ERROR: max count before zero is less than min required count (4) duplicates removed #71

Open
Open
ERROR: max count before zero is less than min required count (4) duplicates removed#71

Description

@colin893
colin893
opened on Mar 27, 2024

Hi,

Even if I found multiple times the error, I can't figure out what's wrong. I got this bam mapped with RNASeq pipeline from Nextflow, and I want to get curve (from SMARTSeq in fact). However, I have this error every time whatever I try.

$preseq lc_extrap -v -o out.nomerge.curve Exp16-12x-FS10-1-A02.sorted.bam
BED_INPUT
TOTAL READS = 137084
DISTINCT READS = 137083
DISTINCT COUNTS = 2
MAX COUNT = 2
COUNTS OF 1 = 137082
MAX TERMS = 2
OBSERVED COUNTS (3)
1	137082
2	1
ERROR:	max count before zero is less than min required count (4) duplicates removed

$preseq lc_extrap -v -o out.nomerge.curve -P -B Exp16-12x-FS10-1-A02.sorted.bam
PAIRED_END_BED_INPUT
ERROR:	problem opening file: -B
root@zddm2-NV-PC:/home/zddm2/Documents# preseq lc_extrap -v -o out.nomerge.curve -B Exp16-12x-FS10-1-A02.sorted.bam
BED_INPUT
ERROR:	problem opening file: -B

Here are my two lasts attempts, it seems there is a problem with the -B parameter? I tried with or without, I have one of the two error message.
I installed preseq with ./configure --enable-hts just to say,

would you have an idea? Thanks for your time!

Activity

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions

      , 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
       blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

      Skip to content
      ERROR:	max count before zero is less than min required count (4) duplicates removed #71
      Open
      Open
      ERROR:	max count before zero is less than min required count (4) duplicates removed#71
      Description
      @colin893
      colin893
      opened on Mar 27, 2024
      Hi,
      Even if I found multiple times the error, I can't figure out what's wrong. I got this bam mapped with RNASeq pipeline from Nextflow, and I want to get curve (from SMARTSeq in fact). However, I have this error every time whatever I try.
      $preseq lc_extrap -v -o out.nomerge.curve Exp16-12x-FS10-1-A02.sorted.bam
BED_INPUT
TOTAL READS = 137084
DISTINCT READS = 137083
DISTINCT COUNTS = 2
MAX COUNT = 2
COUNTS OF 1 = 137082
MAX TERMS = 2
OBSERVED COUNTS (3)
1	137082
2	1
ERROR:	max count before zero is less than min required count (4) duplicates removed

      $preseq lc_extrap -v -o out.nomerge.curve -P -B Exp16-12x-FS10-1-A02.sorted.bam
PAIRED_END_BED_INPUT
ERROR:	problem opening file: -B
root@zddm2-NV-PC:/home/zddm2/Documents# preseq lc_extrap -v -o out.nomerge.curve -B Exp16-12x-FS10-1-A02.sorted.bam
BED_INPUT
ERROR:	problem opening file: -B

      Here are my two lasts attempts, it seems there is a problem with the -B parameter? I tried with or without, I have one of the two error message.
      
I installed preseq with ./configure --enable-hts just to say,
      would you have an idea? Thanks for your time!
      Activity
      Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
      Metadata
      Metadata
      Assignees
      No one assigned
        Labels
        No labels
        No labels
        Type
        No type
        Projects
        No projects
          Milestone
          No milestone
          Relationships
          None yet
          Development
          No branches or pull requests
          Issue actions
          
, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

          Skip to content
          ERROR:	max count before zero is less than min required count (4) duplicates removed #71
          Open
          Open
          ERROR:	max count before zero is less than min required count (4) duplicates removed#71
          Description
          @colin893
          colin893
          opened on Mar 27, 2024
          Hi,
          Even if I found multiple times the error, I can't figure out what's wrong. I got this bam mapped with RNASeq pipeline from Nextflow, and I want to get curve (from SMARTSeq in fact). However, I have this error every time whatever I try.
          $preseq lc_extrap -v -o out.nomerge.curve Exp16-12x-FS10-1-A02.sorted.bam
BED_INPUT
TOTAL READS = 137084
DISTINCT READS = 137083
DISTINCT COUNTS = 2
MAX COUNT = 2
COUNTS OF 1 = 137082
MAX TERMS = 2
OBSERVED COUNTS (3)
1	137082
2	1
ERROR:	max count before zero is less than min required count (4) duplicates removed

          $preseq lc_extrap -v -o out.nomerge.curve -P -B Exp16-12x-FS10-1-A02.sorted.bam
PAIRED_END_BED_INPUT
ERROR:	problem opening file: -B
root@zddm2-NV-PC:/home/zddm2/Documents# preseq lc_extrap -v -o out.nomerge.curve -B Exp16-12x-FS10-1-A02.sorted.bam
BED_INPUT
ERROR:	problem opening file: -B

          Here are my two lasts attempts, it seems there is a problem with the -B parameter? I tried with or without, I have one of the two error message.
          
