Job ID = 6453854 SRX = SRX152113 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:47:47 prefetch.2.10.7: 1) Downloading 'SRR504970'... 2020-06-21T08:47:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:53:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:53:05 prefetch.2.10.7: 1) 'SRR504970' was downloaded successfully Read 23620125 spots for SRR504970/SRR504970.sra Written 23620125 spots for SRR504970/SRR504970.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:56 23620125 reads; of these: 23620125 (100.00%) were unpaired; of these: 4083792 (17.29%) aligned 0 times 14003074 (59.28%) aligned exactly 1 time 5533259 (23.43%) aligned >1 times 82.71% overall alignment rate Time searching: 00:04:56 Overall time: 00:04:56 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2580158 / 19536333 = 0.1321 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:05:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 18:05:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:05:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:05:34: 1000000 INFO @ Sun, 21 Jun 2020 18:05:39: 2000000 INFO @ Sun, 21 Jun 2020 18:05:45: 3000000 INFO @ Sun, 21 Jun 2020 18:05:51: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:05:56: 5000000 INFO @ Sun, 21 Jun 2020 18:05:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 18:05:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:05:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:02: 6000000 INFO @ Sun, 21 Jun 2020 18:06:05: 1000000 INFO @ Sun, 21 Jun 2020 18:06:08: 7000000 INFO @ Sun, 21 Jun 2020 18:06:12: 2000000 INFO @ Sun, 21 Jun 2020 18:06:14: 8000000 INFO @ Sun, 21 Jun 2020 18:06:19: 3000000 INFO @ Sun, 21 Jun 2020 18:06:20: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:06:26: 10000000 INFO @ Sun, 21 Jun 2020 18:06:27: 4000000 INFO @ Sun, 21 Jun 2020 18:06:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 18:06:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:33: 11000000 INFO @ Sun, 21 Jun 2020 18:06:34: 5000000 INFO @ Sun, 21 Jun 2020 18:06:35: 1000000 INFO @ Sun, 21 Jun 2020 18:06:39: 12000000 INFO @ Sun, 21 Jun 2020 18:06:41: 2000000 INFO @ Sun, 21 Jun 2020 18:06:42: 6000000 INFO @ Sun, 21 Jun 2020 18:06:46: 13000000 INFO @ Sun, 21 Jun 2020 18:06:49: 3000000 INFO @ Sun, 21 Jun 2020 18:06:49: 7000000 INFO @ Sun, 21 Jun 2020 18:06:54: 14000000 INFO @ Sun, 21 Jun 2020 18:06:56: 4000000 INFO @ Sun, 21 Jun 2020 18:06:57: 8000000 INFO @ Sun, 21 Jun 2020 18:07:02: 15000000 INFO @ Sun, 21 Jun 2020 18:07:04: 5000000 INFO @ Sun, 21 Jun 2020 18:07:04: 9000000 INFO @ Sun, 21 Jun 2020 18:07:10: 16000000 INFO @ Sun, 21 Jun 2020 18:07:11: 6000000 INFO @ Sun, 21 Jun 2020 18:07:11: 10000000 INFO @ Sun, 21 Jun 2020 18:07:17: #1 tag size is determined as 38 bps INFO @ Sun, 21 Jun 2020 18:07:17: #1 tag size = 38 INFO @ Sun, 21 Jun 2020 18:07:17: #1 total tags in treatment: 16956175 INFO @ Sun, 21 Jun 2020 18:07:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:07:18: #1 tags after filtering in treatment: 16956118 INFO @ Sun, 21 Jun 2020 18:07:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:18: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:19: 7000000 INFO @ Sun, 21 Jun 2020 18:07:19: 11000000 INFO @ Sun, 21 Jun 2020 18:07:19: #2 number of paired peaks: 912 WARNING @ Sun, 21 Jun 2020 18:07:19: Fewer paired peaks (912) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 912 pairs to build model! INFO @ Sun, 21 Jun 2020 18:07:19: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:19: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:19: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:19: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:19: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 18:07:19: #2 alternative fragment length(s) may be 4,99 bps INFO @ Sun, 21 Jun 2020 18:07:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.05_model.r INFO @ Sun, 21 Jun 2020 18:07:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:07:26: 8000000 INFO @ Sun, 21 Jun 2020 18:07:26: 12000000 INFO @ Sun, 21 Jun 2020 18:07:33: 9000000 INFO @ Sun, 21 Jun 2020 18:07:34: 13000000 INFO @ Sun, 21 Jun 2020 18:07:41: 10000000 INFO @ Sun, 21 Jun 2020 18:07:41: 14000000 INFO @ Sun, 21 Jun 2020 18:07:48: 11000000 INFO @ Sun, 21 Jun 2020 18:07:49: 15000000 INFO @ Sun, 21 Jun 2020 