added trace to get the number of lines in huge gzipped file

phagetermvirome/readsCoverage_res.py

@@ -283,8 +283,9 @@ class RCCheckpoint_handler:
                  host_whole_coverage,list_hybrid,insert,paired_mismatch,reads_tested,read_match):
         cur_t = time.perf_counter_ns()
         elapsed_t = cur_t - self.start_t
-        #convert elapsed_t tp to seconds
-        elaspsed_t=elapsed_t * 0.000000001
+        #convert elapsed_t tp to seconds; then minutes
+        elapsed_t=elapsed_t * 0.000000001
+        elapsed_t=elapsed_t/60
         if (self.test_mode==True or (self.chk_freq!=0 and (elapsed_t % self.chk_freq == 0))):  # time to create checkpoint.
             chkp=RCCheckpoint(count_line,core_id,idx_seq,termini_coverage,whole_coverage,paired_whole_coverage,\
                  phage_hybrid_coverage, host_hybrid_coverage, \