I installed preseq with ./configure --enable-hts just to say,
          would you have an idea? Thanks for your time!
          Activity
          Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
          Metadata
          Metadata
          Assignees
          No one assigned
            Labels
            No labels
            No labels
            Type
            No type
            Projects
            No projects
              Milestone
              No milestone
              Relationships
              None yet
              Development
              No branches or pull requests
              Issue actions
              
, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

              Skip to content
              ERROR:	max count before zero is less than min required count (4) duplicates removed #71
              Open
              Open
              ERROR:	max count before zero is less than min required count (4) duplicates removed#71
              Description
              @colin893
              colin893
              opened on Mar 27, 2024
              Hi,
              Even if I found multiple times the error, I can't figure out what's wrong. I got this bam mapped with RNASeq pipeline from Nextflow, and I want to get curve (from SMARTSeq in fact). However, I have this error every time whatever I try.
              $preseq lc_extrap -v -o out.nomerge.curve Exp16-12x-FS10-1-A02.sorted.bam
BED_INPUT
TOTAL READS = 137084
DISTINCT READS = 137083
DISTINCT COUNTS = 2
MAX COUNT = 2
COUNTS OF 1 = 137082
MAX TERMS = 2
OBSERVED COUNTS (3)
1	137082
2	1
ERROR:	max count before zero is less than min required count (4) duplicates removed

              $preseq lc_extrap -v -o out.nomerge.curve -P -B Exp16-12x-FS10-1-A02.sorted.bam
PAIRED_END_BED_INPUT
ERROR:	problem opening file: -B
root@zddm2-NV-PC:/home/zddm2/Documents# preseq lc_extrap -v -o out.nomerge.curve -B Exp16-12x-FS10-1-A02.sorted.bam
BED_INPUT
ERROR:	problem opening file: -B

              Here are my two lasts attempts, it seems there is a problem with the -B parameter? I tried with or without, I have one of the two error message.
              
I installed preseq with ./configure --enable-hts just to say,
              would you have an idea? Thanks for your time!
              Activity
              Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
              Metadata
              Metadata
              Assignees
              No one assigned
                Labels
                No labels
                No labels
                Type
                No type
                Projects
                No projects
                  Milestone
                  No milestone
                  Relationships
                  None yet
                  Development
                  No branches or pull requests
                  Issue actions
                  
, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

                  Skip to content
                  ERROR:	max count before zero is less than min required count (4) duplicates removed #71
                  Open
                  Open
                  ERROR:	max count before zero is less than min required count (4) duplicates removed#71
                  Description
                  @colin893
                  colin893
                  opened on Mar 27, 2024
                  Hi,
                  Even if I found multiple times the error, I can't figure out what's wrong. I got this bam mapped with RNASeq pipeline from Nextflow, and I want to get curve (from SMARTSeq in fact). However, I have this error every time whatever I try.
                  $preseq lc_extrap -v -o out.nomerge.curve Exp16-12x-FS10-1-A02.sorted.bam
BED_INPUT
TOTAL READS = 137084
DISTINCT READS = 137083
DISTINCT COUNTS = 2
MAX COUNT = 2
COUNTS OF 1 = 137082
MAX TERMS = 2
OBSERVED COUNTS (3)
1	137082
2	1
ERROR:	max count before zero is less than min required count (4) duplicates removed

                  $preseq lc_extrap -v -o out.nomerge.curve -P -B Exp16-12x-FS10-1-A02.sorted.bam
PAIRED_END_BED_INPUT
ERROR:	problem opening file: -B
root@zddm2-NV-PC:/home/zddm2/Documents# preseq lc_extrap -v -o out.nomerge.curve -B Exp16-12x-FS10-1-A02.sorted.bam
BED_INPUT
ERROR:	problem opening file: -B

                  Here are my two lasts attempts, it seems there is a problem with the -B parameter? I tried with or without, I have one of the two error message.
                  
I installed preseq with ./configure --enable-hts just to say,
                  would you have an idea? Thanks for your time!
                  Activity
                  Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
                  Metadata
                  Metadata
                  Assignees
                  No one assigned
                    Labels
                    No labels
                    No labels
                    Type
                    No type
                    Projects
                    No projects
                      Milestone
                      No milestone
                      Relationships
                      None yet
                      Development
                      No branches or pull requests
                      Issue actions
                      
, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

                      Skip to content
                      ERROR:	max count before zero is less than min required count (4) duplicates removed #71
                      Open
                      Open
                      ERROR:	max count before zero is less than min required count (4) duplicates removed#71
                      Description
                      @colin893
                      colin893
                      opened on Mar 27, 2024
                      Hi,
                      Even if I found multiple times the error, I can't figure out what's wrong. I got this bam mapped with RNASeq pipeline from Nextflow, and I want to get curve (from SMARTSeq in fact). However, I have this error every time whatever I try.
                      $preseq lc_extrap -v -o out.nomerge.curve Exp16-12x-FS10-1-A02.sorted.bam
BED_INPUT
TOTAL READS = 137084
DISTINCT READS = 137083
DISTINCT COUNTS = 2
MAX COUNT = 2
COUNTS OF 1 = 137082
MAX TERMS = 2
OBSERVED COUNTS (3)
1	137082
2	1
ERROR:	max count before zero is less than min required count (4) duplicates removed

                      $preseq lc_extrap -v -o out.nomerge.curve -P -B Exp16-12x-FS10-1-A02.sorted.bam
PAIRED_END_BED_INPUT
ERROR:	problem opening file: -B
root@zddm2-NV-PC:/home/zddm2/Documents# preseq lc_extrap -v -o out.nomerge.curve -B Exp16-12x-FS10-1-A02.sorted.bam
BED_INPUT
ERROR:	problem opening file: -B

                      Here are my two lasts attempts, it seems there is a problem with the -B parameter? I tried with or without, I have one of the two error message.
                      
