| 120 | | ''' On mini pilot. Split lines-per-file: 8,000,000. Start: 18-12-2010 16:40 ''' |
| 121 | | || '''Lane''' || '''split BWA merge''' || '''Comments''' || '''Elapsed time (s)''' || |
| 122 | | || A4a_L4_HUModqRBUDIBAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-cOunUZ/html/workflow-cOunUZ.html done] || || 22740 || |
| 123 | | || A4a_L6_HUModqRADDIAAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-pqWdc1/html/workflow-pqWdc1.html done] || || 37750 || |
| 124 | | || A4a_L7_HUModqRBVDIBAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-OqeNdv/html/workflow-OqeNdv.html failed] || || || |
| 125 | | || A4b_L3_HUModqRAFDIBAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-GRDX0X/html/workflow-GRDX0X.html done] || || 32256 || |
| 126 | | || A4b_L6_HUModqRBTDIBAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-ZRH98o/html/workflow-ZRH98o.html failed] || || || |
| 127 | | || R2A _L1_HUModqRADDIBAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-1lNDQh/html/workflow-1lNDQh.html failed] || || || |
| 128 | | || R2A _L1_HUModqRAFDIBAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-rufel6/html/workflow-rufel6.html done] || || 35819 || |
| 129 | | || R2A _L5_HUModqRAEDIAAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-wVuMjg/html/workflow-wVuMjg.html failed] || || || |
| 130 | | || R2B _L3_HUModqRBTDIAAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-L3m5Yi/html/workflow-L3m5Yi.html done] || || 23754 || |
| 131 | | || R2B _L4_HUModqRBUDIAAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-alGMJK/html/workflow-alGMJK.html failed] || pair 1 not in correct gzip format? || || |
| 132 | | || R2B _L6_HUModqRBTDIBAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-LCaDkY/html/workflow-LCaDkY.html failed] || || || |
| 133 | | || R2C _L2_HUModqRBUDIBAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-gVXW9i/html/workflow-gVXW9i.html done] || || 40763 || |
| 134 | | || R2C _L2_HUModqRBVDIBAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-8bma4j/html/workflow-8bma4j.html failed] || || || |
| 135 | | || R2C _L7_HUModqRBVDIAAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-Rjh1lC/html/workflow-Rjh1lC.html done] || || 39374 || |
| 136 | | || Unknown_L6_HUModqRBUDIAAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-IG0HAm/html/workflow-IG0HAm.html done] || || 30307 || |
| 137 | | Note: The Merge component is red (marked as failed) in the finished workflows. The bam files where produced successfully. |
| | 120 | || '''#''' || '''Sample''' || '''WF''' || '''Status''' || '''Start''' || |
| | 121 | || 1 || A4a || [http://orange.ebioscience.amc.nl/workflows/workflow-693426f3/html/workflow-693426f3.html F] [http://orange.ebioscience.amc.nl/workflows/workflow-35a9b777/html/workflow-35a9b777.html F] [http://orange.ebioscience.amc.nl/workflows/workflow-4ba3f651/html/workflow-4ba3f651.html F] [http://orange.ebioscience.amc.nl/workflows/workflow-425d9ceb/html/workflow-425d9ceb.html workflow-425d9ceb] || done |||| |
| | 122 | || 2 || Vartest || [http://orange.ebioscience.amc.nl/workflows/workflow-490b15f8/html/workflow-490b15f8.html workflow-490b15f8] || done |||| |
| | 123 | || 3 || Iteration test || [http://orange.ebioscience.amc.nl/workflows/workflow-bf48aff1/html/workflow-bf48aff1.html workflow-bf48aff1] || failed |||| |
| | 124 | || 4 || Iteration test || [http://orange.ebioscience.amc.nl/workflows/workflow-923c6588/html/workflow-923c6588.html workflow-923c6588] || done |||| |
| | 125 | || 5 || 60-samples-batch (15 lanes) || [http://orange.ebioscience.amc.nl/workflows/workflow-d80b5767/html/workflow-d80b5767.html workflow-d80b5767] || 10 / 15 done || 11-02-2011 19:30 || |
| | 126 | || 6 || 60-samples-batch A (55 lanes) || [http://orange.ebioscience.amc.nl/workflows/workflow-cbaca6e5/html/workflow-cbaca6e5.html workflow-cbaca6e5] || 15 / 55 done || 12-02-2011 13:55 || |
