SAM file is not sorted ERROR even if the input file is sorted #260

Open
Open
SAM file is not sorted ERROR even if the input file is sorted#260

Description

@YuanfengZhang
YuanfengZhang
opened on May 12, 2025

Describe the bug
SAM file is not sorted ERROR even if the input file is sorted

cd result/BL/trim-galore/no-pre-dedup/no-pre-calibrate/segemehl/samtools/no-calibrate
mkdir -p dnmtools
samtools sort -@ 16 -o BL.sorted.bam BL.bam
dnmtools counts \
-c /data/BL.fa \
-t 16 \
-o dnmtools/BL.dnmtools.tmp \
BL.sorted.bam
cd dnmtools
awk -F'\t''$6 > 4' \
BL.dnmtools.tmp \
| pigz -p 16 --best > BL.dnmtools.gz

stdout:

[bam_sort_core] merging from 0 files and 16 in-memory blocks...
[error: 0][ERRNO: 0][Success][SAM file is not sorted]

I'm sure that this error is from dnmtools instead of samtools

dnmtools/src/analysis/methcounts.cpp

Line 464 in e18ae72

if (tid < prev_tid) throwdnmt_error("SAM file is not sorted");

I tried samtools index -n but it failed too. I wonder what exact sorting tool and method does dnmtools require?

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      , 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} 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
      SAM file is not sorted ERROR even if the input file is sorted #260
      Open
      Open
      SAM file is not sorted ERROR even if the input file is sorted#260
      Description
      @YuanfengZhang
      YuanfengZhang
      opened on May 12, 2025
      Describe the bug
      
SAM file is not sorted ERROR even if the input file is sorted
      cd result/BL/trim-galore/no-pre-dedup/no-pre-calibrate/segemehl/samtools/no-calibrate
mkdir -p dnmtools
samtools sort -@ 16 -o BL.sorted.bam BL.bam
dnmtools counts \
-c /data/BL.fa \
-t 16 \
-o dnmtools/BL.dnmtools.tmp \
BL.sorted.bam
cd dnmtools
awk -F'\t''$6 > 4' \
BL.dnmtools.tmp \
| pigz -p 16 --best > BL.dnmtools.gz
      stdout:
      [bam_sort_core] merging from 0 files and 16 in-memory blocks...
[error: 0][ERRNO: 0][Success][SAM file is not sorted]

      I'm sure that this error is from dnmtools instead of samtools
      dnmtools/src/analysis/methcounts.cpp
      
Line 464
in
e18ae72
      if (tid < prev_tid) throwdnmt_error("SAM file is not sorted"); 
      I tried samtools index -n but it failed too. I wonder what exact sorting tool and method does dnmtools require?
      Activity
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, '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
          SAM file is not sorted ERROR even if the input file is sorted #260
          Open
          Open
          SAM file is not sorted ERROR even if the input file is sorted#260
          Description
          @YuanfengZhang
          YuanfengZhang
          opened on May 12, 2025
          Describe the bug
          
SAM file is not sorted ERROR even if the input file is sorted
          cd result/BL/trim-galore/no-pre-dedup/no-pre-calibrate/segemehl/samtools/no-calibrate
mkdir -p dnmtools
samtools sort -@ 16 -o BL.sorted.bam BL.bam
dnmtools counts \
-c /data/BL.fa \
-t 16 \
-o dnmtools/BL.dnmtools.tmp \
BL.sorted.bam
cd dnmtools
awk -F'\t''$6 > 4' \
BL.dnmtools.tmp \
| pigz -p 16 --best > BL.dnmtools.gz
          stdout:
          [bam_sort_core] merging from 0 files and 16 in-memory blocks...
[error: 0][ERRNO: 0][Success][SAM file is not sorted]

          I'm sure that this error is from dnmtools instead of samtools
          dnmtools/src/analysis/methcounts.cpp
          
Line 464
in
e18ae72
          if (tid < prev_tid) throwdnmt_error("SAM file is not sorted"); 
          I tried samtools index -n but it failed too. I wonder what exact sorting tool and method does dnmtools require?
          Activity
          Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
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, '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
              SAM file is not sorted ERROR even if the input file is sorted #260
              Open
              Open
              SAM file is not sorted ERROR even if the input file is sorted#260
              Description
              @YuanfengZhang
              YuanfengZhang
              opened on May 12, 2025
              Describe the bug
              
SAM file is not sorted ERROR even if the input file is sorted
              cd result/BL/trim-galore/no-pre-dedup/no-pre-calibrate/segemehl/samtools/no-calibrate
mkdir -p dnmtools
samtools sort -@ 16 -o BL.sorted.bam BL.bam
dnmtools counts \
-c /data/BL.fa \
-t 16 \
-o dnmtools/BL.dnmtools.tmp \
BL.sorted.bam
cd dnmtools
awk -F'\t''$6 > 4' \
BL.dnmtools.tmp \
| pigz -p 16 --best > BL.dnmtools.gz
              stdout:
              [bam_sort_core] merging from 0 files and 16 in-memory blocks...
[error: 0][ERRNO: 0][Success][SAM file is not sorted]

              I'm sure that this error is from dnmtools instead of samtools
              dnmtools/src/analysis/methcounts.cpp
              
Line 464
in
e18ae72
              if (tid < prev_tid) throwdnmt_error("SAM file is not sorted"); 
              I tried samtools index -n but it failed too. I wonder what exact sorting tool and method does dnmtools require?
              Activity
              Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
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                  No branches or pull requests
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, '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
                  SAM file is not sorted ERROR even if the input file is sorted #260
                  Open
                  Open
                  SAM file is not sorted ERROR even if the input file is sorted#260
                  Description
                  @YuanfengZhang
                  YuanfengZhang
                  opened on May 12, 2025
                  Describe the bug
                  
