Job ID = 14172059 SRX = SRX10089758 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 26710604 spots for SRR13700645/SRR13700645.sra Written 26710604 spots for SRR13700645/SRR13700645.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172513 ("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: 00:05:43 26710604 reads; of these: 26710604 (100.00%) were unpaired; of these: 4945447 (18.51%) aligned 0 times 17301204 (64.77%) aligned exactly 1 time 4463953 (16.71%) aligned >1 times 81.49% overall alignment rate Time searching: 00:05:43 Overall time: 00:05:43 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] 4943747 / 21765157 = 0.2271 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 14:05:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.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 14:05:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:05:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:05:23: 1000000 INFO @ Sat, 11 Dec 2021 14:05:28: 2000000 INFO @ Sat, 11 Dec 2021 14:05:32: 3000000 INFO @ Sat, 11 Dec 2021 14:05:37: 4000000 INFO @ Sat, 11 Dec 2021 14:05:42: 5000000 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 14:05:47: 6000000 INFO @ Sat, 11 Dec 2021 14:05:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.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 14:05:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:05:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:05:53: 7000000 INFO @ Sat, 11 Dec 2021 14:05:54: 1000000 INFO @ Sat, 11 Dec 2021 14:05:58: 8000000 INFO @ Sat, 11 Dec 2021 14:05:59: 2000000 INFO @ Sat, 11 Dec 2021 14:06:03: 9000000 INFO @ Sat, 11 Dec 2021 14:06:05: 3000000 INFO @ Sat, 11 Dec 2021 14:06:09: 10000000 INFO @ Sat, 11 Dec 2021 14:06:11: 4000000 INFO @ Sat, 11 Dec 2021 14:06:14: 11000000 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 14:06:16: 5000000 INFO @ Sat, 11 Dec 2021 14:06:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.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 14:06:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:06:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:06:19: 12000000 INFO @ Sat, 11 Dec 2021 14:06:22: 6000000 INFO @ Sat, 11 Dec 2021 14:06:24: 1000000 INFO @ Sat, 11 Dec 2021 14:06:25: 13000000 INFO @ Sat, 11 Dec 2021 14:06:29: 7000000 INFO @ Sat, 11 Dec 2021 14:06:31: 2000000 INFO @ Sat, 11 Dec 2021 14:06:31: 14000000 INFO @ Sat, 11 Dec 2021 14:06:35: 8000000 INFO @ Sat, 11 Dec 2021 14:06:37: 3000000 INFO @ Sat, 11 Dec 2021 14:06:37: 15000000 INFO @ Sat, 11 Dec 2021 14:06:41: 9000000 INFO @ Sat, 11 Dec 2021 14:06:43: 16000000 INFO @ Sat, 11 Dec 2021 14:06:43: 4000000 INFO @ Sat, 11 Dec 2021 14:06:47: 10000000 INFO @ Sat, 11 Dec 2021 14:06:48: #1 tag size is determined as 41 bps INFO @ Sat, 11 Dec 2021 14:06:48: #1 tag size = 41 INFO @ Sat, 11 Dec 2021 14:06:48: #1 total tags in treatment: 16821410 INFO @ Sat, 11 Dec 2021 14:06:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:06:48: #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 14:06:48: #1 tags after filtering in treatment: 16821410 INFO @ Sat, 11 Dec 2021 14:06:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:06:48: #1 finished! INFO @ Sat, 11 Dec 2021 14:06:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:06:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:06:49: #2 number of paired peaks: 579 WARNING @ Sat, 11 Dec 2021 14:06:49: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Sat, 11 Dec 2021 14:06:49: start model_add_line... INFO @ Sat, 11 Dec 2021 14:06:49: start X-correlation... INFO @ Sat, 11 Dec 2021 14:06:49: end of X-cor INFO @ Sat, 11 Dec 2021 14:06:49: #2 finished! INFO @ Sat, 11 Dec 2021 14:06:49: #2 predicted fragment length is 208 bps INFO @ Sat, 11 Dec 2021 14:06:49: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 11 Dec 2021 14:06:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.05_model.r INFO @ Sat, 11 Dec 2021 14:06:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:06:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:06:50: 5000000 INFO @ Sat, 11 Dec 2021 14:06:53: 11000000 INFO @ Sat, 11 Dec 2021 14:06:56: 6000000 INFO @ Sat, 11 Dec 2021 14:06:59: 12000000 INFO @ Sat, 11 Dec 2021 14:07:03: 7000000 INFO @ Sat, 11 Dec 2021 14:07:05: 13000000 INFO @ Sat, 11 Dec 2021 14:07:09: 8000000 INFO @ Sat, 11 Dec 2021 