18:07:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:07:55: 12000000 INFO @ Sun, 21 Jun 2020 18:07:56: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:08:02: 13000000 INFO @ Sun, 21 Jun 2020 18:08:04: #1 tag size is determined as 38 bps INFO @ Sun, 21 Jun 2020 18:08:04: #1 tag size = 38 INFO @ Sun, 21 Jun 2020 18:08:04: #1 total tags in treatment: 16956175 INFO @ Sun, 21 Jun 2020 18:08:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:08:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:08:05: #1 tags after filtering in treatment: 16956118 INFO @ Sun, 21 Jun 2020 18:08:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:08:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:08:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:08:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:08:06: #2 number of paired peaks: 912 WARNING @ Sun, 21 Jun 2020 18:08:06: Fewer paired peaks (912) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 912 pairs to build model! INFO @ Sun, 21 Jun 2020 18:08:06: start model_add_line... INFO @ Sun, 21 Jun 2020 18:08:06: start X-correlation... INFO @ Sun, 21 Jun 2020 18:08:06: end of X-cor INFO @ Sun, 21 Jun 2020 18:08:06: #2 finished! INFO @ Sun, 21 Jun 2020 18:08:06: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 18:08:06: #2 alternative fragment length(s) may be 4,99 bps INFO @ Sun, 21 Jun 2020 18:08:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.10_model.r INFO @ Sun, 21 Jun 2020 18:08:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:08:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:08:10: 14000000 INFO @ Sun, 21 Jun 2020 18:08:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:08:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.05_summits.bed INFO @ Sun, 21 Jun 2020 18:08:13: Done! pass1 - making usageList (677 chroms): 2 millis pass2 - checking and writing primary data (5802 records, 4 fields): 76 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:08:18: 15000000 INFO @ Sun, 21 Jun 2020 18:08:25: 16000000 INFO @ Sun, 21 Jun 2020 18:08:33: #1 tag size is determined as 38 bps INFO @ Sun, 21 Jun 2020 18:08:33: #1 tag size = 38 INFO @ Sun, 21 Jun 2020 18:08:33: #1 total tags in treatment: 16956175 INFO @ Sun, 21 Jun 2020 18:08:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:08:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:08:33: #1 tags after filtering in treatment: 16956118 INFO @ Sun, 21 Jun 2020 18:08:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:08:33: #1 finished! INFO @ Sun, 21 Jun 2020 18:08:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:08:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:08:35: #2 number of paired peaks: 912 WARNING @ Sun, 21 Jun 2020 18:08:35: Fewer paired peaks (912) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 912 pairs to build model! INFO @ Sun, 21 Jun 2020 18:08:35: start model_add_line... INFO @ Sun, 21 Jun 2020 18:08:35: start X-correlation... INFO @ Sun, 21 Jun 2020 18:08:35: end of X-cor INFO @ Sun, 21 Jun 2020 18:08:35: #2 finished! INFO @ Sun, 21 Jun 2020 18:08:35: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 18:08:35: #2 alternative fragment length(s) may be 4,99 bps INFO @ Sun, 21 Jun 2020 18:08:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.20_model.r INFO @ Sun, 21 Jun 2020 18:08:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:08:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:08:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:09:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:09:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:09:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.10_summits.bed INFO @ Sun, 21 Jun 2020 18:09:00: Done! pass1 - making usageList (516 chroms): 2 millis pass2 - checking and writing primary data (2441 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:09:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:09:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:09:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:09:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152113/SRX152113.20_summits.bed INFO @ Sun, 21 Jun 2020 18:09:27: Done! pass1 - making usageList (240 chroms): 2 millis pass2 - checking and writing primary data (725 records, 4 fields): 15 millis CompletedMACS2peakCalling