SAM file is not sorted ERROR even if the input file is sorted
                  cd result/BL/trim-galore/no-pre-dedup/no-pre-calibrate/segemehl/samtools/no-calibrate
mkdir -p dnmtools
samtools sort -@ 16 -o BL.sorted.bam BL.bam
dnmtools counts \
-c /data/BL.fa \
-t 16 \
-o dnmtools/BL.dnmtools.tmp \
BL.sorted.bam
cd dnmtools
awk -F'\t''$6 > 4' \
BL.dnmtools.tmp \
| pigz -p 16 --best > BL.dnmtools.gz
                  stdout:
                  [bam_sort_core] merging from 0 files and 16 in-memory blocks...
[error: 0][ERRNO: 0][Success][SAM file is not sorted]

                  I'm sure that this error is from dnmtools instead of samtools
                  dnmtools/src/analysis/methcounts.cpp
                  
Line 464
in
e18ae72
                  if (tid < prev_tid) throwdnmt_error("SAM file is not sorted"); 
                  I tried samtools index -n but it failed too. I wonder what exact sorting tool and method does dnmtools require?
                  Activity
                  Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
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                      No milestone
                      Relationships
                      None yet
                      Development
                      No branches or pull requests
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, '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
                      SAM file is not sorted ERROR even if the input file is sorted #260
                      Open
                      Open
                      SAM file is not sorted ERROR even if the input file is sorted#260
                      Description
                      @YuanfengZhang
                      YuanfengZhang
                      opened on May 12, 2025
                      Describe the bug
                      
SAM file is not sorted ERROR even if the input file is sorted
                      cd result/BL/trim-galore/no-pre-dedup/no-pre-calibrate/segemehl/samtools/no-calibrate
mkdir -p dnmtools
samtools sort -@ 16 -o BL.sorted.bam BL.bam
dnmtools counts \
-c /data/BL.fa \
-t 16 \
-o dnmtools/BL.dnmtools.tmp \
BL.sorted.bam
cd dnmtools
awk -F'\t''$6 > 4' \
BL.dnmtools.tmp \
| pigz -p 16 --best > BL.dnmtools.gz
                      stdout:
                      [bam_sort_core] merging from 0 files and 16 in-memory blocks...
[error: 0][ERRNO: 0][Success][SAM file is not sorted]

                      I'm sure that this error is from dnmtools instead of samtools
                      dnmtools/src/analysis/methcounts.cpp
                      
Line 464
in
e18ae72
                      if (tid < prev_tid) throwdnmt_error("SAM file is not sorted"); 
                      I tried samtools index -n but it failed too. I wonder what exact sorting tool and method does dnmtools require?
                      Activity
                      Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
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                        Labels
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                          None yet
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                          No branches or pull requests
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, '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
                          SAM file is not sorted ERROR even if the input file is sorted #260
                          Open
                          Open
                          SAM file is not sorted ERROR even if the input file is sorted#260
                          Description
                          @YuanfengZhang
                          YuanfengZhang
                          opened on May 12, 2025
                          Describe the bug
                          
SAM file is not sorted ERROR even if the input file is sorted
                          cd result/BL/trim-galore/no-pre-dedup/no-pre-calibrate/segemehl/samtools/no-calibrate
mkdir -p dnmtools
samtools sort -@ 16 -o BL.sorted.bam BL.bam
dnmtools counts \
-c /data/BL.fa \
-t 16 \
-o dnmtools/BL.dnmtools.tmp \
BL.sorted.bam
cd dnmtools
awk -F'\t''$6 > 4' \
BL.dnmtools.tmp \
| pigz -p 16 --best > BL.dnmtools.gz
                          stdout:
                          [bam_sort_core] merging from 0 files and 16 in-memory blocks...
[error: 0][ERRNO: 0][Success][SAM file is not sorted]

                          I'm sure that this error is from dnmtools instead of samtools
                          dnmtools/src/analysis/methcounts.cpp
                          
Line 464
in
e18ae72
                          if (tid < prev_tid) throwdnmt_error("SAM file is not sorted"); 
                          I tried samtools index -n but it failed too. I wonder what exact sorting tool and method does dnmtools require?
                          Activity
                          Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
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                              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
                              SAM file is not sorted ERROR even if the input file is sorted #260
                              Open
                              Open
                              SAM file is not sorted ERROR even if the input file is sorted#260
                              Description
                              @YuanfengZhang
                              YuanfengZhang
                              opened on May 12, 2025
                              Describe the bug
                              
SAM file is not sorted ERROR even if the input file is sorted
                              cd result/BL/trim-galore/no-pre-dedup/no-pre-calibrate/segemehl/samtools/no-calibrate
mkdir -p dnmtools
samtools sort -@ 16 -o BL.sorted.bam BL.bam
dnmtools counts \
-c /data/BL.fa \
-t 16 \
-o dnmtools/BL.dnmtools.tmp \
BL.sorted.bam
cd dnmtools
awk -F'\t''$6 > 4' \
BL.dnmtools.tmp \
| pigz -p 16 --best > BL.dnmtools.gz
                              stdout:
                              [bam_sort_core] merging from 0 files and 16 in-memory blocks...
[error: 0][ERRNO: 0][Success][SAM file is not sorted]

                              I'm sure that this error is from dnmtools instead of samtools
                              dnmtools/src/analysis/methcounts.cpp
                              
Line 464
in
e18ae72
                              if (tid < prev_tid) throwdnmt_error("SAM file is not sorted"); 
                              I tried samtools index -n but it failed too. I wonder what exact sorting tool and method does dnmtools require?
                              Activity
                              Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
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                              Metadata
                              Assignees
                              No one assigned
                                Labels
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                                  No branches or pull requests
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