-Thread-12] b.c.jlu.asap.genomes.AssemblyStep : genome.id=12: exec: [/asap/bin/groovy, /asap/scripts/asap-assembly.groovy, --project-path, /data, --genome-id, 12] 2019-08-27 11:53:06.174 DEBUG [Mapping-Step-Thread-12] b.comp.jlu.asap.genomes.MappingStep : genome.id=12: exp backoff=1 s 2019-08-27 11:53:23.620 DEBUG [SNPDetection-Step-Thread-12] b.c.j.asap.genomes.SNPDetectionStep : genome.id=12: exec: [/asap/bin/groovy, /asap/scripts/asap-snp.groovy, --project-path, /data, --genome-id, 12] 2019-08-27 11:55:40.666 DEBUG [SNPDetection-Step-Thread-12] b.c.j.asap.genomes.SNPDetectionStep : genome.id=12: exp backoff=1 s 2019-08-27 12:26:30.779 DEBUG [Assembly-Step-Thread-12] b.c.jlu.asap.genomes.AssemblyStep : genome.id=12: exp backoff=1 s 2019-08-27 12:27:21.497 DEBUG [Scaffolding-Step-Thread-12] b.c.j.asap.genomes.ScaffoldingStep : run 12: dir "/data/scaffolds/Agrobacterium_rhizogenes_ST07-17-004" created 2019-08-27 12:27:21.499 DEBUG [Scaffolding-Step-Thread-12] b.c.j.asap.genomes.ScaffoldingStep : genome.id=12: exec=[/asap/bin/groovy, /asap/scripts/asap-scaffolding.groovy, --project-path, /data, --genome-id, 12] 2019-08-27 12:28:53.131 DEBUG [Scaffolding-Step-Thread-12] b.c.j.asap.genomes.ScaffoldingStep : genome.id=12: exp backoff=1 s 2019-08-27 12:29:21.265 DEBUG [Annotation-Step-Thread-12] b.c.jlu.asap.genomes.AnnotationStep : genome.id=12: found user provided pseudo genome: path=/data/scaffolds/Agrobacterium_rhizogenes_ST07-17-004/Agrobacterium_rhizogenes_ST07-17-004-pseudo.fasta 2019-08-27 12:29:21.268 DEBUG [Taxonomy-Step-Thread-12] b.c.jlu.asap.genomes.TaxonomyStep : genome.id=12: exec: [/asap/bin/groovy, /asap/scripts/asap-taxonomy.groovy, --project-path, /data, --genome-id, 12] 2019-08-27 12:29:21.270 DEBUG [ABRDetection-Step-Thread-12] b.c.j.asap.genomes.ABRDetectionStep : genome.id=12: exec: [/asap/bin/groovy, /asap/scripts/asap-abr.groovy, --project-path, /data, --genome-id, 12] 2019-08-27 12:29:21.272 DEBUG [Annotation-Step-Thread-12] b.c.jlu.asap.genomes.AnnotationStep : run 12: dir '/data/annotations/Agrobacterium_rhizogenes_ST07-17-004' created 2019-08-27 12:29:21.275 DEBUG [MLST-Step-Thread-12] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=12: exec: [/asap/bin/groovy, /asap/scripts/asap-mlst.groovy, --project-path, /data, --genome-id, 12] 2019-08-27 12:29:21.295 DEBUG [Annotation-Step-Thread-12] b.c.jlu.asap.genomes.AnnotationStep : genome.id=12: exec: [/asap/share/prokka/bin/prokka, --genus, Agrobacterium, --species, rhizogenes, --strain, ST07-17-004, --prefix, Agrobacterium_rhizogenes_ST07-17-004, --locustag, Arhiz_ST07-17-004, --centre, JLU, --cpus, 8, --outdir, /data/annotations/Agrobacterium_rhizogenes_ST07-17-004, --proteins, /asap/db/sequences/asap-proteins.faa, --usegenus, --force, --addgenes, --rfam, --rawproduct, /data/scaffolds/Agrobacterium_rhizogenes_ST07-17-004/Agrobacterium_rhizogenes_ST07-17-004-pseudo.fasta] 2019-08-27 12:29:39.116 DEBUG [MLST-Step-Thread-12] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=12: exp backoff=1 s 2019-08-27 12:30:19.103 ERROR [Taxonomy-Step-Thread-12] b.comp.jlu.asap.genomes.GenomeStep : taxonomy genome step for genome id=12 aborted! java.lang.IllegalStateException: abnormal taxonomy exit code! exitCode=1 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.genomes.TaxonomyStep.runStep(TaxonomyStep.groovy:146) at bio.comp.jlu.asap.genomes.TaxonomyStep$runStep$2.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at bio.comp.jlu.asap.genomes.ScaffoldingStep$runStep$2.callCurrent(Unknown Source) at bio.comp.jlu.asap.genomes.GenomeStep.run(GenomeStep.groovy:86) 2019-08-27 12:39:26.220 DEBUG [ABRDetection-Step-Thread-12] b.c.j.asap.genomes.ABRDetectionStep : genome.id=12: exp backoff=1 s 2019-08-27 12:54:19.610 DEBUG [VFDetection-Step-Thread-12] b.c.j.asap.genomes.VFDetectionStep : genome.id=12: exec: [/asap/bin/groovy, /asap/scripts/asap-vf.groovy, --project-path, /data, --genome-id, 12] 2019-08-27 12:56:06.607 DEBUG [VFDetection-Step-Thread-12] b.c.j.asap.genomes.VFDetectionStep : genome.id=12: exp backoff=1 s 2019-08-27 12:56:06.775 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : genome-id=13: running... 