Job ID = 14167115 SRX = SRX4712937 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 26232448 spots for SRR7874067/SRR7874067.sra Written 26232448 spots for SRR7874067/SRR7874067.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167554 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:21 26232448 reads; of these: 26232448 (100.00%) were unpaired; of these: 910343 (3.47%) aligned 0 times 20247458 (77.18%) aligned exactly 1 time 5074647 (19.34%) aligned >1 times 96.53% overall alignment rate Time searching: 00:08:21 Overall time: 00:08:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 5961935 / 25322105 = 0.2354 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 10:17:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.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 @ Fri, 10 Dec 2021 10:17:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:17:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:17:36: 1000000 INFO @ Fri, 10 Dec 2021 10:17:42: 2000000 INFO @ Fri, 10 Dec 2021 10:17:48: 3000000 INFO @ Fri, 10 Dec 2021 10:17:55: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 10:18:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.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 @ Fri, 10 Dec 2021 10:18:00: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:18:00: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:18:01: 5000000 INFO @ Fri, 10 Dec 2021 10:18:07: 1000000 INFO @ Fri, 10 Dec 2021 10:18:08: 6000000 INFO @ Fri, 10 Dec 2021 10:18:13: 2000000 INFO @ Fri, 10 Dec 2021 10:18:15: 7000000 INFO @ Fri, 10 Dec 2021 10:18:20: 3000000 INFO @ Fri, 10 Dec 2021 10:18:22: 8000000 INFO @ Fri, 10 Dec 2021 10:18:27: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 10:18:29: 9000000 INFO @ Fri, 10 Dec 2021 10:18:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.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 @ Fri, 10 Dec 2021 10:18:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:18:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:18:33: 5000000 INFO @ Fri, 10 Dec 2021 10:18:36: 10000000 INFO @ Fri, 10 Dec 2021 10:18:36: 1000000 INFO @ Fri, 10 Dec 2021 10:18:40: 6000000 INFO @ Fri, 10 Dec 2021 10:18:43: 2000000 INFO @ Fri, 10 Dec 2021 10:18:43: 11000000 INFO @ Fri, 10 Dec 2021 10:18:47: 7000000 INFO @ Fri, 10 Dec 2021 10:18:50: 3000000 INFO @ Fri, 10 Dec 2021 10:18:50: 12000000 INFO @ Fri, 10 Dec 2021 10:18:54: 8000000 INFO @ Fri, 10 Dec 2021 10:18:56: 4000000 INFO @ Fri, 10 Dec 2021 10:18:57: 13000000 INFO @ Fri, 10 Dec 2021 10:19:00: 9000000 INFO @ Fri, 10 Dec 2021 10:19:03: 5000000 INFO @ Fri, 10 Dec 2021 10:19:04: 14000000 INFO @ Fri, 10 Dec 2021 10:19:07: 10000000 INFO @ Fri, 10 Dec 2021 10:19:09: 6000000 INFO @ Fri, 10 Dec 2021 10:19:11: 15000000 INFO @ Fri, 10 Dec 2021 10:19:13: 11000000 INFO @ Fri, 10 Dec 2021 10:19:16: 7000000 INFO @ Fri, 10 Dec 2021 10:19:19: 16000000 INFO @ Fri, 10 Dec 2021 10:19:20: 12000000 INFO @ Fri, 10 Dec 2021 10:19:22: 8000000 INFO @ Fri, 10 Dec 2021 10:19:26: 17000000 INFO @ Fri, 10 Dec 2021 10:19:26: 13000000 INFO @ Fri, 10 Dec 2021 10:19:29: 9000000 INFO @ Fri, 10 Dec 2021 10:19:33: 18000000 INFO @ Fri, 10 Dec 2021 10:19:33: 14000000 INFO @ Fri, 10 Dec 2021 10:19:36: 10000000 INFO @ Fri, 10 Dec 2021 10:19:39: 15000000 INFO @ Fri, 10 Dec 2021 10:19:40: 19000000 INFO @ Fri, 10 Dec 2021 10:19:42: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:19:42: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:19:42: #1 total tags in treatment: 19360170 INFO @ Fri, 10 Dec 2021 10:19:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:19:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:19:42: 11000000 INFO @ Fri, 10 Dec 2021 10:19:43: #1 tags after filtering in treatment: 19360170 INFO @ Fri, 10 Dec 2021 10:19:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:19:43: #1 finished! INFO @ Fri, 10 Dec 2021 10:19:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:19:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:19:44: #2 number of paired peaks: 131 WARNING @ Fri, 10 Dec 2021 10:19:44: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Fri, 10 Dec 2021 10:19:44: start model_add_line... INFO @ Fri, 10 Dec 2021 10:19:44: start X-correlation... INFO @ Fri, 10 Dec 2021 10:19:44: end of X-cor INFO @ Fri, 10 Dec 2021 10:19:44: #2 finished! INFO @ Fri, 10 Dec 2021 10:19:44: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Dec 2021 10:19:44: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Dec 2021 10:19:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.05_model.r