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Published 20 hours ago • verified publisher icon soedinglab

Numbers of lines in blast-tab output and MSA file doesn't match

Open elevywis opened this issue 2 years ago • 0 comments

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Expected Behavior

Hit list (blast format) should contain information for all sequences present in the MSA

Current Behavior

Hit list (blast format) contains information for only a subset of sequences present in MSA

Steps to Reproduce (for bugs)

Use this sequence as query: cat 2o4t_1A.fa

2o4t_1A GAHVSRVEKLPKDYQIVYKEIQKYLFKVGPVELNEGIGLLSEILGFFEEGAAAGKGVLDVTGTDVAAFCDALIGDSKTYADLYQESIQQHVDKAMKNMKD

Use this command with latest DB and HHblit version.

hhblits -cpu 4 -i 2o4t_1A.fa -d UniRef30_2020_06 -oa3m 2o4t_1A.a3m -blasttab 2o4t_1A.hhblits.tab -alt 1 -cov 70 -n 2 > 2o4t_1A_hhblits.out

NUMBER OF LINES IN BLAST-LIKE OUTPUT (415)

wc -l 2o4t_1A.hhblits.tab 415 2o4t_1A.hhblits.tab

NUMBER OF SEQUENCES IN MSA (1027)

wc -l 2o4t_1A.a3m 2054 2o4t_1A.a3m

Please make sure to execute the reproduction steps.

HH-suite Output (for bugs)

Please make sure to post the complete output of the tool you called. Please use gist.github.com.

  • 18:11:30.810 INFO: Search results will be written to 2o4t_1A.hhr

  • 18:11:34.971 INFO: Searching 25985124 column state sequences.

  • 18:11:35.007 INFO: 2o4t_1A.fa is in A2M, A3M or FASTA format

  • 18:11:35.007 INFO: Iteration 1

  • 18:11:35.038 INFO: Prefiltering database

  • 18:11:44.707 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 466339

  • 18:11:45.267 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 185

  • 18:11:45.267 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 185

  • 18:11:45.267 INFO: Scoring 185 HMMs using HMM-HMM Viterbi alignment

  • 18:11:45.381 INFO: Alternative alignment: 0

  • 18:11:45.393 INFO: 185 alignments done

  • 18:11:45.559 INFO: Premerge done

  • 18:11:45.559 INFO: Realigning 171 HMM-HMM alignments using Maximum Accuracy algorithm

  • 18:11:45.648 INFO: 34 sequences belonging to 34 database HMMs found with an E-value < 0.001

  • 18:11:45.648 INFO: Number of effective sequences of resulting query HMM: Neff = 5.0716

  • 18:11:45.653 INFO: Iteration 2

  • 18:11:45.653 INFO: Set premerge to 0! (premerge: 3 iteration: 2 hits.Size: 31)

  • 18:11:45.679 INFO: Prefiltering database

  • 18:11:55.236 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 711455

  • 18:11:56.121 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 415

  • 18:11:56.121 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 384

  • 18:11:56.121 INFO: Scoring 384 HMMs using HMM-HMM Viterbi alignment

  • 18:11:56.189 INFO: Alternative alignment: 0

  • 18:11:56.239 INFO: 384 alignments done

  • 18:11:56.292 INFO: Rescoring previously found HMMs with Viterbi algorithm

  • 18:11:56.368 INFO: Alternative alignment: 0

  • 18:11:56.370 INFO: 31 alignments done

  • 18:11:56.419 INFO: Realigning 390 HMM-HMM alignments using Maximum Accuracy algorithm

  • 18:11:56.612 INFO: 77 sequences belonging to 77 database HMMs found with an E-value < 0.001

  • 18:11:56.612 INFO: Number of effective sequences of resulting query HMM: Neff = 5.96639

Context

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Your Environment

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  • Version/Git commit used: Cloned on October 20st 2021 at 10:40am

  • Server specifications (especially CPU support for AVX2/SSE and amount of system memory):

processor : 47 vendor_id : AuthenticAMD cpu family : 23 model : 49 model name : AMD Ryzen Threadripper 3960X 24-Core Processor stepping : 0 microcode : 0x8301039 cpu MHz : 2200.000 cache size : 512 KB physical id : 0 siblings : 48 core id : 30 cpu cores : 24 apicid : 61 initial apicid : 61 fpu : yes fpu_exception : yes cpuid level : 16 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb cat_l3 cdp_l3 hw_pstate sme ssbd mba sev ibpb stibp vmmcall sev_es fsgsbase bmi1 avx2 smep bmi2 cqm rdt_a rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local clzero irperf xsaveerptr rdpru wbnoinvd arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif umip rdpid overflow_recov succor smca bugs : sysret_ss_attrs spectre_v1 spectre_v2 spec_store_bypass bogomips : 7600.81 TLB size : 3072 4K pages clflush size : 64 cache_alignment : 64 address sizes : 43 bits physical, 48 bits virtual power management: ts ttp tm hwpstate cpb eff_freq_ro [13] [14]

  • Operating system and version:

Linux els14 5.11.0-37-generic #41~20.04.2-Ubuntu SMP Fri Sep 24 09:06:38 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

elevywis avatar Oct 22 '21 15:10 elevywis