2019-08-27 12:56:06.816 DEBUG [QC-Step-Thread-13] bio.comp.jlu.asap.genomes.QCStep : genome.id=13: found reads: read.type=paired-end 2019-08-27 12:56:06.822 DEBUG [QC-Step-Thread-13] bio.comp.jlu.asap.genomes.QCStep : genome.id=13: dir "/data/reads_qc/Agrobacterium_rhizogenes_ST07-17-018" created 2019-08-27 12:56:06.823 DEBUG [QC-Step-Thread-13] bio.comp.jlu.asap.genomes.QCStep : genome.id=13: exec: [/asap/bin/groovy, /asap/scripts/asap-qc.groovy, --project-path, /data, --genome-id, 13] 2019-08-27 13:05:36.458 DEBUG [QC-Step-Thread-13] bio.comp.jlu.asap.genomes.QCStep : genome.id=13: exp backoff=1 s 2019-08-27 13:06:10.168 DEBUG [Mapping-Step-Thread-13] b.comp.jlu.asap.genomes.MappingStep : genome.id=13: exec: [/asap/bin/groovy, /asap/scripts/asap-mapping.groovy, --project-path, /data, --genome-id, 13] 2019-08-27 13:06:10.551 DEBUG [Assembly-Step-Thread-13] b.c.jlu.asap.genomes.AssemblyStep : genome.id=13: dir "/data/assemblies/Agrobacterium_rhizogenes_ST07-17-018" created 2019-08-27 13:06:10.556 DEBUG [Assembly-Step-Thread-13] b.c.jlu.asap.genomes.AssemblyStep : genome.id=13: exec: [/asap/bin/groovy, /asap/scripts/asap-assembly.groovy, --project-path, /data, --genome-id, 13] 2019-08-27 13:11:25.882 DEBUG [Mapping-Step-Thread-13] b.comp.jlu.asap.genomes.MappingStep : genome.id=13: exp backoff=1 s 2019-08-27 13:12:09.750 DEBUG [SNPDetection-Step-Thread-13] b.c.j.asap.genomes.SNPDetectionStep : genome.id=13: exec: [/asap/bin/groovy, /asap/scripts/asap-snp.groovy, --project-path, /data, --genome-id, 13] 2019-08-27 13:14:37.868 DEBUG [SNPDetection-Step-Thread-13] b.c.j.asap.genomes.SNPDetectionStep : genome.id=13: exp backoff=1 s 2019-08-27 13:47:48.482 DEBUG [Assembly-Step-Thread-13] b.c.jlu.asap.genomes.AssemblyStep : genome.id=13: exp backoff=1 s 2019-08-27 13:48:07.516 DEBUG [Scaffolding-Step-Thread-13] b.c.j.asap.genomes.ScaffoldingStep : run 13: dir "/data/scaffolds/Agrobacterium_rhizogenes_ST07-17-018" created 2019-08-27 13:48:07.518 DEBUG [Scaffolding-Step-Thread-13] b.c.j.asap.genomes.ScaffoldingStep : genome.id=13: exec=[/asap/bin/groovy, /asap/scripts/asap-scaffolding.groovy, --project-path, /data, --genome-id, 13] 2019-08-27 13:49:48.893 DEBUG [Scaffolding-Step-Thread-13] b.c.j.asap.genomes.ScaffoldingStep : genome.id=13: exp backoff=1 s 2019-08-27 13:50:07.218 DEBUG [MLST-Step-Thread-13] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=13: exec: [/asap/bin/groovy, /asap/scripts/asap-mlst.groovy, --project-path, /data, --genome-id, 13] 2019-08-27 13:50:07.224 DEBUG [ABRDetection-Step-Thread-13] b.c.j.asap.genomes.ABRDetectionStep : genome.id=13: exec: [/asap/bin/groovy, /asap/scripts/asap-abr.groovy, --project-path, /data, --genome-id, 13] 2019-08-27 13:50:07.234 DEBUG [Annotation-Step-Thread-13] b.c.jlu.asap.genomes.AnnotationStep : genome.id=13: found user provided pseudo genome: path=/data/scaffolds/Agrobacterium_rhizogenes_ST07-17-018/Agrobacterium_rhizogenes_ST07-17-018-pseudo.fasta 2019-08-27 13:50:07.250 DEBUG [Annotation-Step-Thread-13] b.c.jlu.asap.genomes.AnnotationStep : run 13: dir '/data/annotations/Agrobacterium_rhizogenes_ST07-17-018' created 2019-08-27 13:50:07.256 DEBUG [Annotation-Step-Thread-13] b.c.jlu.asap.genomes.AnnotationStep : genome.id=13: exec: [/asap/share/prokka/bin/prokka, --genus, Agrobacterium, --species, rhizogenes, --strain, ST07-17-018, --prefix, Agrobacterium_rhizogenes_ST07-17-018, --locustag, Arhiz_ST07-17-018, --centre, JLU, --cpus, 8, --outdir, /data/annotations/Agrobacterium_rhizogenes_ST07-17-018, --proteins, /asap/db/sequences/asap-proteins.faa, --usegenus, --force, --addgenes, --rfam, --rawproduct, /data/scaffolds/Agrobacterium_rhizogenes_ST07-17-018/Agrobacterium_rhizogenes_ST07-17-018-pseudo.fasta] 2019-08-27 13:50:07.267 DEBUG [Taxonomy-Step-Thread-13] b.c.jlu.asap.genomes.TaxonomyStep : genome.id=13: exec: [/asap/bin/groovy, /asap/scripts/asap-taxonomy.groovy, --project-path, /data, --genome-id, 13] 2019-08-27 13:50:25.407 DEBUG [MLST-Step-Thread-13] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=13: exp backoff=1 s 2019-08-27 13:51:07.773 ERROR [Taxonomy-Step-Thread-13] b.comp.jlu.asap.genomes.GenomeStep : taxonomy genome step for genome id=13 aborted! java.lang.IllegalStateException: abnormal taxonomy exit code! exitCode=1 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.genomes.TaxonomyStep.runStep(TaxonomyStep.groovy:146) at bio.comp.jlu.asap.genomes.TaxonomyStep$runStep$2.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at bio.comp.jlu.asap.genomes.AnnotationStep$runStep$2.callCurrent(Unknown Source) at bio.comp.jlu.asap.genomes.GenomeStep.run(GenomeStep.groovy:86) 2019-08-27 14:00:29.837 DEBUG [ABRDetection-Step-Thread-13] b.c.j.asap.genomes.ABRDetectionStep : genome.id=13: exp backoff=1 s 2019-08-27 14:16:05.540 DEBUG [VFDetection-Step-Thread-13] b.c.j.asap.genomes.VFDetectionStep : genome.id=13: exec: [/asap/bin/groovy, /asap/scripts/asap-vf.groovy, --project-path, /data, --genome-id, 13] 2019-08-27 14:17:50.080 DEBUG [VFDetection-Step-Thread-13] b.c.j.asap.genomes.VFDetectionStep : genome.id=13: exp backoff=1 s 2019-08-27 14:17:50.257 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : genome-id=14: running... 