INFO @ Fri, 10 Dec 2021 10:19:44: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:19:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:19:46: 16000000 INFO @ Fri, 10 Dec 2021 10:19:49: 12000000 INFO @ Fri, 10 Dec 2021 10:19:52: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:19:55: 13000000 INFO @ Fri, 10 Dec 2021 10:19:59: 18000000 INFO @ Fri, 10 Dec 2021 10:20:01: 14000000 INFO @ Fri, 10 Dec 2021 10:20:05: 19000000 INFO @ Fri, 10 Dec 2021 10:20:07: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:20:07: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:20:07: #1 total tags in treatment: 19360170 INFO @ Fri, 10 Dec 2021 10:20:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:20:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:20:07: 15000000 INFO @ Fri, 10 Dec 2021 10:20:08: #1 tags after filtering in treatment: 19360170 INFO @ Fri, 10 Dec 2021 10:20:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:20:08: #1 finished! INFO @ Fri, 10 Dec 2021 10:20:08: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:20:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:20:09: #2 number of paired peaks: 131 WARNING @ Fri, 10 Dec 2021 10:20:09: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Fri, 10 Dec 2021 10:20:09: start model_add_line... INFO @ Fri, 10 Dec 2021 10:20:09: start X-correlation... INFO @ Fri, 10 Dec 2021 10:20:09: end of X-cor INFO @ Fri, 10 Dec 2021 10:20:09: #2 finished! INFO @ Fri, 10 Dec 2021 10:20:09: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Dec 2021 10:20:09: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Dec 2021 10:20:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.10_model.r INFO @ Fri, 10 Dec 2021 10:20:09: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:20:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:20:13: 16000000 INFO @ Fri, 10 Dec 2021 10:20:19: 17000000 INFO @ Fri, 10 Dec 2021 10:20:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:20:24: 18000000 INFO @ Fri, 10 Dec 2021 10:20:30: 19000000 INFO @ Fri, 10 Dec 2021 10:20:32: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:20:32: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:20:32: #1 total tags in treatment: 19360170 INFO @ Fri, 10 Dec 2021 10:20:32: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:20:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:20:33: #1 tags after filtering in treatment: 19360170 INFO @ Fri, 10 Dec 2021 10:20:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:20:33: #1 finished! INFO @ Fri, 10 Dec 2021 10:20:33: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:20:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:20:34: #2 number of paired peaks: 131 WARNING @ Fri, 10 Dec 2021 10:20:34: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Fri, 10 Dec 2021 10:20:34: start model_add_line... INFO @ Fri, 10 Dec 2021 10:20:34: start X-correlation... INFO @ Fri, 10 Dec 2021 10:20:34: end of X-cor INFO @ Fri, 10 Dec 2021 10:20:34: #2 finished! INFO @ Fri, 10 Dec 2021 10:20:34: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Dec 2021 10:20:34: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Dec 2021 10:20:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.20_model.r INFO @ Fri, 10 Dec 2021 10:20:34: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:20:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:20:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:20:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:20:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.05_summits.bed INFO @ Fri, 10 Dec 2021 10:20:37: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5431 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:20:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:21:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:21:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:21:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.10_summits.bed INFO @ Fri, 10 Dec 2021 10:21:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3381 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:21:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:21:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:21:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:21:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712937/SRX4712937.20_summits.bed INFO @ Fri, 10 Dec 2021 10:21:28: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1858 records, 4 fields): 4 millis CompletedMACS2peakCalling