Additional warning messages

src/tools/ComponentCutterMain.java

@@ -75,6 +75,9 @@ protected void runImpl() throws ExecutionFailedException {
         BigLong2ShortHashMap hm = IOUtils.loadReads(sequencesFiles.get(), k.get(), minLen.get(),
                 availableProcessors.get(), logger);
         debug("Memory used = " + Misc.usedMemoryAsString() + ", time = " + t);
+        if (hm.size() == 0) {
+            throw new ExecutionFailedException("No sequences were found in input files! The following steps will be useless");
+        }
 
 
         info("Searching for components...");
@@ -91,6 +94,9 @@ protected void runImpl() throws ExecutionFailedException {
             return;
         }
         info("Total " + NumUtils.groupDigits(components.size()) + " components were found");
+        if (components.size() == 0) {
+            warn("No components were extracted! Perhaps you should decrease --min-component-size value");
+        }
 
         try {
             ConnectedComponent.saveComponents(components, componentsFile.get().getAbsolutePath());

src/tools/FeaturesCalculatorMain.java

@@ -76,8 +76,7 @@ protected void runImpl() throws ExecutionFailedException {
         info(NumUtils.groupDigits(components.size()) + " components loaded from " + componentsFile.get());
 
         if (components.size() == 0) {
-            error("No components were found!!! Can't continue the calculations.");
-            System.exit(1);
+            throw new ExecutionFailedException("No components were found in input files! Can't continue the calculations.");
         }
 
         String compName = FileUtils.removeExtension(componentsFile.get().getName(), ".bin");

src/tools/KmersCounterMain.java

@@ -105,6 +105,11 @@ protected void runImpl() throws ExecutionFailedException {
         info(NumUtils.groupDigits(hm.size()) + " k-mers found, "
                 + NumUtils.groupDigits(c) + " (" + String.format("%.1f", c * 100.0 / hm.size()) + "%) of them is good (not erroneous)");
 
+        if (hm.size() == 0) {
+            warn("No k-mers found in reads! Perhaps you reads file is empty or k-mer size is too big");
+        } else if (c == 0 || c < (long) (hm.size() * 0.03)) {
+            warn("Too few good k-mers were found! Perhaps you should decrease k-mer size or --maximal-bad-frequency value");
+        }
         long allKmersNumber = (1L << (2*k.get())) / 2;  // (4^k)/2
         if (hm.size() == allKmersNumber) {
             warn("All possible k-mers were found in reads! Perhaps you should increase k-mer size");

src/tools/SeqBuilderMain.java

@@ -151,6 +151,9 @@ protected void runImpl() throws ExecutionFailedException {
             return;
         }
         info(NumUtils.groupDigits(sequences.size()) + " sequences found");
+        if (sequences.size() == 0) {
+            warn("No sequences were found! Perhaps you should decrease --min-seq-len or --maximal-bad-frequency values");
+        }
         debug("Memory used (without running GC) = " + Misc.usedMemoryWithoutRunningGCAsString());
 
         try {