I installed preseq with ./configure --enable-hts just to say,
                      would you have an idea? Thanks for your time!
                      Activity
                      Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
                      Metadata
                      Metadata
                      Assignees
                      No one assigned
                        Labels
                        No labels
                        No labels
                        Type
                        No type
                        Projects
                        No projects
                          Milestone
                          No milestone
                          Relationships
                          None yet
                          Development
                          No branches or pull requests
                          Issue actions
                          
, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

                          Skip to content
                          ERROR:	max count before zero is less than min required count (4) duplicates removed #71
                          Open
                          Open
                          ERROR:	max count before zero is less than min required count (4) duplicates removed#71
                          Description
                          @colin893
                          colin893
                          opened on Mar 27, 2024
                          Hi,
                          Even if I found multiple times the error, I can't figure out what's wrong. I got this bam mapped with RNASeq pipeline from Nextflow, and I want to get curve (from SMARTSeq in fact). However, I have this error every time whatever I try.
                          $preseq lc_extrap -v -o out.nomerge.curve Exp16-12x-FS10-1-A02.sorted.bam
BED_INPUT
TOTAL READS = 137084
DISTINCT READS = 137083
DISTINCT COUNTS = 2
MAX COUNT = 2
COUNTS OF 1 = 137082
MAX TERMS = 2
OBSERVED COUNTS (3)
1	137082
2	1
ERROR:	max count before zero is less than min required count (4) duplicates removed

                          $preseq lc_extrap -v -o out.nomerge.curve -P -B Exp16-12x-FS10-1-A02.sorted.bam
PAIRED_END_BED_INPUT
ERROR:	problem opening file: -B
root@zddm2-NV-PC:/home/zddm2/Documents# preseq lc_extrap -v -o out.nomerge.curve -B Exp16-12x-FS10-1-A02.sorted.bam
BED_INPUT
ERROR:	problem opening file: -B

                          Here are my two lasts attempts, it seems there is a problem with the -B parameter? I tried with or without, I have one of the two error message.
                          
I installed preseq with ./configure --enable-hts just to say,
                          would you have an idea? Thanks for your time!
                          Activity
                          Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
                          Metadata
                          Metadata
                          Assignees
                          No one assigned
                            Labels
                            No labels
                            No labels
                            Type
                            No type
                            Projects
                            No projects
                              Milestone
                              No milestone
                              Relationships
                              None yet
                              Development
                              No branches or pull requests
                              Issue actions
                              
, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

                              Skip to content
                              ERROR:	max count before zero is less than min required count (4) duplicates removed #71
                              Open
                              Open
                              ERROR:	max count before zero is less than min required count (4) duplicates removed#71
                              Description
                              @colin893
                              colin893
                              opened on Mar 27, 2024
                              Hi,
                              Even if I found multiple times the error, I can't figure out what's wrong. I got this bam mapped with RNASeq pipeline from Nextflow, and I want to get curve (from SMARTSeq in fact). However, I have this error every time whatever I try.
                              $preseq lc_extrap -v -o out.nomerge.curve Exp16-12x-FS10-1-A02.sorted.bam
BED_INPUT
TOTAL READS = 137084
DISTINCT READS = 137083
DISTINCT COUNTS = 2
MAX COUNT = 2
COUNTS OF 1 = 137082
MAX TERMS = 2
OBSERVED COUNTS (3)
1	137082
2	1
ERROR:	max count before zero is less than min required count (4) duplicates removed

                              $preseq lc_extrap -v -o out.nomerge.curve -P -B Exp16-12x-FS10-1-A02.sorted.bam
PAIRED_END_BED_INPUT
ERROR:	problem opening file: -B
root@zddm2-NV-PC:/home/zddm2/Documents# preseq lc_extrap -v -o out.nomerge.curve -B Exp16-12x-FS10-1-A02.sorted.bam
BED_INPUT
ERROR:	problem opening file: -B

                              Here are my two lasts attempts, it seems there is a problem with the -B parameter? I tried with or without, I have one of the two error message.
                              
I installed preseq with ./configure --enable-hts just to say,
                              would you have an idea? Thanks for your time!
                              Activity
                              Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
                              Metadata
                              Metadata
                              Assignees
                              No one assigned
                                Labels
                                No labels
                                No labels
                                Type
                                No type
                                Projects
                                No projects
                                  Milestone
                                  No milestone
                                  Relationships
                                  None yet
                                  Development
                                  No branches or pull requests
                                  Issue actions