| | 127 | || 7 || 60-samples-batch A remaining 1 (17 lanes) || [http://orange.ebioscience.amc.nl/workflows/workflow-835250b1/html/workflow-835250b1.html workflow-835250b1] || failed (grid very busy) || 07-03-2011 17:45 || |
| | 128 | || 8 || 60-samples-batch A remaining 1 (17 lanes) || [http://orange.ebioscience.amc.nl/workflows/workflow-31eb952d/html/workflow-31eb952d.html workflow-31eb952d] || 1/17 done || 08-03-2011 14:15 || |
| | 129 | || 9 || 60-samples-batch A remaining (27 lanes) || [http://orange.ebioscience.amc.nl/workflows/workflow-fd98c7c8/html/workflow-fd98c7c8.html workflow-fd98c7c8] || running || 15-03-2011 10:45 || |
| | 130 | || x || 60-samples-batch G (54 lanes) || || || || |
| | 131 | || x || 60-samples-batch R (60 lanes) || || || || |
| 139 | | ''' BWA alignment on mini pilot without splitting the data ''' |
| 140 | | * 19-12-2010 14:00 [https://hangplek.nikhef.nl:443/workflows/workflow-rIUQ2N/html/workflow-rIUQ2N.html done] - elapsed time 325886 s |
| 141 | | |
| 142 | | '''PicardQC on finished bam files''' |
| 143 | | * 20-12-2010 11:30 [https://hangplek.nikhef.nl:443/workflows/workflow-3T5uMC/html/workflow-3T5uMC.html done] - elapsed time (10 bam files) 8730 s |
| 144 | | * [http://www.bbmriwiki.nl/attachment/wiki/BigCompute/log-picardqc-20101220.ods Info runtime and used disk space] (ods) |
| 145 | | |
| 146 | | '''Coverage-per-base on finished bam files''' |
| 147 | | * 20-12-2010 12:40 [https://hangplek.nikhef.nl:443/workflows/workflow-qwMQka/html/workflow-qwMQka.html done] - elapsed time 89634 s |
| 148 | | |
| 149 | | '''Mark-duplicates on finished bam files''' |
| 150 | | * 20-12-2010 12:47 [https://hangplek.nikhef.nl:443/workflows/workflow-E6tgrW/html/workflow-E6tgrW.html done] - elapsed time 10614 s |
| 151 | | |
| 152 | | '''Re-align on finished bam files''' |
| 153 | | * 20-12-2010 17:48 [https://hangplek.nikhef.nl:443/workflows/workflow-ICmgZF/html/workflow-ICmgZF.html done] - elapsed time 9165 s |
| 154 | | |
| 155 | | '''Gvnl pipeline on remaining samples (split, bwa, merge, coverage-per-base, picard-qc, mark-duplicates, re-align) Start: 20-12-2010 18:50''' |
| 156 | | || '''Lane''' || '''Progress''' || '''Elapsed time''' || |
| 157 | | || A4a_L7_HUModqRBVDIBAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-RllyLv/html/workflow-RllyLv.html done] || 208542 || |
| 158 | | || A4b_L6_HUModqRBTDIBAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-A6WSPB/html/workflow-A6WSPB.html done] || 74476 || |
| 159 | | || R2A _L1_HUModqRADDIBAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-L2NZUb/html/workflow-L2NZUb.html done] || 72636 || |
| 160 | | || R2A _L5_HUModqRAEDIAAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-VoZud6/html/workflow-VoZud6.html done] || 55242 || |
| 161 | | || R2B _L4_HUModqRBUDIAAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-ldqezK/html/workflow-ldqezK.html failed] || || |
| 162 | | || R2B _L6_HUModqRBTDIBAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-q9PKaQ/html/workflow-q9PKaQ.html done] || 227859 || |
| 163 | | || R2C _L2_HUModqRBVDIBAPE || [https://hangplek.nikhef.nl:443/workflows/workflow-jroCmW/html/workflow-jroCmW.html done] || 44730 || |
| 164 | | * Note1: Workflow stops after merge-bam. Working on it. |
| 165 | | * Note2: The Dutch grid seems very busy at the moment. That could explain the longer execution times. |
| 166 | | |
| 167 | | '''Gvnl pipeline on theoretical reads''' |
| 168 | | * 22-12-2010 19:14 [https://hangplek.nikhef.nl/workflows//workflow-FRErry/html/workflow-FRErry.html done] - elapsed time 38587 s |
| 169 | | * Workflow does continue after the merge-bam now |
| 170 | | * To do: implement recalibration step, and a check on all bam files of the split input before the merge step |
