133994 reads; of these: 133994 (100.00%) were paired; of these: 33777 (25.21%) aligned concordantly 0 times 99762 (74.45%) aligned concordantly exactly 1 time 455 (0.34%) aligned concordantly >1 times ---- 33777 pairs aligned concordantly 0 times; of these: 28538 (84.49%) aligned discordantly 1 time ---- 5239 pairs aligned 0 times concordantly or discordantly; of these: 10478 mates make up the pairs; of these: 6318 (60.30%) aligned 0 times 3744 (35.73%) aligned exactly 1 time 416 (3.97%) aligned >1 times 97.64% overall alignment rate [bam_header_read] EOF marker is absent. The input is probably truncated. [samopen] SAM header is present: 1367 sequences. 20517 reads; of these: 20517 (100.00%) were unpaired; of these: 3060 (14.91%) aligned 0 times 17407 (84.84%) aligned exactly 1 time 50 (0.24%) aligned >1 times 85.09% overall alignment rate [bam_header_read] EOF marker is absent. The input is probably truncated. [samopen] SAM header is present: 1367 sequences. [mpileup] 1 samples in 1 input files (mpileup) Max depth is above 1M. Potential memory hog! 133994 reads; of these: 133994 (100.00%) were paired; of these: 31623 (23.60%) aligned concordantly 0 times 100140 (74.73%) aligned concordantly exactly 1 time 2231 (1.66%) aligned concordantly >1 times ---- 31623 pairs aligned concordantly 0 times; of these: 29187 (92.30%) aligned discordantly 1 time ---- 2436 pairs aligned 0 times concordantly or discordantly; of these: 4872 mates make up the pairs; of these: 2660 (54.60%) aligned 0 times 1594 (32.72%) aligned exactly 1 time 618 (12.68%) aligned >1 times 99.01% overall alignment rate [samopen] SAM header is present: 1 sequences. [bam_header_read] EOF marker is absent. The input is probably truncated. 20517 reads; of these: 20517 (100.00%) were unpaired; of these: 196 (0.96%) aligned 0 times 19746 (96.24%) aligned exactly 1 time 575 (2.80%) aligned >1 times 99.04% overall alignment rate [samopen] SAM header is present: 1 sequences. [bam_header_read] EOF marker is absent. The input is probably truncated. [mpileup] 1 samples in 1 input files Set max per-file depth to 8000 [mpileup] 1 samples in 1 input files (mpileup) Max depth is above 1M. Potential memory hog! ** (inkscape:11576): WARNING **: Unable to create profile directory (Permission denied) (13) ** Message: Cannot create profile directory /var/www/.config/inkscape. ** Message: Inkscape will run with default settings, and new settings will not be saved. ** (inkscape:11576): WARNING **: Could not create extension error log file '/var/www/.config/inkscape/extension-errors.log' ** (inkscape:11579): WARNING **: Unable to create profile directory (Permission denied) (13) ** Message: Cannot create profile directory /var/www/.config/inkscape. ** Message: Inkscape will run with default settings, and new settings will not be saved. ** (inkscape:11579): WARNING **: Could not create extension error log file '/var/www/.config/inkscape/extension-errors.log' ** (inkscape:11582): WARNING **: Unable to create profile directory (Permission denied) (13) ** Message: Cannot create profile directory /var/www/.config/inkscape. ** Message: Inkscape will run with default settings, and new settings will not be saved. ** (inkscape:11582): WARNING **: Could not create extension error log file '/var/www/.config/inkscape/extension-errors.log' ** (inkscape:11585): WARNING **: Unable to create profile directory (Permission denied) (13) ** Message: Cannot create profile directory /var/www/.config/inkscape. ** Message: Inkscape will run with default settings, and new settings will not be saved. ** (inkscape:11585): WARNING **: Could not create extension error log file '/var/www/.config/inkscape/extension-errors.log' [00:00:00] Loading SNP file [00:00:00] Loading Genbank [00:00:11] Processing NC_000913 [00:00:28] Processing SNP files [00:00:32] Printing result to contigsToRef.SNPs_report.txt and contigsToRef.Indels_report.txt [00:00:32] Finished [00:00:00] Loading Gap file [00:00:00] Loading Genbank [00:00:11] Processing NC_000913 [00:00:39] Finished parallel: Warning: $SHELL not set. Using /bin/sh. parallel: Warning: $HOME not set. Using /tmp Generate plots in R...Done. 0.10user 0.02system 0:00.84elapsed 15%CPU (0avgtext+0avgdata 47948maxresident)k 8inputs+9776outputs (0major+10018minor)pagefaults 0swaps [bam_header_read] EOF marker is absent. The input is probably truncated. [samopen] SAM header is present: 1367 sequences. [bam_header_read] EOF marker is absent. The input is probably truncated.