2019-08-27 14:17:50.263 DEBUG [QC-Step-Thread-14] bio.comp.jlu.asap.genomes.QCStep : genome.id=14: found reads: read.type=paired-end 2019-08-27 14:17:50.268 DEBUG [QC-Step-Thread-14] bio.comp.jlu.asap.genomes.QCStep : genome.id=14: dir "/data/reads_qc/Agrobacterium_rhizogenes_ST07-17-026" created 2019-08-27 14:17:50.272 DEBUG [QC-Step-Thread-14] bio.comp.jlu.asap.genomes.QCStep : genome.id=14: exec: [/asap/bin/groovy, /asap/scripts/asap-qc.groovy, --project-path, /data, --genome-id, 14] 2019-08-27 14:27:31.163 DEBUG [QC-Step-Thread-14] bio.comp.jlu.asap.genomes.QCStep : genome.id=14: exp backoff=1 s 2019-08-27 14:27:49.607 DEBUG [Mapping-Step-Thread-14] b.comp.jlu.asap.genomes.MappingStep : genome.id=14: exec: [/asap/bin/groovy, /asap/scripts/asap-mapping.groovy, --project-path, /data, --genome-id, 14] 2019-08-27 14:27:49.614 DEBUG [Assembly-Step-Thread-14] b.c.jlu.asap.genomes.AssemblyStep : genome.id=14: dir "/data/assemblies/Agrobacterium_rhizogenes_ST07-17-026" created 2019-08-27 14:27:49.616 DEBUG [Assembly-Step-Thread-14] b.c.jlu.asap.genomes.AssemblyStep : genome.id=14: exec: [/asap/bin/groovy, /asap/scripts/asap-assembly.groovy, --project-path, /data, --genome-id, 14] 2019-08-27 14:33:07.393 DEBUG [Mapping-Step-Thread-14] b.comp.jlu.asap.genomes.MappingStep : genome.id=14: exp backoff=1 s 2019-08-27 14:33:49.209 DEBUG [SNPDetection-Step-Thread-14] b.c.j.asap.genomes.SNPDetectionStep : genome.id=14: exec: [/asap/bin/groovy, /asap/scripts/asap-snp.groovy, --project-path, /data, --genome-id, 14] 2019-08-27 14:36:00.464 DEBUG [SNPDetection-Step-Thread-14] b.c.j.asap.genomes.SNPDetectionStep : genome.id=14: exp backoff=1 s 2019-08-27 15:11:25.224 DEBUG [Assembly-Step-Thread-14] b.c.jlu.asap.genomes.AssemblyStep : genome.id=14: exp backoff=1 s 2019-08-27 15:11:46.826 DEBUG [Scaffolding-Step-Thread-14] b.c.j.asap.genomes.ScaffoldingStep : run 14: dir "/data/scaffolds/Agrobacterium_rhizogenes_ST07-17-026" created 2019-08-27 15:11:46.831 DEBUG [Scaffolding-Step-Thread-14] b.c.j.asap.genomes.ScaffoldingStep : genome.id=14: exec=[/asap/bin/groovy, /asap/scripts/asap-scaffolding.groovy, --project-path, /data, --genome-id, 14] 2019-08-27 15:13:37.349 DEBUG [Scaffolding-Step-Thread-14] b.c.j.asap.genomes.ScaffoldingStep : genome.id=14: exp backoff=1 s 2019-08-27 15:13:46.582 DEBUG [ABRDetection-Step-Thread-14] b.c.j.asap.genomes.ABRDetectionStep : genome.id=14: exec: [/asap/bin/groovy, /asap/scripts/asap-abr.groovy, --project-path, /data, --genome-id, 14] 2019-08-27 15:13:46.585 DEBUG [MLST-Step-Thread-14] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=14: exec: [/asap/bin/groovy, /asap/scripts/asap-mlst.groovy, --project-path, /data, --genome-id, 14] 2019-08-27 15:13:46.585 DEBUG [Taxonomy-Step-Thread-14] b.c.jlu.asap.genomes.TaxonomyStep : genome.id=14: exec: [/asap/bin/groovy, /asap/scripts/asap-taxonomy.groovy, --project-path, /data, --genome-id, 14] 2019-08-27 15:13:46.585 DEBUG [Annotation-Step-Thread-14] b.c.jlu.asap.genomes.AnnotationStep : genome.id=14: found user provided pseudo genome: path=/data/scaffolds/Agrobacterium_rhizogenes_ST07-17-026/Agrobacterium_rhizogenes_ST07-17-026-pseudo.fasta 2019-08-27 15:13:47.005 DEBUG [Annotation-Step-Thread-14] b.c.jlu.asap.genomes.AnnotationStep : run 14: dir '/data/annotations/Agrobacterium_rhizogenes_ST07-17-026' created 2019-08-27 15:13:47.043 DEBUG [Annotation-Step-Thread-14] b.c.jlu.asap.genomes.AnnotationStep : genome.id=14: exec: [/asap/share/prokka/bin/prokka, --genus, Agrobacterium, --species, rhizogenes, --strain, ST07-17-026, --prefix, Agrobacterium_rhizogenes_ST07-17-026, --locustag, Arhiz_ST07-17-026, --centre, JLU, --cpus, 8, --outdir, /data/annotations/Agrobacterium_rhizogenes_ST07-17-026, --proteins, /asap/db/sequences/asap-proteins.faa, --usegenus, --force, --addgenes, --rfam, --rawproduct, /data/scaffolds/Agrobacterium_rhizogenes_ST07-17-026/Agrobacterium_rhizogenes_ST07-17-026-pseudo.fasta] 2019-08-27 15:14:05.759 DEBUG [MLST-Step-Thread-14] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=14: exp backoff=1 s 2019-08-27 15:14:45.550 ERROR [Taxonomy-Step-Thread-14] b.comp.jlu.asap.genomes.GenomeStep : taxonomy genome step for genome id=14 aborted! java.lang.IllegalStateException: abnormal taxonomy exit code! exitCode=1 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.genomes.TaxonomyStep.runStep(TaxonomyStep.groovy:146) at bio.comp.jlu.asap.genomes.TaxonomyStep$runStep$2.