Job ID = 14167700 SRX = SRX4712960 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:41 35463852 reads; of these: 35463852 (100.00%) were unpaired; of these: 1900592 (5.36%) aligned 0 times 23836277 (67.21%) aligned exactly 1 time 9726983 (27.43%) aligned >1 times 94.64% overall alignment rate Time searching: 00:11:41 Overall time: 00:11:41 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 9495337 / 33563260 = 0.2829 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 @ Fri, 10 Dec 2021 13:27:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.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 @ Fri, 10 Dec 2021 13:27:35: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:27:35: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:27:41: 1000000 INFO @ Fri, 10 Dec 2021 13:27:46: 2000000 INFO @ Fri, 10 Dec 2021 13:27:51: 3000000 INFO @ Fri, 10 Dec 2021 13:27:57: 4000000 INFO @ Fri, 10 Dec 2021 13:28:03: 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 @ Fri, 10 Dec 2021 13:28:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.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 @ Fri, 10 Dec 2021 13:28:05: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:28:05: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:28:08: 6000000 INFO @ Fri, 10 Dec 2021 13:28:11: 1000000 INFO @ Fri, 10 Dec 2021 13:28:14: 7000000 INFO @ Fri, 10 Dec 2021 13:28:17: 2000000 INFO @ Fri, 10 Dec 2021 13:28:20: 8000000 INFO @ Fri, 10 Dec 2021 13:28:22: 3000000 INFO @ Fri, 10 Dec 2021 13:28:26: 9000000 INFO @ Fri, 10 Dec 2021 13:28:28: 4000000 INFO @ Fri, 10 Dec 2021 13:28:32: 10000000 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 @ Fri, 10 Dec 2021 13:28:34: 5000000 INFO @ Fri, 10 Dec 2021 13:28:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.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 @ Fri, 10 Dec 2021 13:28:35: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:28:35: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:28:38: 11000000 INFO @ Fri, 10 Dec 2021 13:28:40: 6000000 INFO @ Fri, 10 Dec 2021 13:28:41: 1000000 INFO @ Fri, 10 Dec 2021 13:28:43: 12000000 INFO @ Fri, 10 Dec 2021 13:28:45: 7000000 INFO @ Fri, 10 Dec 2021 13:28:46: 2000000 INFO @ Fri, 10 Dec 2021 13:28:49: 13000000 INFO @ Fri, 10 Dec 2021 13:28:51: 3000000 INFO @ Fri, 10 Dec 2021 13:28:51: 8000000 INFO @ Fri, 10 Dec 2021 13:28:55: 14000000 INFO @ Fri, 10 Dec 2021 13:28:56: 4000000 INFO @ Fri, 10 Dec 2021 13:28:57: 9000000 INFO @ Fri, 10 Dec 2021 13:29:01: 15000000 INFO @ Fri, 10 Dec 2021 13:29:01: 5000000 INFO @ Fri, 10 Dec 2021 13:29:03: 10000000 INFO @ Fri, 10 Dec 2021 13:29:06: 6000000 INFO @ Fri, 10 Dec 2021 13:29:07: 16000000 INFO @ Fri, 10 Dec 2021 13:29:08: 11000000 INFO @ Fri, 10 Dec 2021 13:29:11: 7000000 INFO @ Fri, 10 Dec 2021 13:29:12: 17000000 INFO @ Fri, 10 Dec 2021 13:29:14: 12000000 INFO @ Fri, 10 Dec 2021 13:29:16: 8000000 INFO @ Fri, 10 Dec 2021 13:29:18: 18000000 INFO @ Fri, 10 Dec 2021 13:29:20: 13000000 INFO @ Fri, 10 Dec 2021 13:29:22: 9000000 INFO @ Fri, 10 Dec 2021 13:29:24: 19000000 INFO @ Fri, 10 Dec 2021 13:29:26: 14000000 INFO @ Fri, 10 Dec 2021 13:29:27: 10000000 INFO @ Fri, 10 Dec 2021 13:29:30: 20000000 INFO @ Fri, 10 Dec 2021 13:29:32: 15000000 INFO @ Fri, 10 Dec 2021 13:29:32: 11000000 INFO @ Fri, 10 Dec 2021 13:29:36: 21000000 INFO @ Fri, 10 Dec 2021 13:29:37: 12000000 INFO @ Fri, 10 Dec 2021 13:29:38: 16000000 INFO @ Fri, 10 Dec 2021 13:29:42: 22000000 INFO @ Fri, 10 Dec 2021 13:29:42: 13000000 INFO @ Fri, 10 Dec 2021 13:29:43: 17000000 INFO @ Fri, 10 Dec 2021 13:29:47: 14000000 INFO @ Fri, 10 Dec 2021 13:29:47: 23000000 INFO @ Fri, 10 Dec 2021 13:29:49: 18000000 INFO @ Fri, 10 Dec 2021 13:29:52: 15000000 INFO @ Fri, 10 Dec 2021 13:29:53: 24000000 INFO @ Fri, 10 Dec 2021 13:29:54: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 13:29:54: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 13:29:54: #1 total tags in treatment: 24067923 INFO @ Fri, 10 Dec 2021 13:29:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:29:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:29:55: #1 tags after filtering in treatment: 24067915 INFO @ Fri, 10 Dec 2021 13:29:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:29:55: #1 finished! INFO @ Fri, 10 Dec 2021 13:29:55: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:29:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:29:55: 19000000 INFO @ Fri, 10 Dec 2021 13:29:56: #2 number of paired peaks: 362 WARNING @ Fri, 10 Dec 2021 13:29:56: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Fri, 10 Dec 2021 13:29:56: start model_add_line... INFO @ Fri, 10 Dec 2021 13:29:56: start X-correlation... INFO @ Fri, 10 Dec 2021 13:29:56: end of X-cor INFO @ Fri, 10 Dec 2021 13:29:56: #2 finished! INFO @ Fri, 10 Dec 2021 13:29:56: #2 predicted fragment length is 108 bps INFO @ Fri, 10 Dec 2021 13:29:56: #2 alternative fragment