Job ID = 14170788 SRX = SRX9720908 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: 00:08:36 31458708 reads; of these: 31458708 (100.00%) were unpaired; of these: 1561413 (4.96%) aligned 0 times 21985517 (69.89%) aligned exactly 1 time 7911778 (25.15%) aligned >1 times 95.04% overall alignment rate Time searching: 00:08:36 Overall time: 00:08:36 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] 6521040 / 29897295 = 0.2181 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 08:56:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.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 08:56:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:56:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:56:53: 1000000 INFO @ Sat, 11 Dec 2021 08:57:01: 2000000 INFO @ Sat, 11 Dec 2021 08:57:09: 3000000 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 08:57:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.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 08:57:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:57:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:57:17: 4000000 INFO @ Sat, 11 Dec 2021 08:57:22: 1000000 INFO @ Sat, 11 Dec 2021 08:57:25: 5000000 INFO @ Sat, 11 Dec 2021 08:57:29: 2000000 INFO @ Sat, 11 Dec 2021 08:57:34: 6000000 INFO @ Sat, 11 Dec 2021 08:57:35: 3000000 INFO @ Sat, 11 Dec 2021 08:57:42: 7000000 INFO @ Sat, 11 Dec 2021 08:57:42: 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 08:57:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.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 08:57:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:57:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:57:48: 5000000 INFO @ Sat, 11 Dec 2021 08:57:50: 8000000 INFO @ Sat, 11 Dec 2021 08:57:54: 1000000 INFO @ Sat, 11 Dec 2021 08:57:55: 6000000 INFO @ Sat, 11 Dec 2021 08:57:58: 9000000 INFO @ Sat, 11 Dec 2021 08:58:02: 7000000 INFO @ Sat, 11 Dec 2021 08:58:02: 2000000 INFO @ Sat, 11 Dec 2021 08:58:06: 10000000 INFO @ Sat, 11 Dec 2021 08:58:09: 8000000 INFO @ Sat, 11 Dec 2021 08:58:11: 3000000 INFO @ Sat, 11 Dec 2021 08:58:14: 11000000 INFO @ Sat, 11 Dec 2021 08:58:16: 9000000 INFO @ Sat, 11 Dec 2021 08:58:19: 4000000 INFO @ Sat, 11 Dec 2021 08:58:22: 12000000 INFO @ Sat, 11 Dec 2021 08:58:22: 10000000 INFO @ Sat, 11 Dec 2021 08:58:27: 5000000 INFO @ Sat, 11 Dec 2021 08:58:29: 11000000 INFO @ Sat, 11 Dec 2021 08:58:30: 13000000 INFO @ Sat, 11 Dec 2021 08:58:35: 6000000 INFO @ Sat, 11 Dec 2021 08:58:36: 12000000 INFO @ Sat, 11 Dec 2021 08:58:38: 14000000 INFO @ Sat, 11 Dec 2021 08:58:42: 13000000 INFO @ Sat, 11 Dec 2021 08:58:44: 7000000 INFO @ Sat, 11 Dec 2021 08:58:47: 15000000 INFO @ Sat, 11 Dec 2021 08:58:49: 14000000 INFO @ Sat, 11 Dec 2021 08:58:52: 8000000 INFO @ Sat, 11 Dec 2021 08:58:55: 16000000 INFO @ Sat, 11 Dec 2021 08:58:55: 15000000 INFO @ Sat, 11 Dec 2021 08:59:00: 9000000 INFO @ Sat, 11 Dec 2021 08:59:02: 16000000 INFO @ Sat, 11 Dec 2021 08:59:03: 17000000 INFO @ Sat, 11 Dec 2021 08:59:08: 10000000 INFO @ Sat, 11 Dec 2021 08:59:08: 17000000 INFO @ Sat, 11 Dec 2021 08:59:11: 18000000 INFO @ Sat, 11 Dec 2021 08:59:15: 18000000 INFO @ Sat, 11 Dec 2021 08:59:16: 11000000 INFO @ Sat, 11 Dec 2021 08:59:19: 19000000 INFO @ Sat, 11 Dec 2021 08:59:21: 19000000 INFO @ Sat, 11 Dec 2021 08:59:25: 12000000 INFO @ Sat, 11 Dec 2021 08:59:28: 20000000 INFO @ Sat, 11 Dec 2021 08:59:29: 20000000 INFO @ Sat, 11 Dec 2021 08:59:33: 13000000 INFO @ Sat, 11 Dec 2021 08:59:36: 21000000 INFO @ Sat, 11 Dec 2021 08:59:36: 21000000 INFO @ Sat, 11 Dec 2021 08:59:41: 14000000 INFO @ Sat, 11 Dec 2021 08:59:42: 22000000 INFO @ Sat, 11 Dec 2021 08:59:45: 22000000 INFO @ Sat, 11 Dec 2021 08:59:49: 23000000 INFO @ Sat, 11 Dec 2021 08:59:49: 15000000 INFO @ Sat, 11 Dec 2021 08:59:52: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:59:52: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:59:52: #1 total tags in treatment: 23376255 INFO @ Sat, 11 Dec 2021 08:59:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:59:52: #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 08:59:53: #1 tags after filtering in treatment: 23376199 INFO @ Sat, 11 Dec 2021 08:59:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:59:53: #1 finished! INFO @ Sat, 11 Dec 2021 08:59:53: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:59:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:59:53: 23000000 INFO @ Sat, 11 Dec 2021 08:59:54: #2 number of paired peaks: 639 WARNING @ Sat, 11 Dec 2021 08:59:54: Fewer paired peaks (639) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 639 pairs to build model! INFO @ Sat, 11 Dec 2021 08:59:54: start model_add_line... INFO @ Sat, 11 Dec 2021 08:59:55: start X-correlation... INFO @ Sat, 11 Dec 2021 08:59:55: end of X-cor INFO @ Sat, 11 Dec 2021 08:59:55: #2 finished! INFO @ Sat, 11 Dec 2021 08:59:55: #2 