Job ID = 16437480 SRX = SRX15046047 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: 00:07:27 30902359 reads; of these: 30902359 (100.00%) were unpaired; of these: 4456081 (14.42%) aligned 0 times 21879455 (70.80%) aligned exactly 1 time 4566823 (14.78%) aligned >1 times 85.58% overall alignment rate Time searching: 00:07:27 Overall time: 00:07:27 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 12 files... [bam_rmdupse_core] 7790700 / 26446278 = 0.2946 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:53:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.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, 02 Aug 2022 12:53:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:53:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:53:34: 1000000 INFO @ Tue, 02 Aug 2022 12:53:39: 2000000 INFO @ Tue, 02 Aug 2022 12:53:44: 3000000 INFO @ Tue, 02 Aug 2022 12:53:49: 4000000 INFO @ Tue, 02 Aug 2022 12:53:54: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:53:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.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, 02 Aug 2022 12:53:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:53:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:53:58: 6000000 INFO @ Tue, 02 Aug 2022 12:54:03: 7000000 INFO @ Tue, 02 Aug 2022 12:54:03: 1000000 INFO @ Tue, 02 Aug 2022 12:54:08: 8000000 INFO @ Tue, 02 Aug 2022 12:54:09: 2000000 INFO @ Tue, 02 Aug 2022 12:54:13: 9000000 INFO @ Tue, 02 Aug 2022 12:54:14: 3000000 INFO @ Tue, 02 Aug 2022 12:54:18: 10000000 INFO @ Tue, 02 Aug 2022 12:54:19: 4000000 INFO @ Tue, 02 Aug 2022 12:54:23: 11000000 INFO @ Tue, 02 Aug 2022 12:54:24: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:54:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.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, 02 Aug 2022 12:54:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:54:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:54:29: 12000000 INFO @ Tue, 02 Aug 2022 12:54:29: 6000000 INFO @ Tue, 02 Aug 2022 12:54:34: 13000000 INFO @ Tue, 02 Aug 2022 12:54:34: 7000000 INFO @ Tue, 02 Aug 2022 12:54:34: 1000000 INFO @ Tue, 02 Aug 2022 12:54:39: 14000000 INFO @ Tue, 02 Aug 2022 12:54:39: 8000000 INFO @ Tue, 02 Aug 2022 12:54:40: 2000000 INFO @ Tue, 02 Aug 2022 12:54:44: 15000000 INFO @ Tue, 02 Aug 2022 12:54:44: 9000000 INFO @ Tue, 02 Aug 2022 12:54:46: 3000000 INFO @ Tue, 02 Aug 2022 12:54:49: 16000000 INFO @ Tue, 02 Aug 2022 12:54:49: 10000000 INFO @ Tue, 02 Aug 2022 12:54:52: 4000000 INFO @ Tue, 02 Aug 2022 12:54:54: 17000000 INFO @ Tue, 02 Aug 2022 12:54:55: 11000000 INFO @ Tue, 02 Aug 2022 12:54:58: 5000000 INFO @ Tue, 02 Aug 2022 12:55:00: 18000000 INFO @ Tue, 02 Aug 2022 12:55:00: 12000000 INFO @ Tue, 02 Aug 2022 12:55:03: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:55:03: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:55:03: #1 total tags in treatment: 18655578 INFO @ Tue, 02 Aug 2022 12:55:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:55:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:55:04: #1 tags after filtering in treatment: 18655578 INFO @ Tue, 02 Aug 2022 12:55:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:55:04: #1 finished! INFO @ Tue, 02 Aug 2022 12:55:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:55:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:55:04: 6000000 INFO @ Tue, 02 Aug 2022 12:55:05: 13000000 INFO @ Tue, 02 Aug 2022 12:55:05: #2 number of paired peaks: 338 WARNING @ Tue, 02 Aug 2022 12:55:05: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 02 Aug 2022 12:55:05: start model_add_line... INFO @ Tue, 02 Aug 2022 12:55:05: start X-correlation... INFO @ Tue, 02 Aug 2022 12:55:05: end of X-cor INFO @ Tue, 02 Aug 2022 12:55:05: #2 finished! INFO @ Tue, 02 Aug 2022 12:55:05: #2 predicted fragment length is 115 bps INFO @ Tue, 02 Aug 2022 12:55:05: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 02 Aug 2022 12:55:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.05_model.r INFO @ Tue, 02 Aug 2022 12:55:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:55:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:55:10: 14000000 INFO @ Tue, 02 Aug 2022 12:55:10: 7000000 INFO @ Tue, 02 Aug 2022 12:55:15: 15000000 INFO @ Tue, 02 Aug 2022 12:55:16: 8000000 INFO @ Tue, 02 Aug 2022 12:55:20: 16000000 INFO @ Tue, 02 Aug 2022 12:55:22: 9000000 INFO @ Tue, 02 Aug 2022 12:55:25: 