Job ID = 6529219 SRX = SRX1032388 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: 00:09:28 36758378 reads; of these: 36758378 (100.00%) were unpaired; of these: 1128213 (3.07%) aligned 0 times 28387234 (77.23%) aligned exactly 1 time 7242931 (19.70%) aligned >1 times 96.93% overall alignment rate Time searching: 00:09:29 Overall time: 00:09:29 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] 7685699 / 35630165 = 0.2157 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:05:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.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 @ Tue, 30 Jun 2020 02:05:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:05:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:05:08: 1000000 INFO @ Tue, 30 Jun 2020 02:05:16: 2000000 INFO @ Tue, 30 Jun 2020 02:05:23: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:05:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.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 @ Tue, 30 Jun 2020 02:05:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:05:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:05:31: 4000000 INFO @ Tue, 30 Jun 2020 02:05:38: 1000000 INFO @ Tue, 30 Jun 2020 02:05:39: 5000000 INFO @ Tue, 30 Jun 2020 02:05:45: 2000000 INFO @ Tue, 30 Jun 2020 02:05:47: 6000000 INFO @ Tue, 30 Jun 2020 02:05:52: 3000000 INFO @ Tue, 30 Jun 2020 02:05:55: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:05:59: 4000000 INFO @ Tue, 30 Jun 2020 02:06:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.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 @ Tue, 30 Jun 2020 02:06:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:06:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:06:03: 8000000 INFO @ Tue, 30 Jun 2020 02:06:06: 5000000 INFO @ Tue, 30 Jun 2020 02:06:09: 1000000 INFO @ Tue, 30 Jun 2020 02:06:11: 9000000 INFO @ Tue, 30 Jun 2020 02:06:13: 6000000 INFO @ Tue, 30 Jun 2020 02:06:17: 2000000 INFO @ Tue, 30 Jun 2020 02:06:19: 10000000 INFO @ Tue, 30 Jun 2020 02:06:21: 7000000 INFO @ Tue, 30 Jun 2020 02:06:24: 3000000 INFO @ Tue, 30 Jun 2020 02:06:26: 11000000 INFO @ Tue, 30 Jun 2020 02:06:28: 8000000 INFO @ Tue, 30 Jun 2020 02:06:32: 4000000 INFO @ Tue, 30 Jun 2020 02:06:34: 12000000 INFO @ Tue, 30 Jun 2020 02:06:35: 9000000 INFO @ Tue, 30 Jun 2020 02:06:39: 5000000 INFO @ Tue, 30 Jun 2020 02:06:40: 13000000 INFO @ Tue, 30 Jun 2020 02:06:43: 10000000 INFO @ Tue, 30 Jun 2020 02:06:46: 6000000 INFO @ Tue, 30 Jun 2020 02:06:48: 14000000 INFO @ Tue, 30 Jun 2020 02:06:50: 11000000 INFO @ Tue, 30 Jun 2020 02:06:53: 7000000 INFO @ Tue, 30 Jun 2020 02:06:55: 15000000 INFO @ Tue, 30 Jun 2020 02:06:57: 12000000 INFO @ Tue, 30 Jun 2020 02:07:00: 8000000 INFO @ Tue, 30 Jun 2020 02:07:02: 16000000 INFO @ Tue, 30 Jun 2020 02:07:04: 13000000 INFO @ Tue, 30 Jun 2020 02:07:08: 9000000 INFO @ Tue, 30 Jun 2020 02:07:09: 17000000 INFO @ Tue, 30 Jun 2020 02:07:11: 14000000 INFO @ Tue, 30 Jun 2020 02:07:15: 10000000 INFO @ Tue, 30 Jun 2020 02:07:16: 18000000 INFO @ Tue, 30 Jun 2020 02:07:18: 15000000 INFO @ Tue, 30 Jun 2020 02:07:22: 11000000 INFO @ Tue, 30 Jun 2020 02:07:23: 19000000 INFO @ Tue, 30 Jun 2020 02:07:25: 16000000 INFO @ Tue, 30 Jun 2020 02:07:29: 12000000 INFO @ Tue, 30 Jun 2020 02:07:30: 20000000 INFO @ Tue, 30 Jun 2020 02:07:33: 17000000 INFO @ Tue, 30 Jun 2020 02:07:36: 13000000 INFO @ Tue, 30 Jun 2020 02:07:37: 21000000 INFO @ Tue, 30 Jun 2020 02:07:40: 18000000 INFO @ Tue, 30 Jun 2020 02:07:43: 14000000 INFO @ Tue, 30 Jun 2020 02:07:44: 22000000 INFO @ Tue, 30 Jun 2020 02:07:47: 19000000 INFO @ Tue, 30 Jun 2020 02:07:50: 15000000 INFO @ Tue, 30 Jun 2020 02:07:51: 23000000 INFO @ Tue, 30 Jun 2020 02:07:54: 20000000 INFO @ Tue, 30 Jun 2020 02:07:57: 16000000 INFO @ Tue, 30 Jun 2020 02:07:58: 24000000 INFO @ Tue, 30 Jun 2020 02:08:01: 21000000 INFO @ Tue, 30 Jun 2020 02:08:04: 17000000 INFO @ Tue, 30 Jun 2020 02:08:05: 25000000 INFO @ Tue, 30 Jun 2020 02:08:07: 22000000 INFO @ Tue, 30 Jun 2020 02:08:11: 18000000 INFO @ Tue, 30 Jun 2020 02:08:12: 26000000 INFO @ Tue, 30 Jun 2020 02:08:15: 23000000 INFO @ Tue, 30 Jun 2020 02:08:17: 19000000 INFO @ Tue, 30 Jun 2020 02:08:19: 27000000 INFO @ Tue, 30 Jun 2020 02:08:22: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:08:24: 20000000 INFO @ Tue, 30 Jun 2020 02:08:26: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:08:26: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:08:26: #1 total tags in treatment: 27944466 INFO @ Tue, 30 Jun 2020 02:08:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:08:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:08:27: #1 tags after filtering in treatment: 27944462 INFO @ Tue, 30 Jun 2020 02:08:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:08:27: #1 finished! INFO @ Tue, 30 Jun 2020 02:08:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:08:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:08:28: #2 number of paired peaks: 294 WARNING @ Tue, 30 Jun 2020 02:08:28: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Tue, 