Job ID = 14171151 SRX = SRX9986100 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 18409282 spots for SRR13591503/SRR13591503.sra Written 18409282 spots for SRR13591503/SRR13591503.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171624 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:37 18409282 reads; of these: 18409282 (100.00%) were unpaired; of these: 809422 (4.40%) aligned 0 times 8543082 (46.41%) aligned exactly 1 time 9056778 (49.20%) aligned >1 times 95.60% overall alignment rate Time searching: 00:07:38 Overall time: 00:07:38 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 8 files... [bam_rmdupse_core] 6477666 / 17599860 = 0.3681 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 10:20:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.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 10:20:53: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:20:53: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:21:00: 1000000 INFO @ Sat, 11 Dec 2021 10:21:07: 2000000 INFO @ Sat, 11 Dec 2021 10:21:14: 3000000 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 10:21:21: 4000000 INFO @ Sat, 11 Dec 2021 10:21:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.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 10:21:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:21:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:21:29: 5000000 INFO @ Sat, 11 Dec 2021 10:21:29: 1000000 INFO @ Sat, 11 Dec 2021 10:21:36: 2000000 INFO @ Sat, 11 Dec 2021 10:21:36: 6000000 INFO @ Sat, 11 Dec 2021 10:21:44: 3000000 INFO @ Sat, 11 Dec 2021 10:21:44: 7000000 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 10:21:51: 4000000 INFO @ Sat, 11 Dec 2021 10:21:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.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 10:21:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:21:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:21:52: 8000000 INFO @ Sat, 11 Dec 2021 10:21:58: 5000000 INFO @ Sat, 11 Dec 2021 10:21:59: 1000000 INFO @ Sat, 11 Dec 2021 10:22:00: 9000000 INFO @ Sat, 11 Dec 2021 10:22:05: 6000000 INFO @ Sat, 11 Dec 2021 10:22:07: 2000000 INFO @ Sat, 11 Dec 2021 10:22:08: 10000000 INFO @ Sat, 11 Dec 2021 10:22:13: 7000000 INFO @ Sat, 11 Dec 2021 10:22:14: 3000000 INFO @ Sat, 11 Dec 2021 10:22:16: 11000000 INFO @ Sat, 11 Dec 2021 10:22:17: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 10:22:17: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 10:22:17: #1 total tags in treatment: 11122194 INFO @ Sat, 11 Dec 2021 10:22:17: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:22:17: #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 10:22:17: #1 tags after filtering in treatment: 11122194 INFO @ Sat, 11 Dec 2021 10:22:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:22:17: #1 finished! INFO @ Sat, 11 Dec 2021 10:22:17: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:22:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:22:18: #2 number of paired peaks: 790 WARNING @ Sat, 11 Dec 2021 10:22:18: Fewer paired peaks (790) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 790 pairs to build model! INFO @ Sat, 11 Dec 2021 10:22:18: start model_add_line... INFO @ Sat, 11 Dec 2021 10:22:18: start X-correlation... INFO @ Sat, 11 Dec 2021 10:22:18: end of X-cor INFO @ Sat, 11 Dec 2021 10:22:18: #2 finished! INFO @ Sat, 11 Dec 2021 10:22:18: #2 predicted fragment length is 142 bps INFO @ Sat, 11 Dec 2021 10:22:18: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 11 Dec 2021 10:22:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.05_model.r INFO @ Sat, 11 Dec 2021 10:22:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:22:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:22:20: 8000000 INFO @ Sat, 11 Dec 2021 10:22:21: 4000000 INFO @ Sat, 11 Dec 2021 10:22:27: 9000000 INFO @ Sat, 11 Dec 2021 10:22:28: 5000000 INFO @ Sat, 11 Dec 2021 10:22:33: 10000000 INFO @ Sat, 11 Dec 2021 10:22:34: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 10:22:40: 11000000 INFO @ Sat, 11 Dec 2021 10:22:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 10:22:41: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 10:22:41: #1 total tags in treatment: 11122194 INFO @ Sat, 11 Dec 2021 10:22:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:22:41: #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 10:22:41: 7000000 INFO @ Sat, 11 Dec 2021 10:22:41: #1 tags after filtering in treatment: 11122194 INFO @ Sat, 11 Dec 2021 10:22:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:22:41: #1 finished! INFO @ Sat, 11 Dec 2021 10:22:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:22:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:22:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:22:42: #2 number of paired peaks: 790 WARNING @ Sat, 11 Dec 2021 10:22:42: Fewer paired peaks (790) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 790 pairs to build model! INFO @ Sat, 11 Dec 2021 10:22:42: start model_add_line... INFO @ Sat, 11 Dec 2021 10:22:42: start X-correlation... INFO @ Sat, 11 Dec 2021 10:22:42: end of X-cor INFO @ Sat, 11 Dec 2021 10:22:42: #2 finished! INFO @ Sat, 11 Dec 2021 10:22:42: #2 predicted fragment length is 142 bps INFO @ Sat, 11 Dec 2021 10:22:42: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 11 Dec 2021 10:22:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.10_model.r INFO @ Sat, 11 Dec 2021 10:22:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:22:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:22:48: 8000000 INFO @ Sat, 11 Dec 2021 10:22:53: 9000000 INFO @ Sat, 11 Dec 2021 10:22:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:22:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:22:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.05_summits.bed INFO @ Sat, 11 Dec 2021 10:22:54: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11277 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 10:22:59: 10000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 10:23:05: 11000000 INFO @ Sat, 11 Dec 2021 10:23:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:23:05: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 10:23:05: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 10:23:05: #1 total tags in treatment: 11122194 INFO @ Sat, 11 Dec 2021 10:23:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:23:05: #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 10:23:05: #1 tags after filtering in treatment: 11122194 INFO @ Sat, 11 Dec 2021 10:23:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:23:05: #1 finished! INFO @ Sat, 11 Dec 2021 10:23:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:23:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:23:06: #2 number of paired peaks: 790 WARNING @ Sat, 11 Dec 2021 10:23:06: Fewer paired peaks (790) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 790 pairs to build model! INFO @ Sat, 11 Dec 2021 10:23:06: start model_add_line... INFO @ Sat, 11 Dec 2021 10:23:06: start X-correlation... INFO @ Sat, 11 Dec 2021 10:23:06: end of X-cor INFO @ Sat, 11 Dec 2021 10:23:06: #2 finished! INFO @ Sat, 11 Dec 2021 10:23:06: #2 predicted fragment length is 142 bps INFO @ Sat, 11 Dec 2021 10:23:06: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 11 Dec 2021 10:23:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.20_model.r INFO @ Sat, 11 Dec 2021 10:23:06: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:23:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:23:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:23:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:23:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.10_summits.bed INFO @ Sat, 11 Dec 2021 10:23:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4014 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 10:23:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:23:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:23:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:23:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986100/SRX9986100.20_summits.bed INFO @ Sat, 11 Dec 2021 10:23:40: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1232 records, 4 fields): 3 millis CompletedMACS2peakCalling