Job ID = 14172229 SRX = SRX9281741 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8792472 spots for SRR12813253/SRR12813253.sra Written 8792472 spots for SRR12813253/SRR12813253.sra Read 8770410 spots for SRR12813254/SRR12813254.sra Written 8770410 spots for SRR12813254/SRR12813254.sra Read 8920098 spots for SRR12813255/SRR12813255.sra Written 8920098 spots for SRR12813255/SRR12813255.sra Read 8735433 spots for SRR12813256/SRR12813256.sra Written 8735433 spots for SRR12813256/SRR12813256.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172732 ("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: 00:09:33 35218413 reads; of these: 35218413 (100.00%) were paired; of these: 33006254 (93.72%) aligned concordantly 0 times 1659390 (4.71%) aligned concordantly exactly 1 time 552769 (1.57%) aligned concordantly >1 times ---- 33006254 pairs aligned concordantly 0 times; of these: 7032 (0.02%) aligned discordantly 1 time ---- 32999222 pairs aligned 0 times concordantly or discordantly; of these: 65998444 mates make up the pairs; of these: 65408464 (99.11%) aligned 0 times 251966 (0.38%) aligned exactly 1 time 338014 (0.51%) aligned >1 times 7.14% overall alignment rate Time searching: 00:09:33 Overall time: 00:09:33 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 90453 / 2215238 = 0.0408 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 15:05:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.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 15:05:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:05:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:05:47: 1000000 INFO @ Sat, 11 Dec 2021 15:05:52: 2000000 INFO @ Sat, 11 Dec 2021 15:05:58: 3000000 INFO @ Sat, 11 Dec 2021 15:06:03: 4000000 INFO @ Sat, 11 Dec 2021 15:06:08: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:06:08: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:06:08: #1 total tags in treatment: 2121798 INFO @ Sat, 11 Dec 2021 15:06:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:06:08: #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 15:06:08: #1 tags after filtering in treatment: 2040304 INFO @ Sat, 11 Dec 2021 15:06:08: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 15:06:08: #1 finished! INFO @ Sat, 11 Dec 2021 15:06:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:06:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:06:08: #2 number of paired peaks: 970 WARNING @ Sat, 11 Dec 2021 15:06:08: Fewer paired peaks (970) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 970 pairs to build model! INFO @ Sat, 11 Dec 2021 15:06:08: start model_add_line... INFO @ Sat, 11 Dec 2021 15:06:08: start X-correlation... INFO @ Sat, 11 Dec 2021 15:06:08: end of X-cor INFO @ Sat, 11 Dec 2021 15:06:08: #2 finished! INFO @ Sat, 11 Dec 2021 15:06:08: #2 predicted fragment length is 100 bps INFO @ Sat, 11 Dec 2021 15:06:08: #2 alternative fragment length(s) may be 100,137 bps INFO @ Sat, 11 Dec 2021 15:06:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.05_model.r INFO @ Sat, 11 Dec 2021 15:06:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:06:08: #3 Pre-compute pvalue-qvalue table... 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 15:06:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.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 15:06:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:06:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:06:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:06:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:06:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:06:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.05_summits.bed INFO @ Sat, 11 Dec 2021 15:06:14: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (337 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:06:17: 1000000 INFO @ Sat, 11 Dec 2021 15:06:22: 2000000 INFO @ Sat, 11 Dec 2021 15:06:27: 3000000 INFO @ Sat, 11 Dec 2021 15:06:31: 4000000 INFO @ Sat, 11 Dec 2021 15:06:36: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:06:36: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:06:36: #1 total tags in treatment: 2121798 INFO @ Sat, 11 Dec 2021 15:06:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:06:36: #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 15:06:36: #1 tags after filtering in treatment: 2040304 INFO @ Sat, 11 Dec 2021 15:06:36: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 15:06:36: #1 finished! INFO @ Sat, 11 Dec 2021 15:06:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:06:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:06:36: #2 number of paired peaks: 970 WARNING @ Sat, 11 Dec 2021 15:06:36: Fewer paired peaks (970) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 970 pairs to build model! INFO @ Sat, 11 Dec 2021 15:06:36: start model_add_line... INFO @ Sat, 11 Dec 2021 15:06:36: start X-correlation... INFO @ Sat, 11 Dec 2021 15:06:36: end of X-cor INFO @ Sat, 11 Dec 2021 15:06:36: #2 finished! INFO @ Sat, 11 Dec 2021 15:06:36: #2 predicted fragment length is 100 bps INFO @ Sat, 11 Dec 2021 15:06:36: #2 alternative fragment length(s) may be 100,137 bps INFO @ Sat, 11 Dec 2021 15:06:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.10_model.r INFO @ Sat, 11 Dec 2021 15:06:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:06:36: #3 Pre-compute pvalue-qvalue table... 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 15:06:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:06:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.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 15:06:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:06:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:06:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:06:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:06:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.10_summits.bed INFO @ Sat, 11 Dec 2021 15:06:43: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (156 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:06:47: 1000000 INFO @ Sat, 11 Dec 2021 15:06:52: 2000000 INFO @ Sat, 11 Dec 2021 15:06:57: 3000000 INFO @ Sat, 11 Dec 2021 15:07:02: 4000000 INFO @ Sat, 11 Dec 2021 15:07:06: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:07:06: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:07:06: #1 total tags in treatment: 2121798 INFO @ Sat, 11 Dec 2021 15:07:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:07:06: #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 15:07:06: #1 tags after filtering in treatment: 2040304 INFO @ Sat, 11 Dec 2021 15:07:06: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 15:07:06: #1 finished! INFO @ Sat, 11 Dec 2021 15:07:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:07:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:07:06: #2 number of paired peaks: 970 WARNING @ Sat, 11 Dec 2021 15:07:06: Fewer paired peaks (970) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 970 pairs to build model! INFO @ Sat, 11 Dec 2021 15:07:06: start model_add_line... INFO @ Sat, 11 Dec 2021 15:07:06: start X-correlation... INFO @ Sat, 11 Dec 2021 15:07:06: end of X-cor INFO @ Sat, 11 Dec 2021 15:07:06: #2 finished! INFO @ Sat, 11 Dec 2021 15:07:06: #2 predicted fragment length is 100 bps INFO @ Sat, 11 Dec 2021 15:07:06: #2 alternative fragment length(s) may be 100,137 bps INFO @ Sat, 11 Dec 2021 15:07:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.20_model.r INFO @ Sat, 11 Dec 2021 15:07:06: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:07:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:07:10: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:07:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:07:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:07:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281741/SRX9281741.20_summits.bed INFO @ Sat, 11 Dec 2021 15:07:13: Done! pass1 - making usageList (3 chroms): 8 millis pass2 - checking and writing primary data (74 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。