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at bio.comp.jlu.asap.genomes.ABRDetectionStep$runStep$2.callCurrent(Unknown Source) at bio.comp.jlu.asap.genomes.GenomeStep.run(GenomeStep.groovy:86) 2019-08-27 15:23:37.905 DEBUG [ABRDetection-Step-Thread-14] b.c.j.asap.genomes.ABRDetectionStep : genome.id=14: exp backoff=1 s 2019-08-27 15:38:44.938 DEBUG [VFDetection-Step-Thread-14] b.c.j.asap.genomes.VFDetectionStep : genome.id=14: exec: [/asap/bin/groovy, /asap/scripts/asap-vf.groovy, --project-path, /data, --genome-id, 14] 2019-08-27 15:40:33.827 DEBUG [VFDetection-Step-Thread-14] b.c.j.asap.genomes.VFDetectionStep : genome.id=14: exp backoff=1 s 2019-08-27 15:40:33.932 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : genome-id=15: running... 2019-08-27 15:40:33.964 DEBUG [QC-Step-Thread-15] bio.comp.jlu.asap.genomes.QCStep : genome.id=15: found reads: read.type=paired-end 2019-08-27 15:40:33.972 DEBUG [QC-Step-Thread-15] bio.comp.jlu.asap.genomes.QCStep : genome.id=15: dir "/data/reads_qc/Agrobacterium_rhizogenes_ST15-13-042" created 2019-08-27 15:40:33.977 DEBUG [QC-Step-Thread-15] bio.comp.jlu.asap.genomes.QCStep : genome.id=15: exec: [/asap/bin/groovy, /asap/scripts/asap-qc.groovy, --project-path, /data, --genome-id, 15] 2019-08-27 15:51:02.210 DEBUG [QC-Step-Thread-15] bio.comp.jlu.asap.genomes.QCStep : genome.id=15: exp backoff=1 s 2019-08-27 15:51:33.249 DEBUG [Mapping-Step-Thread-15] b.comp.jlu.asap.genomes.MappingStep : genome.id=15: exec: [/asap/bin/groovy, /asap/scripts/asap-mapping.groovy, --project-path, /data, --genome-id, 15] 2019-08-27 15:51:33.272 DEBUG [Assembly-Step-Thread-15] b.c.jlu.asap.genomes.AssemblyStep : genome.id=15: dir "/data/assemblies/Agrobacterium_rhizogenes_ST15-13-042" created 2019-08-27 15:51:33.274 DEBUG [Assembly-Step-Thread-15] b.c.jlu.asap.genomes.AssemblyStep : genome.id=15: exec: [/asap/bin/groovy, /asap/scripts/asap-assembly.groovy, --project-path, /data, --genome-id, 15] 2019-08-27 15:57:09.207 DEBUG [Mapping-Step-Thread-15] b.comp.jlu.asap.genomes.MappingStep : genome.id=15: exp backoff=1 s 2019-08-27 15:57:32.935 DEBUG [SNPDetection-Step-Thread-15] b.c.j.asap.genomes.SNPDetectionStep : genome.id=15: exec: [/asap/bin/groovy, /asap/scripts/asap-snp.groovy, --project-path, /data, --genome-id, 15] 2019-08-27 15:58:02.079 DEBUG [SNPDetection-Step-Thread-15] b.c.j.asap.genomes.SNPDetectionStep : genome.id=15: exp backoff=1 s 2019-08-27 16:57:14.410 DEBUG [Assembly-Step-Thread-15] b.c.jlu.asap.genomes.AssemblyStep : genome.id=15: exp backoff=1 s 2019-08-27 16:57:29.084 DEBUG [Scaffolding-Step-Thread-15] b.c.j.asap.genomes.ScaffoldingStep : run 15: dir "/data/scaffolds/Agrobacterium_rhizogenes_ST15-13-042" created 2019-08-27 16:57:29.086 DEBUG [Scaffolding-Step-Thread-15] b.c.j.asap.genomes.ScaffoldingStep : genome.id=15: exec=[/asap/bin/groovy, /asap/scripts/asap-scaffolding.groovy, --project-path, /data, --genome-id, 15] 2019-08-27 16:58:02.430 DEBUG [Scaffolding-Step-Thread-15] b.c.j.asap.genomes.ScaffoldingStep : genome.id=15: exp backoff=1 s 2019-08-27 16:58:28.896 DEBUG [ABRDetection-Step-Thread-15] b.c.j.asap.genomes.ABRDetectionStep : genome.id=15: exec: [/asap/bin/groovy, /asap/scripts/asap-abr.groovy, --project-path, /data, --genome-id, 15] 2019-08-27 16:58:28.899 DEBUG [Taxonomy-Step-Thread-15] b.c.jlu.asap.genomes.TaxonomyStep : genome.id=15: exec: [/asap/bin/groovy, /asap/scripts/asap-taxonomy.groovy, --project-path, /data, --genome-id, 15] 2019-08-27 16:58:28.912 DEBUG [Annotation-Step-Thread-15] b.c.jlu.asap.genomes.AnnotationStep : genome.id=15: found user provided pseudo genome: path=/data/scaffolds/Agrobacterium_rhizogenes_ST15-13-042/Agrobacterium_rhizogenes_ST15-13-042-pseudo.fasta 2019-08-27 16:58:28.917 DEBUG [MLST-Step-Thread-15] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=15: exec: [/asap/bin/groovy, /asap/scripts/asap-mlst.groovy, --project-path, /data, --genome-id, 15] 2019-08-27 16:58:29.035 DEBUG [Annotation-Step-Thread-15] b.c.jlu.asap.genomes.AnnotationStep : run 15: dir '/data/annotations/Agrobacterium_rhizogenes_ST15-13-042' created 2019-08-27 16:58:29.089 DEBUG [Annotation-Step-Thread-15] b.c.jlu.asap.genomes.AnnotationStep : genome.id=15: exec: [/asap/share/prokka/bin/prokka, --genus, Agrobacterium, --species, rhizogenes, --strain, ST15-13-042, --prefix, Agrobacterium_rhizogenes_ST15-13-042, --locustag, Arhiz_ST15-13-042, --centre, JLU, --cpus, 8, --outdir, /data/annotations/Agrobacterium_rhizogenes_ST15-13-042, --proteins, /asap/db/sequences/asap-proteins.faa, --usegenus, --force, --addgenes, --rfam, --rawproduct, /data/scaffolds/Agrobacterium_rhizogenes_ST15-13-042/Agrobacterium_rhizogenes_ST15-13-042-pseudo.fasta] 2019-08-27 16:58:46.588 DEBUG [MLST-Step-Thread-15] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=15: exp backoff=1 s 2019-08-27 16:59:29.856 ERROR [Taxonomy-Step-Thread-15] b.comp.jlu.asap.genomes.GenomeStep : taxonomy genome step for genome id=15 aborted! java.lang.IllegalStateException: abnormal taxonomy exit code! exitCode=1 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.genomes.TaxonomyStep.runStep(TaxonomyStep.groovy:146) at bio.comp.jlu.asap.genomes.TaxonomyStep$runStep$2.