predicted fragment length is 124 bps INFO @ Sat, 11 Dec 2021 08:59:55: #2 alternative fragment length(s) may be 4,124 bps INFO @ Sat, 11 Dec 2021 08:59:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.10_model.r INFO @ Sat, 11 Dec 2021 08:59:55: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:59:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:59:57: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:59:57: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:59:57: #1 total tags in treatment: 23376255 INFO @ Sat, 11 Dec 2021 08:59:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:59:57: #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 08:59:57: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:59:58: #1 tags after filtering in treatment: 23376199 INFO @ Sat, 11 Dec 2021 08:59:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:59:58: #1 finished! INFO @ Sat, 11 Dec 2021 08:59:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:59:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:59:59: #2 number of paired peaks: 639 WARNING @ Sat, 11 Dec 2021 08:59:59: Fewer paired peaks (639) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 639 pairs to build model! INFO @ Sat, 11 Dec 2021 08:59:59: start model_add_line... INFO @ Sat, 11 Dec 2021 09:00:00: start X-correlation... INFO @ Sat, 11 Dec 2021 09:00:00: end of X-cor INFO @ Sat, 11 Dec 2021 09:00:00: #2 finished! INFO @ Sat, 11 Dec 2021 09:00:00: #2 predicted fragment length is 124 bps INFO @ Sat, 11 Dec 2021 09:00:00: #2 alternative fragment length(s) may be 4,124 bps INFO @ Sat, 11 Dec 2021 09:00:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.05_model.r INFO @ Sat, 11 Dec 2021 09:00:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:00:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:00:05: 17000000 INFO @ Sat, 11 Dec 2021 09:00:13: 18000000 INFO @ Sat, 11 Dec 2021 09:00:21: 19000000 INFO @ Sat, 11 Dec 2021 09:00:30: 20000000 INFO @ Sat, 11 Dec 2021 09:00:39: 21000000 INFO @ Sat, 11 Dec 2021 09:00:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:00:47: 22000000 INFO @ Sat, 11 Dec 2021 09:00:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:00:55: 23000000 INFO @ Sat, 11 Dec 2021 09:00:59: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:00:59: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:00:59: #1 total tags in treatment: 23376255 INFO @ Sat, 11 Dec 2021 09:00:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:00:59: #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 09:01:00: #1 tags after filtering in treatment: 23376199 INFO @ Sat, 11 Dec 2021 09:01:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:01:00: #1 finished! INFO @ Sat, 11 Dec 2021 09:01:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:01:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:01:01: #2 number of paired peaks: 639 WARNING @ Sat, 11 Dec 2021 09:01:01: Fewer paired peaks (639) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 639 pairs to build model! INFO @ Sat, 11 Dec 2021 09:01:01: start model_add_line... INFO @ Sat, 11 Dec 2021 09:01:01: start X-correlation... INFO @ Sat, 11 Dec 2021 09:01:01: end of X-cor INFO @ Sat, 11 Dec 2021 09:01:01: #2 finished! INFO @ Sat, 11 Dec 2021 09:01:01: #2 predicted fragment length is 124 bps INFO @ Sat, 11 Dec 2021 09:01:01: #2 alternative fragment length(s) may be 4,124 bps INFO @ Sat, 11 Dec 2021 09:01:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.20_model.r INFO @ Sat, 11 Dec 2021 09:01:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:01:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:01:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:01:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:01:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.10_summits.bed INFO @ Sat, 11 Dec 2021 09:01:05: Done! pass1 - making usageList (601 chroms): 2 millis pass2 - checking and writing primary data (4166 records, 4 fields): 41 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:01:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:01:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:01:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.05_summits.bed INFO @ Sat, 11 Dec 2021 09:01:12: Done! pass1 - making usageList (715 chroms): 2 millis pass2 - checking and writing primary data (6025 records, 4 fields): 54 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:01:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:02:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:02:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:02:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9720908/SRX9720908.20_summits.bed INFO @ Sat, 11 Dec 2021 09:02:14: Done! pass1 - making usageList (469 chroms): 1 millis pass2 - checking and writing primary data (2879 records, 4 fields): 34 millis CompletedMACS2peakCalling