length(s) may be 108 bps INFO @ Fri, 10 Dec 2021 13:29:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.05_model.r INFO @ Fri, 10 Dec 2021 13:29:56: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:29:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:29:57: 16000000 INFO @ Fri, 10 Dec 2021 13:30:01: 20000000 INFO @ Fri, 10 Dec 2021 13:30:02: 17000000 INFO @ Fri, 10 Dec 2021 13:30:07: 21000000 INFO @ Fri, 10 Dec 2021 13:30:07: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:30:12: 22000000 INFO @ Fri, 10 Dec 2021 13:30:13: 19000000 INFO @ Fri, 10 Dec 2021 13:30:18: 23000000 INFO @ Fri, 10 Dec 2021 13:30:18: 20000000 INFO @ Fri, 10 Dec 2021 13:30:23: 21000000 INFO @ Fri, 10 Dec 2021 13:30:24: 24000000 INFO @ Fri, 10 Dec 2021 13:30:24: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 13:30:25: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 13:30:25: #1 total tags in treatment: 24067923 INFO @ Fri, 10 Dec 2021 13:30:25: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:30:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:30:25: #1 tags after filtering in treatment: 24067915 INFO @ Fri, 10 Dec 2021 13:30:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:30:25: #1 finished! INFO @ Fri, 10 Dec 2021 13:30:25: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:30:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:30:27: #2 number of paired peaks: 362 WARNING @ Fri, 10 Dec 2021 13:30:27: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Fri, 10 Dec 2021 13:30:27: start model_add_line... INFO @ Fri, 10 Dec 2021 13:30:27: start X-correlation... INFO @ Fri, 10 Dec 2021 13:30:27: end of X-cor INFO @ Fri, 10 Dec 2021 13:30:27: #2 finished! INFO @ Fri, 10 Dec 2021 13:30:27: #2 predicted fragment length is 108 bps INFO @ Fri, 10 Dec 2021 13:30:27: #2 alternative fragment length(s) may be 108 bps INFO @ Fri, 10 Dec 2021 13:30:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.10_model.r INFO @ Fri, 10 Dec 2021 13:30:27: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:30:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:30:28: 22000000 INFO @ Fri, 10 Dec 2021 13:30:33: 23000000 INFO @ Fri, 10 Dec 2021 13:30:38: 24000000 INFO @ Fri, 10 Dec 2021 13:30:38: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 13:30:38: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 13:30:38: #1 total tags in treatment: 24067923 INFO @ Fri, 10 Dec 2021 13:30:38: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:30:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:30:39: #1 tags after filtering in treatment: 24067915 INFO @ Fri, 10 Dec 2021 13:30:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:30:39: #1 finished! INFO @ Fri, 10 Dec 2021 13:30:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:30:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:30:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:30:40: #2 number of paired peaks: 362 WARNING @ Fri, 10 Dec 2021 13:30:40: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Fri, 10 Dec 2021 13:30:40: start model_add_line... INFO @ Fri, 10 Dec 2021 13:30:40: start X-correlation... INFO @ Fri, 10 Dec 2021 13:30:40: end of X-cor INFO @ Fri, 10 Dec 2021 13:30:40: #2 finished! INFO @ Fri, 10 Dec 2021 13:30:40: #2 predicted fragment length is 108 bps INFO @ Fri, 10 Dec 2021 13:30:40: #2 alternative fragment length(s) may be 108 bps INFO @ Fri, 10 Dec 2021 13:30:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.20_model.r INFO @ Fri, 10 Dec 2021 13:30:41: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:30:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:31:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:31:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:31:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.05_summits.bed INFO @ Fri, 10 Dec 2021 13:31:02: Done! pass1 - making usageList (738 chroms): 5 millis pass2 - checking and writing primary data (33379 records, 4 fields): 47 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:31:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:31:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:31:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:31:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:31:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.10_summits.bed INFO @ Fri, 10 Dec 2021 13:31:34: Done! pass1 - making usageList (599 chroms): 3 millis pass2 - checking and writing primary data (16998 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:31:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:31:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:31:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712960/SRX4712960.20_summits.bed INFO @ Fri, 10 Dec 2021 13:31:44: Done! pass1 - making usageList (340 chroms): 2 millis pass2 - checking and writing primary data (4942 records, 4 fields): 14 millis CompletedMACS2peakCalling