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at bio.comp.jlu.asap.genomes.ABRDetectionStep$runStep$2.callCurrent(Unknown Source) at bio.comp.jlu.asap.genomes.GenomeStep.run(GenomeStep.groovy:86) 2019-08-27 17:02:32.192 DEBUG [ABRDetection-Step-Thread-15] b.c.j.asap.genomes.ABRDetectionStep : genome.id=15: exp backoff=1 s 2019-08-27 17:11:28.066 DEBUG [VFDetection-Step-Thread-15] b.c.j.asap.genomes.VFDetectionStep : genome.id=15: exec: [/asap/bin/groovy, /asap/scripts/asap-vf.groovy, --project-path, /data, --genome-id, 15] 2019-08-27 17:12:26.468 DEBUG [VFDetection-Step-Thread-15] b.c.j.asap.genomes.VFDetectionStep : genome.id=15: exp backoff=1 s 2019-08-27 17:12:26.653 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : genome-id=16: running... 2019-08-27 17:12:26.761 DEBUG [QC-Step-Thread-16] bio.comp.jlu.asap.genomes.QCStep : genome.id=16: found reads: read.type=paired-end 2019-08-27 17:12:26.773 DEBUG [QC-Step-Thread-16] bio.comp.jlu.asap.genomes.QCStep : genome.id=16: dir "/data/reads_qc/Agrobacterium_rhizogenes_ST15-13-056" created 2019-08-27 17:12:26.774 DEBUG [QC-Step-Thread-16] bio.comp.jlu.asap.genomes.QCStep : genome.id=16: exec: [/asap/bin/groovy, /asap/scripts/asap-qc.groovy, --project-path, /data, --genome-id, 16] 2019-08-27 17:21:03.546 DEBUG [QC-Step-Thread-16] bio.comp.jlu.asap.genomes.QCStep : genome.id=16: exp backoff=1 s 2019-08-27 17:21:26.181 DEBUG [Mapping-Step-Thread-16] b.comp.jlu.asap.genomes.MappingStep : genome.id=16: exec: [/asap/bin/groovy, /asap/scripts/asap-mapping.groovy, --project-path, /data, --genome-id, 16] 2019-08-27 17:21:26.296 DEBUG [Assembly-Step-Thread-16] b.c.jlu.asap.genomes.AssemblyStep : genome.id=16: dir "/data/assemblies/Agrobacterium_rhizogenes_ST15-13-056" created 2019-08-27 17:21:26.305 DEBUG [Assembly-Step-Thread-16] b.c.jlu.asap.genomes.AssemblyStep : genome.id=16: exec: [/asap/bin/groovy, /asap/scripts/asap-assembly.groovy, --project-path, /data, --genome-id, 16] 2019-08-27 17:25:27.996 DEBUG [Mapping-Step-Thread-16] b.comp.jlu.asap.genomes.MappingStep : genome.id=16: exp backoff=1 s 2019-08-27 17:26:25.837 DEBUG [SNPDetection-Step-Thread-16] b.c.j.asap.genomes.SNPDetectionStep : genome.id=16: exec: [/asap/bin/groovy, /asap/scripts/asap-snp.groovy, --project-path, /data, --genome-id, 16] 2019-08-27 17:27:56.328 DEBUG [SNPDetection-Step-Thread-16] b.c.j.asap.genomes.SNPDetectionStep : genome.id=16: exp backoff=1 s 2019-08-27 17:57:42.651 DEBUG [Assembly-Step-Thread-16] b.c.jlu.asap.genomes.AssemblyStep : genome.id=16: exp backoff=1 s 2019-08-27 17:58:23.854 DEBUG [Scaffolding-Step-Thread-16] b.c.j.asap.genomes.ScaffoldingStep : run 16: dir "/data/scaffolds/Agrobacterium_rhizogenes_ST15-13-056" created 2019-08-27 17:58:23.860 DEBUG [Scaffolding-Step-Thread-16] b.c.j.asap.genomes.ScaffoldingStep : genome.id=16: exec=[/asap/bin/groovy, /asap/scripts/asap-scaffolding.groovy, --project-path, /data, --genome-id, 16] 2019-08-27 18:00:24.792 DEBUG [Scaffolding-Step-Thread-16] b.c.j.asap.genomes.ScaffoldingStep : genome.id=16: exp backoff=1 s 2019-08-27 18:01:23.540 DEBUG [Taxonomy-Step-Thread-16] b.c.jlu.asap.genomes.TaxonomyStep : genome.id=16: exec: [/asap/bin/groovy, /asap/scripts/asap-taxonomy.groovy, --project-path, /data, --genome-id, 16] 2019-08-27 18:01:23.571 DEBUG [Annotation-Step-Thread-16] b.c.jlu.asap.genomes.AnnotationStep : genome.id=16: found user provided pseudo genome: path=/data/scaffolds/Agrobacterium_rhizogenes_ST15-13-056/Agrobacterium_rhizogenes_ST15-13-056-pseudo.fasta 2019-08-27 18:01:23.633 DEBUG [Annotation-Step-Thread-16] b.c.jlu.asap.genomes.AnnotationStep : run 16: dir '/data/annotations/Agrobacterium_rhizogenes_ST15-13-056' created 2019-08-27 18:01:23.636 DEBUG [MLST-Step-Thread-16] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=16: exec: [/asap/bin/groovy, /asap/scripts/asap-mlst.groovy, --project-path, /data, --genome-id, 16] 2019-08-27 18:01:23.637 DEBUG [ABRDetection-Step-Thread-16] b.c.j.asap.genomes.ABRDetectionStep : genome.id=16: exec: [/asap/bin/groovy, /asap/scripts/asap-abr.groovy, --project-path, /data, --genome-id, 