Job ID = 14171255 SRX = SRX9986129 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16295896 spots for SRR13591548/SRR13591548.sra Written 16295896 spots for SRR13591548/SRR13591548.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171708 ("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: 00:03:48 16295896 reads; of these: 16295896 (100.00%) were unpaired; of these: 1280004 (7.85%) aligned 0 times 12410929 (76.16%) aligned exactly 1 time 2604963 (15.99%) aligned >1 times 92.15% overall alignment rate Time searching: 00:03:48 Overall time: 00:03:48 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] 4391914 / 15015892 = 0.2925 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 10:51:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.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 10:51:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:51:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:51:06: 1000000 INFO @ Sat, 11 Dec 2021 10:51:11: 2000000 INFO @ Sat, 11 Dec 2021 10:51:17: 3000000 INFO @ Sat, 11 Dec 2021 10:51:22: 4000000 INFO @ Sat, 11 Dec 2021 10:51:27: 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 10:51:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.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 10:51:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:51:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:51:32: 6000000 INFO @ Sat, 11 Dec 2021 10:51:36: 1000000 INFO @ Sat, 11 Dec 2021 10:51:38: 7000000 INFO @ Sat, 11 Dec 2021 10:51:42: 2000000 INFO @ Sat, 11 Dec 2021 10:51:43: 8000000 INFO @ Sat, 11 Dec 2021 10:51:47: 3000000 INFO @ Sat, 11 Dec 2021 10:51:48: 9000000 INFO @ Sat, 11 Dec 2021 10:51:53: 10000000 INFO @ Sat, 11 Dec 2021 10:51:53: 4000000 INFO @ Sat, 11 Dec 2021 10:51:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 10:51:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 10:51:56: #1 total tags in treatment: 10623978 INFO @ Sat, 11 Dec 2021 10:51:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:51:56: #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 10:51:56: #1 tags after filtering in treatment: 10623978 INFO @ Sat, 11 Dec 2021 10:51:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:51:56: #1 finished! INFO @ Sat, 11 Dec 2021 10:51:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:51:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:51:57: #2 number of paired peaks: 468 WARNING @ Sat, 11 Dec 2021 10:51:57: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Sat, 11 Dec 2021 10:51:57: start model_add_line... INFO @ Sat, 11 Dec 2021 10:51:57: start X-correlation... INFO @ Sat, 11 Dec 2021 10:51:57: end of X-cor INFO @ Sat, 11 Dec 2021 10:51:57: #2 finished! INFO @ Sat, 11 Dec 2021 10:51:57: #2 predicted fragment length is 225 bps INFO @ Sat, 11 Dec 2021 10:51:57: #2 alternative fragment length(s) may be 4,173,225 bps INFO @ Sat, 11 Dec 2021 10:51:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.05_model.r INFO @ Sat, 11 Dec 2021 10:51:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:51:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:51:58: 5000000 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 10:52:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.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 10:52:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:52:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:52:04: 6000000 INFO @ Sat, 11 Dec 2021 10:52:06: 1000000 INFO @ Sat, 11 Dec 2021 10:52:09: 7000000 INFO @ Sat, 11 Dec 2021 10:52:12: 2000000 INFO @ Sat, 11 Dec 2021 10:52:15: 8000000 INFO @ Sat, 11 Dec 2021 10:52:18: 3000000 INFO @ Sat, 11 Dec 2021 10:52:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:52:20: 9000000 INFO @ Sat, 11 Dec 2021 10:52:23: 4000000 INFO @ Sat, 11 Dec 2021 10:52:26: 10000000 INFO @ Sat, 11 Dec 2021 10:52:28: 5000000 INFO @ Sat, 11 Dec 2021 10:52:29: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 10:52:29: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 10:52:29: #1 total tags in treatment: 10623978 INFO @ Sat, 11 Dec 2021 10:52:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:52:29: #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 10:52:29: #1 tags after filtering in treatment: 10623978 INFO @ Sat, 11 Dec 2021 10:52:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:52:29: #1 finished! INFO @ Sat, 11 Dec 2021 10:52:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:52:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:52:30: #2 number of paired peaks: 468 WARNING @ Sat, 11 Dec 2021 10:52:30: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Sat, 11 Dec 2021 10:52:30: start model_add_line... INFO @ Sat, 11 Dec 2021 10:52:30: start X-correlation... INFO @ Sat, 11 Dec 2021 10:52:30: end of X-cor INFO @ Sat, 11 Dec 2021 10:52:30: #2 finished! INFO @ Sat, 11 Dec 2021 10:52:30: #2 predicted fragment length is 225 bps INFO @ Sat, 11 Dec 2021 10:52:30: #2 alternative fragment length(s) may be 4,173,225 bps INFO @ Sat, 11 Dec 2021 10:52:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.10_model.r INFO @ Sat, 11 Dec 2021 10:52:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:52:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:52:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:52:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:52:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.05_summits.bed INFO @ Sat, 11 Dec 2021 10:52:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4749 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 10:52:33: 6000000 INFO @ Sat, 11 Dec 2021 10:52:38: 7000000 INFO @ Sat, 11 Dec 2021 10:52:43: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 10:52:49: 9000000 INFO @ Sat, 11 Dec 2021 10:52:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:52:54: 10000000 INFO @ Sat, 11 Dec 2021 10:52:58: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 10:52:58: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 10:52:58: #1 total tags in treatment: 10623978 INFO @ Sat, 11 Dec 2021 10:52:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:52:58: #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 10:52:58: #1 tags after filtering in treatment: 10623978 INFO @ Sat, 11 Dec 2021 10:52:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:52:58: #1 finished! INFO @ Sat, 11 Dec 2021 10:52:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:52:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:52:58: #2 number of paired peaks: 468 WARNING @ Sat, 11 Dec 2021 10:52:58: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Sat, 11 Dec 2021 10:52:58: start model_add_line... INFO @ Sat, 11 Dec 2021 10:52:58: start X-correlation... INFO @ Sat, 11 Dec 2021 10:52:58: end of X-cor INFO @ Sat, 11 Dec 2021 10:52:58: #2 finished! INFO @ Sat, 11 Dec 2021 10:52:58: #2 predicted fragment length is 225 bps INFO @ Sat, 11 Dec 2021 10:52:58: #2 alternative fragment length(s) may be 4,173,225 bps INFO @ Sat, 11 Dec 2021 10:52:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.20_model.r INFO @ Sat, 11 Dec 2021 10:52:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:52:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:53:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:53:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:53:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.10_summits.bed INFO @ Sat, 11 Dec 2021 10:53:06: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1521 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 10:53:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:53:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:53:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:53:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986129/SRX9986129.20_summits.bed INFO @ Sat, 11 Dec 2021 10:53:36: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (309 records, 4 fields): 2 millis CompletedMACS2peakCalling