Job ID = 14171845 SRX = SRX9986166 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: 00:04:40 20061360 reads; of these: 20061360 (100.00%) were unpaired; of these: 2103574 (10.49%) aligned 0 times 15070314 (75.12%) aligned exactly 1 time 2887472 (14.39%) aligned >1 times 89.51% overall alignment rate Time searching: 00:04:40 Overall time: 00:04:40 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 8 files... [bam_rmdupse_core] 5161221 / 17957786 = 0.2874 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 13:15:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.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 13:15:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:15:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:15:31: 1000000 INFO @ Sat, 11 Dec 2021 13:15:36: 2000000 INFO @ Sat, 11 Dec 2021 13:15:41: 3000000 INFO @ Sat, 11 Dec 2021 13:15:46: 4000000 INFO @ Sat, 11 Dec 2021 13:15:52: 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 13:15:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.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 13:15:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:15:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:15:57: 6000000 INFO @ Sat, 11 Dec 2021 13:16:02: 1000000 INFO @ Sat, 11 Dec 2021 13:16:03: 7000000 INFO @ Sat, 11 Dec 2021 13:16:09: 2000000 INFO @ Sat, 11 Dec 2021 13:16:10: 8000000 INFO @ Sat, 11 Dec 2021 13:16:16: 3000000 INFO @ Sat, 11 Dec 2021 13:16:16: 9000000 INFO @ Sat, 11 Dec 2021 13:16:23: 10000000 INFO @ Sat, 11 Dec 2021 13:16:23: 4000000 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 13:16:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.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 13:16:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:16:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:16:30: 11000000 INFO @ Sat, 11 Dec 2021 13:16:30: 5000000 INFO @ Sat, 11 Dec 2021 13:16:33: 1000000 INFO @ Sat, 11 Dec 2021 13:16:36: 12000000 INFO @ Sat, 11 Dec 2021 13:16:37: 6000000 INFO @ Sat, 11 Dec 2021 13:16:40: 2000000 INFO @ Sat, 11 Dec 2021 13:16:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:16:41: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:16:41: #1 total tags in treatment: 12796565 INFO @ Sat, 11 Dec 2021 13:16:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:16:41: #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 13:16:42: #1 tags after filtering in treatment: 12796458 INFO @ Sat, 11 Dec 2021 13:16:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:16:42: #1 finished! INFO @ Sat, 11 Dec 2021 13:16:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:16:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:16:43: #2 number of paired peaks: 491 WARNING @ Sat, 11 Dec 2021 13:16:43: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Sat, 11 Dec 2021 13:16:43: start model_add_line... INFO @ Sat, 11 Dec 2021 13:16:43: start X-correlation... INFO @ Sat, 11 Dec 2021 13:16:43: end of X-cor INFO @ Sat, 11 Dec 2021 13:16:43: #2 finished! INFO @ Sat, 11 Dec 2021 13:16:43: #2 predicted fragment length is 142 bps INFO @ Sat, 11 Dec 2021 13:16:43: #2 alternative fragment length(s) may be 79,142,161,168,198,247,261,282,314,330,462,563 bps INFO @ Sat, 11 Dec 2021 13:16:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.05_model.r INFO @ Sat, 11 Dec 2021 13:16:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:16:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:16:44: 7000000 INFO @ Sat, 11 Dec 2021 13:16:47: 3000000 INFO @ Sat, 11 Dec 2021 13:16:51: 8000000 INFO @ Sat, 11 Dec 2021 13:16:54: 4000000 INFO @ Sat, 11 Dec 2021 13:16:59: 9000000 INFO @ Sat, 11 Dec 2021 13:17:01: 5000000 INFO @ Sat, 11 Dec 2021 13:17:06: 10000000 INFO @ Sat, 11 Dec 2021 13:17:08: 6000000 INFO @ Sat, 11 Dec 2021 13:17:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:17:13: 11000000 INFO @ Sat, 11 Dec 2021 13:17:15: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:17:20: 12000000 INFO @ Sat, 11 Dec 2021 13:17:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:17:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:17:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.05_summits.bed INFO @ Sat, 11 Dec 2021 13:17:22: Done! pass1 - making usageList (109 chroms): 1 millis pass2 - checking and writing primary data (1038 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:17:23: 8000000 INFO @ Sat, 11 Dec 2021 13:17:26: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:17:26: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:17:26: #1 total tags in treatment: 12796565 INFO @ Sat, 11 Dec 2021 13:17:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:17:26: #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 13:17:27: #1 tags after filtering in treatment: 12796458 INFO @ Sat, 11 Dec 2021 13:17:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:17:27: #1 finished! INFO @ Sat, 11 Dec 2021 13:17:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:17:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:17:28: #2 number of paired peaks: 491 WARNING @ Sat, 11 Dec 2021 13:17:28: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Sat, 11 Dec 2021 13:17:28: start model_add_line... INFO @ Sat, 11 Dec 2021 13:17:28: start X-correlation... INFO @ Sat, 11 Dec 2021 13:17:28: end of X-cor INFO @ Sat, 11 Dec 2021 13:17:28: #2 finished! INFO @ Sat, 11 Dec 2021 13:17:28: #2 predicted fragment length is 142 bps INFO @ Sat, 11 Dec 2021 13:17:28: #2 alternative fragment length(s) may be 79,142,161,168,198,247,261,282,314,330,462,563 bps INFO @ Sat, 11 Dec 2021 13:17:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.10_model.r INFO @ Sat, 11 Dec 2021 13:17:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:17:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:17:30: 9000000 INFO @ Sat, 11 Dec 2021 13:17:36: 10000000 INFO @ Sat, 11 Dec 2021 13:17:43: 11000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:17:49: 12000000 INFO @ Sat, 11 Dec 2021 13:17:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:17:55: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:17:55: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:17:55: #1 total tags in treatment: 12796565 INFO @ Sat, 11 Dec 2021 13:17:55: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:17:55: #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 13:17:55: #1 tags after filtering in treatment: 12796458 INFO @ Sat, 11 Dec 2021 13:17:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:17:55: #1 finished! INFO @ Sat, 11 Dec 2021 13:17:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:17:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:17:56: #2 number of paired peaks: 491 WARNING @ Sat, 11 Dec 2021 13:17:56: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Sat, 11 Dec 2021 13:17:56: start model_add_line... INFO @ Sat, 11 Dec 2021 13:17:56: start X-correlation... INFO @ Sat, 11 Dec 2021 13:17:56: end of X-cor INFO @ Sat, 11 Dec 2021 13:17:56: #2 finished! INFO @ Sat, 11 Dec 2021 13:17:56: #2 predicted fragment length is 142 bps INFO @ Sat, 11 Dec 2021 13:17:56: #2 alternative fragment length(s) may be 79,142,161,168,198,247,261,282,314,330,462,563 bps INFO @ Sat, 11 Dec 2021 13:17:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.20_model.r INFO @ Sat, 11 Dec 2021 13:17:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:17:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:18:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:18:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:18:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.10_summits.bed INFO @ Sat, 11 Dec 2021 13:18:05: Done! pass1 - making usageList (67 chroms): 1 millis pass2 - checking and writing primary data (196 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:18:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:18:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:18:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:18:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986166/SRX9986166.20_summits.bed INFO @ Sat, 11 Dec 2021 13:18:35: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (69 records, 4 fields): 2 millis CompletedMACS2peakCalling