16] 2019-08-27 18:01:23.648 DEBUG [Annotation-Step-Thread-16] b.c.jlu.asap.genomes.AnnotationStep : genome.id=16: exec: [/asap/share/prokka/bin/prokka, --genus, Agrobacterium, --species, rhizogenes, --strain, ST15-13-056, --prefix, Agrobacterium_rhizogenes_ST15-13-056, --locustag, Arhiz_ST15-13-056, --centre, JLU, --cpus, 8, --outdir, /data/annotations/Agrobacterium_rhizogenes_ST15-13-056, --proteins, /asap/db/sequences/asap-proteins.faa, --usegenus, --force, --addgenes, --rfam, --rawproduct, /data/scaffolds/Agrobacterium_rhizogenes_ST15-13-056/Agrobacterium_rhizogenes_ST15-13-056-pseudo.fasta] 2019-08-27 18:01:45.139 DEBUG [MLST-Step-Thread-16] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=16: exp backoff=1 s 2019-08-27 18:02:21.497 ERROR [Taxonomy-Step-Thread-16] b.comp.jlu.asap.genomes.GenomeStep : taxonomy genome step for genome id=16 aborted! java.lang.IllegalStateException: abnormal taxonomy exit code! exitCode=1 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.genomes.TaxonomyStep.runStep(TaxonomyStep.groovy:146) at bio.comp.jlu.asap.genomes.TaxonomyStep$runStep$2.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at bio.comp.jlu.asap.genomes.ScaffoldingStep$runStep$2.callCurrent(Unknown Source) at bio.comp.jlu.asap.genomes.GenomeStep.run(GenomeStep.groovy:86) 2019-08-27 18:10:37.336 DEBUG [ABRDetection-Step-Thread-16] b.c.j.asap.genomes.ABRDetectionStep : genome.id=16: exp backoff=1 s 2019-08-27 18:24:22.047 DEBUG [VFDetection-Step-Thread-16] b.c.j.asap.genomes.VFDetectionStep : genome.id=16: exec: [/asap/bin/groovy, /asap/scripts/asap-vf.groovy, --project-path, /data, --genome-id, 16] 2019-08-27 18:26:04.658 DEBUG [VFDetection-Step-Thread-16] b.c.j.asap.genomes.VFDetectionStep : genome.id=16: exp backoff=1 s 2019-08-27 18:26:04.786 INFO [ASAP-RUN-THREAD-1] b.c.jlu.asap.genomes.GenomeRunner : genome-id=17: running... 2019-08-27 18:26:04.905 DEBUG [QC-Step-Thread-17] bio.comp.jlu.asap.genomes.QCStep : genome.id=17: found reads: read.type=paired-end 2019-08-27 18:26:04.938 DEBUG [QC-Step-Thread-17] bio.comp.jlu.asap.genomes.QCStep : genome.id=17: dir "/data/reads_qc/Agrobacterium_rhizogenes_ST15-13-057" created 2019-08-27 18:26:04.943 DEBUG [QC-Step-Thread-17] bio.comp.jlu.asap.genomes.QCStep : genome.id=17: exec: [/asap/bin/groovy, /asap/scripts/asap-qc.groovy, --project-path, /data, --genome-id, 17] 2019-08-27 18:38:13.949 DEBUG [QC-Step-Thread-17] bio.comp.jlu.asap.genomes.QCStep : genome.id=17: exp backoff=1 s 2019-08-27 18:39:04.114 DEBUG [Assembly-Step-Thread-17] b.c.jlu.asap.genomes.AssemblyStep : genome.id=17: dir "/data/assemblies/Agrobacterium_rhizogenes_ST15-13-057" created 2019-08-27 18:39:04.142 DEBUG [Assembly-Step-Thread-17] b.c.jlu.asap.genomes.AssemblyStep : genome.id=17: exec: [/asap/bin/groovy, /asap/scripts/asap-assembly.groovy, --project-path, /data, --genome-id, 17] 2019-08-27 18:39:04.143 DEBUG [Mapping-Step-Thread-17] b.comp.jlu.asap.genomes.MappingStep : genome.id=17: exec: [/asap/bin/groovy, /asap/scripts/asap-mapping.groovy, --project-path, /data, --genome-id, 17] 2019-08-27 18:45:05.251 DEBUG [Mapping-Step-Thread-17] b.comp.jlu.asap.genomes.MappingStep : genome.id=17: exp backoff=1 s 2019-08-27 18:46:03.619 DEBUG [SNPDetection-Step-Thread-17] b.c.j.asap.genomes.SNPDetectionStep : genome.id=17: exec: [/asap/bin/groovy, /asap/scripts/asap-snp.groovy, --project-path, /data, --genome-id, 17] 2019-08-27 18:48:12.387 DEBUG [SNPDetection-Step-Thread-17] b.c.j.asap.genomes.SNPDetectionStep : genome.id=17: exp backoff=1 s 2019-08-27 19:58:11.104 DEBUG [Assembly-Step-Thread-17] b.c.jlu.asap.genomes.AssemblyStep : genome.id=17: exp backoff=1 s 2019-08-27 19:58:14.385 DEBUG [Scaffolding-Step-Thread-17] b.c.j.asap.genomes.ScaffoldingStep : run 17: dir "/data/scaffolds/Agrobacterium_rhizogenes_ST15-13-057" created 2019-08-27 19:58:14.396 DEBUG [Scaffolding-Step-Thread-17] b.c.j.asap.genomes.ScaffoldingStep : genome.id=17: exec=[/asap/bin/groovy, /asap/scripts/asap-scaffolding.groovy, --project-path, /data, --genome-id, 17] 2019-08-27 20:00:08.244 DEBUG [Scaffolding-Step-Thread-17] b.c.j.asap.genomes.ScaffoldingStep : genome.id=17: exp backoff=1 s 2019-08-27 20:00:14.053 DEBUG [Annotation-Step-Thread-17] b.c.jlu.asap.genomes.AnnotationStep : genome.id=17: found user provided pseudo genome: path=/data/scaffolds/Agrobacterium_rhizogenes_ST15-13-057/Agrobacterium_rhizogenes_ST15-13-057-pseudo.fasta 2019-08-27 20:00:14.062 DEBUG [MLST-Step-Thread-17] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=17: exec: [/asap/bin/groovy, /asap/scripts/asap-mlst.groovy, --project-path, /data, --genome-id, 