30 Jun 2020 02:08:28: start model_add_line... INFO @ Tue, 30 Jun 2020 02:08:29: start X-correlation... INFO @ Tue, 30 Jun 2020 02:08:29: end of X-cor INFO @ Tue, 30 Jun 2020 02:08:29: #2 finished! INFO @ Tue, 30 Jun 2020 02:08:29: #2 predicted fragment length is 119 bps INFO @ Tue, 30 Jun 2020 02:08:29: #2 alternative fragment length(s) may be 3,119 bps INFO @ Tue, 30 Jun 2020 02:08:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.05_model.r INFO @ Tue, 30 Jun 2020 02:08:29: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:08:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:08:29: 25000000 INFO @ Tue, 30 Jun 2020 02:08:30: 21000000 INFO @ Tue, 30 Jun 2020 02:08:36: 26000000 INFO @ Tue, 30 Jun 2020 02:08:37: 22000000 INFO @ Tue, 30 Jun 2020 02:08:43: 27000000 INFO @ Tue, 30 Jun 2020 02:08:44: 23000000 INFO @ Tue, 30 Jun 2020 02:08:50: 24000000 INFO @ Tue, 30 Jun 2020 02:08:50: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:08:50: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:08:50: #1 total tags in treatment: 27944466 INFO @ Tue, 30 Jun 2020 02:08:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:08:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:08:51: #1 tags after filtering in treatment: 27944462 INFO @ Tue, 30 Jun 2020 02:08:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:08:51: #1 finished! INFO @ Tue, 30 Jun 2020 02:08:51: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:08:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:08:53: #2 number of paired peaks: 294 WARNING @ Tue, 30 Jun 2020 02:08:53: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Tue, 30 Jun 2020 02:08:53: start model_add_line... INFO @ Tue, 30 Jun 2020 02:08:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:08:53: end of X-cor INFO @ Tue, 30 Jun 2020 02:08:53: #2 finished! INFO @ Tue, 30 Jun 2020 02:08:53: #2 predicted fragment length is 119 bps INFO @ Tue, 30 Jun 2020 02:08:53: #2 alternative fragment length(s) may be 3,119 bps INFO @ Tue, 30 Jun 2020 02:08:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.10_model.r INFO @ Tue, 30 Jun 2020 02:08:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:08:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:08:56: 25000000 INFO @ Tue, 30 Jun 2020 02:09:02: 26000000 INFO @ Tue, 30 Jun 2020 02:09:09: 27000000 INFO @ Tue, 30 Jun 2020 02:09:15: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:09:15: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:09:15: #1 total tags in treatment: 27944466 INFO @ Tue, 30 Jun 2020 02:09:15: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:09:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:09:16: #1 tags after filtering in treatment: 27944462 INFO @ Tue, 30 Jun 2020 02:09:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:09:16: #1 finished! INFO @ Tue, 30 Jun 2020 02:09:16: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:09:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:09:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:09:18: #2 number of paired peaks: 294 WARNING @ Tue, 30 Jun 2020 02:09:18: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Tue, 30 Jun 2020 02:09:18: start model_add_line... INFO @ Tue, 30 Jun 2020 02:09:18: start X-correlation... INFO @ Tue, 30 Jun 2020 02:09:18: end of X-cor INFO @ Tue, 30 Jun 2020 02:09:18: #2 finished! INFO @ Tue, 30 Jun 2020 02:09:18: #2 predicted fragment length is 119 bps INFO @ Tue, 30 Jun 2020 02:09:18: #2 alternative fragment length(s) may be 3,119 bps INFO @ Tue, 30 Jun 2020 02:09:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.20_model.r INFO @ Tue, 30 Jun 2020 02:09:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:09:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:09:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:09:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:09:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.05_summits.bed INFO @ Tue, 30 Jun 2020 02:09:40: Done! pass1 - making usageList (639 chroms): 3 millis pass2 - checking and writing primary data (8429 records, 4 fields): 44 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:09:44: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:10:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:10:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:10:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:10:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.10_summits.bed INFO @ Tue, 30 Jun 2020 02:10:10: Done! pass1 - making usageList (519 chroms): 2 millis pass2 - checking and writing primary data (3427 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:10:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:10:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:10:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032388/SRX1032388.20_summits.bed INFO @ Tue, 30 Jun 2020 02:10:29: Done! pass1 - making usageList (290 chroms): 2 millis pass2 - checking and writing primary data (1092 records, 4 fields): 18 millis CompletedMACS2peakCalling