Job ID = 14171284 SRX = SRX9986136 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 28711233 spots for SRR13591555/SRR13591555.sra Written 28711233 spots for SRR13591555/SRR13591555.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171749 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:13:05 28711233 reads; of these: 28711233 (100.00%) were unpaired; of these: 1445806 (5.04%) aligned 0 times 8256153 (28.76%) aligned exactly 1 time 19009274 (66.21%) aligned >1 times 94.96% overall alignment rate Time searching: 00:13:06 Overall time: 00:13:06 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] 16660263 / 27265427 = 0.6110 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 @ Sat, 11 Dec 2021 11:13:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.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 @ Sat, 11 Dec 2021 11:13:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:13:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:13:55: 1000000 INFO @ Sat, 11 Dec 2021 11:14:01: 2000000 INFO @ Sat, 11 Dec 2021 11:14:07: 3000000 INFO @ Sat, 11 Dec 2021 11:14:12: 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 @ Sat, 11 Dec 2021 11:14:18: 5000000 INFO @ Sat, 11 Dec 2021 11:14:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.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 @ Sat, 11 Dec 2021 11:14:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:14:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:14:24: 6000000 INFO @ Sat, 11 Dec 2021 11:14:25: 1000000 INFO @ Sat, 11 Dec 2021 11:14:30: 7000000 INFO @ Sat, 11 Dec 2021 11:14:32: 2000000 INFO @ Sat, 11 Dec 2021 11:14:36: 8000000 INFO @ Sat, 11 Dec 2021 11:14:38: 3000000 INFO @ Sat, 11 Dec 2021 11:14:42: 9000000 INFO @ Sat, 11 Dec 2021 11:14:45: 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 @ Sat, 11 Dec 2021 11:14:48: 10000000 INFO @ Sat, 11 Dec 2021 11:14:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.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 @ Sat, 11 Dec 2021 11:14:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:14:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:14:51: 5000000 INFO @ Sat, 11 Dec 2021 11:14:52: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:14:52: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:14:52: #1 total tags in treatment: 10605164 INFO @ Sat, 11 Dec 2021 11:14:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:14:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:14:52: #1 tags after filtering in treatment: 10605164 INFO @ Sat, 11 Dec 2021 11:14:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:14:52: #1 finished! INFO @ Sat, 11 Dec 2021 11:14:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:14:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:14:53: #2 number of paired peaks: 726 WARNING @ Sat, 11 Dec 2021 11:14:53: Fewer paired peaks (726) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 726 pairs to build model! INFO @ Sat, 11 Dec 2021 11:14:53: start model_add_line... INFO @ Sat, 11 Dec 2021 11:14:53: start X-correlation... INFO @ Sat, 11 Dec 2021 11:14:53: end of X-cor INFO @ Sat, 11 Dec 2021 11:14:53: #2 finished! INFO @ Sat, 11 Dec 2021 11:14:53: #2 predicted fragment length is 137 bps INFO @ Sat, 11 Dec 2021 11:14:53: #2 alternative fragment length(s) may be 137 bps INFO @ Sat, 11 Dec 2021 11:14:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.05_model.r INFO @ Sat, 11 Dec 2021 11:14:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:14:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:14:55: 1000000 INFO @ Sat, 11 Dec 2021 11:14:57: 6000000 INFO @ Sat, 11 Dec 2021 11:15:02: 2000000 INFO @ Sat, 11 Dec 2021 11:15:04: 7000000 INFO @ Sat, 11 Dec 2021 11:15:09: 3000000 INFO @ Sat, 11 Dec 2021 11:15:11: 8000000 INFO @ Sat, 11 Dec 2021 11:15:15: 4000000 INFO @ Sat, 11 Dec 2021 11:15:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:15:17: 9000000 INFO @ Sat, 11 Dec 2021 11:15:22: 5000000 INFO @ Sat, 11 Dec 2021 11:15:24: 10000000 INFO @ Sat, 11 Dec 2021 11:15:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:15:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:15:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.05_summits.bed INFO @ Sat, 11 Dec 2021 11:15:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5706 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:15:28: 6000000 INFO @ Sat, 11 Dec 2021 11:15:28: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:15:28: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:15:28: #1 total tags in treatment: 10605164 INFO @ Sat, 11 Dec 2021 11:15:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:15:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:15:28: #1 tags after filtering in treatment: 10605164 INFO @ Sat, 11 Dec 2021 11:15:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:15:28: #1 finished! INFO @ Sat, 11 Dec 2021 11:15:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:15:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:15:29: #2 number of paired peaks: 726 WARNING @ Sat, 11 Dec 2021 11:15:29: Fewer paired peaks (726) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 726 pairs to build model! INFO @ Sat, 11 Dec 2021 11:15:29: start model_add_line... INFO @ Sat, 11 Dec 2021 11:15:29: start X-correlation... INFO @ Sat, 11 Dec 2021 11:15:29: end of X-cor INFO @ Sat, 11 Dec 2021 11:15:29: #2 finished! INFO @ Sat, 11 Dec 2021 11:15:29: #2 predicted fragment length is 137 bps INFO @ Sat, 11 Dec 2021 11:15:29: #2 alternative fragment length(s) may be 137 bps INFO @ Sat, 11 Dec 2021 11:15:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.10_model.r INFO @ Sat, 11 Dec 2021 11:15:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:15:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:15:35: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:15:41: 8000000 INFO @ Sat, 11 Dec 2021 11:15:47: 9000000 INFO @ Sat, 11 Dec 2021 11:15:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:15:53: 10000000 INFO @ Sat, 11 Dec 2021 11:15:57: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:15:57: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:15:57: #1 total tags in treatment: 10605164 INFO @ Sat, 11 Dec 2021 11:15:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:15:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:15:57: #1 tags after filtering in treatment: 10605164 INFO @ Sat, 11 Dec 2021 11:15:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:15:57: #1 finished! INFO @ Sat, 11 Dec 2021 11:15:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:15:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:15:58: #2 number of paired peaks: 726 WARNING @ Sat, 11 Dec 2021 11:15:58: Fewer paired peaks (726) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 726 pairs to build model! INFO @ Sat, 11 Dec 2021 11:15:58: start model_add_line... INFO @ Sat, 11 Dec 2021 11:15:58: start X-correlation... INFO @ Sat, 11 Dec 2021 11:15:58: end of X-cor INFO @ Sat, 11 Dec 2021 11:15:58: #2 finished! INFO @ Sat, 11 Dec 2021 11:15:58: #2 predicted fragment length is 137 bps INFO @ Sat, 11 Dec 2021 11:15:58: #2 alternative fragment length(s) may be 137 bps INFO @ Sat, 11 Dec 2021 11:15:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.20_model.r INFO @ Sat, 11 Dec 2021 11:15:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:15:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:16:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:16:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:16:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.10_summits.bed INFO @ Sat, 11 Dec 2021 11:16:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3062 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:16:20: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:16:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:16:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:16:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986136/SRX9986136.20_summits.bed INFO @ Sat, 11 Dec 2021 11:16:32: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1394 records, 4 fields): 4 millis CompletedMACS2peakCalling