17] 2019-08-27 20:00:14.065 DEBUG [ABRDetection-Step-Thread-17] b.c.j.asap.genomes.ABRDetectionStep : genome.id=17: exec: [/asap/bin/groovy, /asap/scripts/asap-abr.groovy, --project-path, /data, --genome-id, 17] 2019-08-27 20:00:14.066 DEBUG [Taxonomy-Step-Thread-17] b.c.jlu.asap.genomes.TaxonomyStep : genome.id=17: exec: [/asap/bin/groovy, /asap/scripts/asap-taxonomy.groovy, --project-path, /data, --genome-id, 17] 2019-08-27 20:00:14.086 DEBUG [Annotation-Step-Thread-17] b.c.jlu.asap.genomes.AnnotationStep : run 17: dir '/data/annotations/Agrobacterium_rhizogenes_ST15-13-057' created 2019-08-27 20:00:14.130 DEBUG [Annotation-Step-Thread-17] b.c.jlu.asap.genomes.AnnotationStep : genome.id=17: exec: [/asap/share/prokka/bin/prokka, --genus, Agrobacterium, --species, rhizogenes, --strain, ST15-13-057, --prefix, Agrobacterium_rhizogenes_ST15-13-057, --locustag, Arhiz_ST15-13-057, --centre, JLU, --cpus, 8, --outdir, /data/annotations/Agrobacterium_rhizogenes_ST15-13-057, --proteins, /asap/db/sequences/asap-proteins.faa, --usegenus, --force, --addgenes, --rfam, --rawproduct, /data/scaffolds/Agrobacterium_rhizogenes_ST15-13-057/Agrobacterium_rhizogenes_ST15-13-057-pseudo.fasta] 2019-08-27 20:00:35.022 DEBUG [MLST-Step-Thread-17] bio.comp.jlu.asap.genomes.MLSTStep : genome.id=17: exp backoff=1 s 2019-08-27 20:01:16.088 ERROR [Taxonomy-Step-Thread-17] b.comp.jlu.asap.genomes.GenomeStep : taxonomy genome step for genome id=17 aborted! java.lang.IllegalStateException: abnormal taxonomy exit code! exitCode=1 at sun.reflect.GeneratedConstructorAccessor84.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:60) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:235) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.genomes.TaxonomyStep.runStep(TaxonomyStep.groovy:146) at bio.comp.jlu.asap.genomes.TaxonomyStep$runStep$2.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at bio.comp.jlu.asap.genomes.ScaffoldingStep$runStep$2.callCurrent(Unknown Source) at bio.comp.jlu.asap.genomes.GenomeStep.run(GenomeStep.groovy:86) 2019-08-27 20:10:47.884 DEBUG [ABRDetection-Step-Thread-17] b.c.j.asap.genomes.ABRDetectionStep : genome.id=17: exp backoff=1 s 2019-08-27 20:26:12.371 DEBUG [VFDetection-Step-Thread-17] b.c.j.asap.genomes.VFDetectionStep : genome.id=17: exec: [/asap/bin/groovy, /asap/scripts/asap-vf.groovy, --project-path, /data, --genome-id, 17] 2019-08-27 20:28:10.671 DEBUG [VFDetection-Step-Thread-17] b.c.j.asap.genomes.VFDetectionStep : genome.id=17: exp backoff=1 s 2019-08-27 20:28:11.160 DEBUG [Phylogeny-Analysis-Thread] b.c.j.a.analyses.PhylogenyAnalysis : check analyses/phylotree dir... 2019-08-27 20:28:11.163 DEBUG [Phylogeny-Analysis-Thread] b.c.j.a.analyses.PhylogenyAnalysis : dir "/data/phylogeny" created 2019-08-27 20:28:11.164 DEBUG [CorePan-Analysis-Thread] b.c.j.a.a.CorePanGenomeAnalysis : check corepan dir... 2019-08-27 20:28:11.172 DEBUG [CorePan-Analysis-Thread] b.c.j.a.a.CorePanGenomeAnalysis : dir "/data/corepan" created 2019-08-27 20:34:36.866 ERROR [Phylogeny-Analysis-Thread] b.c.jlu.asap.analyses.AnalysisStep : phylogeny analysis step aborted! java.io.IOException: abnormal phylo tree exit code! exitCode=1 at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:77) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:60) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:235) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.analyses.PhylogenyAnalysis.runStep(PhylogenyAnalysis.groovy:115) at bio.comp.jlu.asap.analyses.PhylogenyAnalysis$runStep$1.callCurrent(Unknown Source) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:52) at bio.comp.jlu.asap.analyses.AnalysesRunner$runStep$1.callCurrent(Unknown Source) at bio.comp.jlu.asap.analyses.AnalysisStep.run(AnalysisStep.groovy:79) 2019-08-28 00:04:56.743 DEBUG [Report-Runner-Thread] b.c.jlu.asap.reports.ReportRunner : recreated reports folder: /data/reports 2019-08-28 00:04:57.927 DEBUG [Thread-204] b.c.jlu.asap.reports.MLSTReportStep : st: [:] 2019-08-28 00:04:58.089 DEBUG [Thread-204] b.c.jlu.asap.reports.MLSTReportStep : cc: [:] 2019-08-28 00:04:58.116 DEBUG [Thread-204] b.c.jlu.asap.reports.MLSTReportStep : st: [:] 2019-08-28 00:05:16.612 ERROR [Thread-210] b.comp.jlu.asap.reports.ReportStep : corepan reporting step aborted! java.lang.OutOfMemoryError: Java heap space at sun.nio.cs.StreamEncoder.write(StreamEncoder.java:133) at java.io.OutputStreamWriter.write(OutputStreamWriter.java:220) at java.io.Writer.write(Writer.java:157) at org.codehaus.groovy.runtime.InvokerHelper.write(InvokerHelper.java:504) at