14:07:12: 14000000 INFO @ Sat, 11 Dec 2021 14:07:15: 9000000 INFO @ Sat, 11 Dec 2021 14:07:18: 15000000 INFO @ Sat, 11 Dec 2021 14:07:22: 10000000 INFO @ Sat, 11 Dec 2021 14:07:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:07:24: 16000000 INFO @ Sat, 11 Dec 2021 14:07:28: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:07:29: #1 tag size is determined as 41 bps INFO @ Sat, 11 Dec 2021 14:07:29: #1 tag size = 41 INFO @ Sat, 11 Dec 2021 14:07:29: #1 total tags in treatment: 16821410 INFO @ Sat, 11 Dec 2021 14:07:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:07:29: #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 14:07:30: #1 tags after filtering in treatment: 16821410 INFO @ Sat, 11 Dec 2021 14:07:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:07:30: #1 finished! INFO @ Sat, 11 Dec 2021 14:07:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:07:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:07:31: #2 number of paired peaks: 579 WARNING @ Sat, 11 Dec 2021 14:07:31: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Sat, 11 Dec 2021 14:07:31: start model_add_line... INFO @ Sat, 11 Dec 2021 14:07:31: start X-correlation... INFO @ Sat, 11 Dec 2021 14:07:31: end of X-cor INFO @ Sat, 11 Dec 2021 14:07:31: #2 finished! INFO @ Sat, 11 Dec 2021 14:07:31: #2 predicted fragment length is 208 bps INFO @ Sat, 11 Dec 2021 14:07:31: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 11 Dec 2021 14:07:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.10_model.r INFO @ Sat, 11 Dec 2021 14:07:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:07:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:07:34: 12000000 INFO @ Sat, 11 Dec 2021 14:07:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:07:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:07:40: 13000000 INFO @ Sat, 11 Dec 2021 14:07:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.05_summits.bed INFO @ Sat, 11 Dec 2021 14:07:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5947 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:07:46: 14000000 INFO @ Sat, 11 Dec 2021 14:07:52: 15000000 INFO @ Sat, 11 Dec 2021 14:07:58: 16000000 INFO @ Sat, 11 Dec 2021 14:08:03: #1 tag size is determined as 41 bps INFO @ Sat, 11 Dec 2021 14:08:03: #1 tag size = 41 INFO @ Sat, 11 Dec 2021 14:08:03: #1 total tags in treatment: 16821410 INFO @ Sat, 11 Dec 2021 14:08:03: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:08:03: #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 14:08:04: #1 tags after filtering in treatment: 16821410 INFO @ Sat, 11 Dec 2021 14:08:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:08:04: #1 finished! INFO @ Sat, 11 Dec 2021 14:08:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:08:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:08:05: #2 number of paired peaks: 579 WARNING @ Sat, 11 Dec 2021 14:08:05: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Sat, 11 Dec 2021 14:08:05: start model_add_line... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:08:05: start X-correlation... INFO @ Sat, 11 Dec 2021 14:08:05: end of X-cor INFO @ Sat, 11 Dec 2021 14:08:05: #2 finished! INFO @ Sat, 11 Dec 2021 14:08:05: #2 predicted fragment length is 208 bps INFO @ Sat, 11 Dec 2021 14:08:05: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 11 Dec 2021 14:08:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.20_model.r INFO @ Sat, 11 Dec 2021 14:08:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:08:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:08:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:08:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:08:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:08:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.10_summits.bed INFO @ Sat, 11 Dec 2021 14:08:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3991 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:08:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:08:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:08:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:08:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089758/SRX10089758.20_summits.bed INFO @ Sat, 11 Dec 2021 14:08:56: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (2265 records, 4 fields): 4 millis CompletedMACS2peakCalling