...
The alignment log will have a "I ran successfully" message at the end if all went well, and if there was an error, the important information should also be at the end of the log file. So you can use tail to check the status of an alignment; for example
:
| Code Block | ||||
|---|---|---|---|---|
| ||||
tail aln.yeast_chip.log |
This will show something like this:
| Code Block |
|---|
..samstats file 'yeast_chip.samstats.txt' exists Thu May 28 16:36:01 CDT 2015 ..samstats file file 'yeast_chip.samstats.txt' size ok Thu May 28 16:36:01 CDT 2015 --------------------------------------------------------- Cleaning up files... --------------------------------------------------------- ckRes 0 cleanup --------------------------------------------------------- All bwa alignment tasks completed successfully! Thu May 28 16:36:01 CDT 2015 --------------------------------------------------------- |
...
For example, suppose I have run 6 alignments and have these 6 log files:
| Code Block |
|---|
aln.delswr1_htz1_tap1t0.log aln.delswr1_htz1_tap1t30.log aln.wt_htz1_tap1t15.log aln.delswr1_htz1_tap1t15.log aln.wt_htz1_tap1t0.log aln.wt_htz1_tap1t30.log |
I can check that all 6 completed with this command:
| Code Block | ||||
|---|---|---|---|---|
| ||||
grep 'completed successfully' aln.*.log | wc -l |
...
The <prefix>.samstats.txt statistics file produced by the alignment pipeline has a lot of good information in one place. If you use cat or more to view it you'll see this:
| Code Block |
|---|
-----------------------------------------------
Aligner: bwa
Total sequences: 1184360
Total mapped: 547664 (46.2 %)
Total unmapped: 636696 (53.8 %)
Primary: 547664 (100.0 %)
Secondary:
Duplicates: 324280 (59.2 %)
Fwd strand: 272898 (49.8 %)
Rev strand: 274766 (50.2 %)
Multi hit: 18688 (3.4 %)
Soft clip: 222451 (40.6 %)
All match: 319429 (58.3 %)
Indels: 6697 (1.2 %)
Spliced:
-----------------------------------------------
Total PE seqs: 1184360
PE seqs mapped: 547664 (46.2 %)
Num PE pairs: 592180
F5 1st end mapped: 300477 (50.7 %)
F3 2nd end mapped: 247187 (41.7 %)
PE pairs mapped: 241180 (40.7 %)
PE proper pairs: 236557 (39.9 %)
-----------------------------------------------
Insert size stats for: yeast_chip
Number of pairs: 236557 (proper)
Number of insert sizes: 212
Mean [-/+ 1 SD]: 215 [153 277] (sd 62)
Mode [Fivenum]: 223 [105 210 220 229 321]
----------------------------------------------- |
...
A quick way to check alignment stats if you have run multiple alignments is again to use grep. For example, for the 6 alignment files shown earlier, running this:
| Code Block | ||||
|---|---|---|---|---|
| ||||
grep 'Total map' *samstats.txt |
will produce output like this:
| Code Block |
|---|
delswr1_htz1_tap1t0.samstats.txt: Total mapped: 32761761 (86.8 %) delswr1_htz1_tap1t15.samstats.txt: Total mapped: 33699464 (89.2 %) delswr1_htz1_tap1t30.samstats.txt: Total mapped: 28441655 (87.6 %) wt_htz1_tap1t0.samstats.txt: Total mapped: 28454847 (89.5 %) wt_htz1_tap1t15.samstats.txt: Total mapped: 33245627 (90.9 %) wt_htz1_tap1t30.samstats.txt: Total mapped: 32567026 (90.7 %) |
...