17000000 INFO @ Tue, 02 Aug 2022 12:55:28: 10000000 INFO @ Tue, 02 Aug 2022 12:55:31: 18000000 INFO @ Tue, 02 Aug 2022 12:55:34: 11000000 INFO @ Tue, 02 Aug 2022 12:55:34: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:55:34: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:55:34: #1 total tags in treatment: 18655578 INFO @ Tue, 02 Aug 2022 12:55:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:55:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:55:35: #1 tags after filtering in treatment: 18655578 INFO @ Tue, 02 Aug 2022 12:55:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:55:35: #1 finished! INFO @ Tue, 02 Aug 2022 12:55:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:55:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:55:36: #2 number of paired peaks: 338 WARNING @ Tue, 02 Aug 2022 12:55:36: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 02 Aug 2022 12:55:36: start model_add_line... INFO @ Tue, 02 Aug 2022 12:55:36: start X-correlation... INFO @ Tue, 02 Aug 2022 12:55:36: end of X-cor INFO @ Tue, 02 Aug 2022 12:55:36: #2 finished! INFO @ Tue, 02 Aug 2022 12:55:36: #2 predicted fragment length is 115 bps INFO @ Tue, 02 Aug 2022 12:55:36: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 02 Aug 2022 12:55:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.10_model.r INFO @ Tue, 02 Aug 2022 12:55:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:55:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:55:40: 12000000 INFO @ Tue, 02 Aug 2022 12:55:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:55:45: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:55:51: 14000000 INFO @ Tue, 02 Aug 2022 12:55:56: 15000000 INFO @ Tue, 02 Aug 2022 12:56:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:56:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:56:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.05_summits.bed INFO @ Tue, 02 Aug 2022 12:56:02: Done! INFO @ Tue, 02 Aug 2022 12:56:02: 16000000 pass1 - making usageList (480 chroms): 2 millis pass2 - checking and writing primary data (4303 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:56:08: 17000000 INFO @ Tue, 02 Aug 2022 12:56:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:56:13: 18000000 INFO @ Tue, 02 Aug 2022 12:56:17: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:56:17: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:56:17: #1 total tags in treatment: 18655578 INFO @ Tue, 02 Aug 2022 12:56:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:56:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:56:18: #1 tags after filtering in treatment: 18655578 INFO @ Tue, 02 Aug 2022 12:56:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:56:18: #1 finished! INFO @ Tue, 02 Aug 2022 12:56:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:56:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:56:19: #2 number of paired peaks: 338 WARNING @ Tue, 02 Aug 2022 12:56:19: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 02 Aug 2022 12:56:19: start model_add_line... INFO @ Tue, 02 Aug 2022 12:56:19: start X-correlation... INFO @ Tue, 02 Aug 2022 12:56:19: end of X-cor INFO @ Tue, 02 Aug 2022 12:56:19: #2 finished! INFO @ Tue, 02 Aug 2022 12:56:19: #2 predicted fragment length is 115 bps INFO @ Tue, 02 Aug 2022 12:56:19: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 02 Aug 2022 12:56:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.20_model.r INFO @ Tue, 02 Aug 2022 12:56:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:56:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:56:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:56:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:56:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.10_summits.bed INFO @ Tue, 02 Aug 2022 12:56:31: Done! pass1 - making usageList (391 chroms): 2 millis pass2 - checking and writing primary data (2754 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:56:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:57:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:57:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:57:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15046047/SRX15046047.20_summits.bed INFO @ Tue, 02 Aug 2022 12:57:13: Done! pass1 - making usageList (221 chroms): 1 millis pass2 - checking and writing primary data (1342 records, 4 fields): 87 millis CompletedMACS2peakCalling