org.codehaus.groovy.runtime.ResourceGroovyMethods.append(ResourceGroovyMethods.java:869) at org.codehaus.groovy.runtime.ResourceGroovyMethods.leftShift(ResourceGroovyMethods.java:797) at org.codehaus.groovy.runtime.dgm$971.invoke(Unknown Source) at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274) at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125) at bio.comp.jlu.asap.reports.CorePanReportStep$_runStep_closure1.doCall(CorePanReportStep.groovy:119) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022) at groovy.lang.Closure.call(Closure.java:414) at groovy.lang.Closure.call(Closure.java:430) at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2040) at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2025) at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2066) at org.codehaus.groovy.runtime.dgm$163.invoke(Unknown Source) at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite$PojoMetaMethodSiteNoUnwrapNoCoerce.invoke(PojoMetaMethodSite.java:274) at org.codehaus.groovy.runtime.callsite.PojoMetaMethodSite.call(PojoMetaMethodSite.java:56) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:48) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:113) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125) at bio.comp.jlu.asap.reports.CorePanReportStep.runStep(CorePanReportStep.groovy:93) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) 2019-08-28 00:05:20.855 ERROR [Thread-205] b.comp.jlu.asap.reports.ReportStep : annotation reporting step aborted! java.lang.OutOfMemoryError: Java heap space at java.lang.AbstractStringBuilder.<init>(AbstractStringBuilder.java:68) at java.lang.StringBuilder.<init>(StringBuilder.java:101) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:83) at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:105) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:247) at bio.comp.jlu.asap.reports.AnnotationReportStep.setupCircularGenomePlot(AnnotationReportStep.groovy:258) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:384) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022) at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:69) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:190) at bio.comp.jlu.asap.reports.AnnotationReportStep$_runStep_closure2.doCall(AnnotationReportStep.groovy:141) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:93) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:325) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:294) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1022) at groovy.lang.Closure.call(Closure.java:414) at groovy.lang.Closure.call(Closure.java:430) at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:2040) 2019-08-28 00:06:29.955 DEBUG [ConfigWriterThread] b.comp.jlu.asap.ConfigWriterThread : shutdown json writer...

Thank you very much for your support! I really appreciate it.

Cheers, Pablo

oschwengers commented 5 years ago

Hi @pavlo888 , Ok, now I have a better overview on this issue. There are several things going on:

  1. The taxonomic classification fails due to a wrong core parameter for blastn. I'll fix this in a minor release as soon as possible
  2. There are no MLST hits -> unfortunately, there is no MLST scheme for Agrobacterium rhizogenes (https://pubmlst.org/databases/)
  3. There are no ABR hits -> Might it be that there are indeed no ABR genes? This is fairly often the case in non-human pathogenic bacteria. Due you have additional data supporting the existence of AMR genes?
  4. There are no annotation and core/pan report files -> Due to your log, ASA³P suffered from an Java OutOfMemoryError. In this case ASA³P just needs more RAM. Can you execute ASA³P on a bigger machine? If this in not an additional option four you, you might simply analyse your genomes in chunks, i.e. split them up into 4 genomes for each execution.
  5. The phylogeny step aborts without error message. From personal experience I know that FastTreeMP just aborts if it doesn't have enough memory, so the issue as 4. .

In short: I'll work on the "taxonomic classification - number of cores" issue but you have to either analyse your data on a larger machine or split it into chunks. I'll get back to you and close this issue as soon as I've published a patch version (1.1.3). Cheers!

oschwengers commented 5 years ago

Hi @pavlo888 , I just release a new patch release v1.1.3 (https://github.com/oschwengers/asap/releases/tag/v1.1.3) which fixes the wrong cpu/core parameter bug.

The remaining issues you observed are mostly out of memory errors. So you have to analyse your data on a bigger machine or split it into smaller chunks if possible. Best regards!