Job ID = 6529218 SRX = SRX101480 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: 00:07:47 33954493 reads; of these: 33954493 (100.00%) were unpaired; of these: 5383774 (15.86%) aligned 0 times 22641955 (66.68%) aligned exactly 1 time 5928764 (17.46%) aligned >1 times 84.14% overall alignment rate Time searching: 00:07:47 Overall time: 00:07:47 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] 6352769 / 28570719 = 0.2224 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 01:52:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.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 01:52:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:52:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:52:17: 1000000 INFO @ Tue, 30 Jun 2020 01:52:23: 2000000 INFO @ Tue, 30 Jun 2020 01:52:29: 3000000 INFO @ Tue, 30 Jun 2020 01:52:35: 4000000 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 01:52:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.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 01:52:41: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:52:41: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:52:41: 5000000 INFO @ Tue, 30 Jun 2020 01:52:47: 1000000 INFO @ Tue, 30 Jun 2020 01:52:48: 6000000 INFO @ Tue, 30 Jun 2020 01:52:53: 2000000 INFO @ Tue, 30 Jun 2020 01:52:54: 7000000 INFO @ Tue, 30 Jun 2020 01:53:00: 3000000 INFO @ Tue, 30 Jun 2020 01:53:01: 8000000 INFO @ Tue, 30 Jun 2020 01:53:06: 4000000 INFO @ Tue, 30 Jun 2020 01:53:07: 9000000 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 01:53:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.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 01:53:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:53:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:53:12: 5000000 INFO @ Tue, 30 Jun 2020 01:53:13: 10000000 INFO @ Tue, 30 Jun 2020 01:53:17: 1000000 INFO @ Tue, 30 Jun 2020 01:53:18: 6000000 INFO @ Tue, 30 Jun 2020 01:53:19: 11000000 INFO @ Tue, 30 Jun 2020 01:53:23: 2000000 INFO @ Tue, 30 Jun 2020 01:53:25: 7000000 INFO @ Tue, 30 Jun 2020 01:53:26: 12000000 INFO @ Tue, 30 Jun 2020 01:53:29: 3000000 INFO @ Tue, 30 Jun 2020 01:53:31: 8000000 INFO @ Tue, 30 Jun 2020 01:53:32: 13000000 INFO @ Tue, 30 Jun 2020 01:53:36: 4000000 INFO @ Tue, 30 Jun 2020 01:53:37: 9000000 INFO @ Tue, 30 Jun 2020 01:53:38: 14000000 INFO @ Tue, 30 Jun 2020 01:53:42: 5000000 INFO @ Tue, 30 Jun 2020 01:53:43: 10000000 INFO @ Tue, 30 Jun 2020 01:53:45: 15000000 INFO @ Tue, 30 Jun 2020 01:53:48: 6000000 INFO @ Tue, 30 Jun 2020 01:53:49: 11000000 INFO @ Tue, 30 Jun 2020 01:53:51: 16000000 INFO @ Tue, 30 Jun 2020 01:53:55: 7000000 INFO @ Tue, 30 Jun 2020 01:53:55: 12000000 INFO @ Tue, 30 Jun 2020 01:53:57: 17000000 INFO @ Tue, 30 Jun 2020 01:54:01: 8000000 INFO @ Tue, 30 Jun 2020 01:54:02: 13000000 INFO @ Tue, 30 Jun 2020 01:54:04: 18000000 INFO @ Tue, 30 Jun 2020 01:54:07: 9000000 INFO @ Tue, 30 Jun 2020 01:54:08: 14000000 INFO @ Tue, 30 Jun 2020 01:54:10: 19000000 INFO @ Tue, 30 Jun 2020 01:54:14: 10000000 INFO @ Tue, 30 Jun 2020 01:54:14: 15000000 INFO @ Tue, 30 Jun 2020 01:54:16: 20000000 INFO @ Tue, 30 Jun 2020 01:54:20: 11000000 INFO @ Tue, 30 Jun 2020 01:54:20: 16000000 INFO @ Tue, 30 Jun 2020 01:54:22: 21000000 INFO @ Tue, 30 Jun 2020 01:54:26: 17000000 INFO @ Tue, 30 Jun 2020 01:54:26: 12000000 INFO @ Tue, 30 Jun 2020 01:54:28: 22000000 INFO @ Tue, 30 Jun 2020 01:54:29: #1 tag size is determined as 41 bps INFO @ Tue, 30 Jun 2020 01:54:29: #1 tag size = 41 INFO @ Tue, 30 Jun 2020 01:54:29: #1 total tags in treatment: 22217950 INFO @ Tue, 30 Jun 2020 01:54:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:54:29: #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 01:54:30: #1 tags after filtering in treatment: 22217878 INFO @ Tue, 30 Jun 2020 01:54:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:54:30: #1 finished! INFO @ Tue, 30 Jun 2020 01:54:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:54:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:54:32: #2 number of paired peaks: 241 WARNING @ Tue, 30 Jun 2020 01:54:32: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Tue, 30 Jun 2020 01:54:32: start model_add_line... INFO @ Tue, 30 Jun 2020 01:54:32: start X-correlation... INFO @ Tue, 30 Jun 2020 01:54:32: end of X-cor INFO @ Tue, 30 Jun 2020 01:54:32: #2 finished! INFO @ Tue, 30 Jun 2020 01:54:32: #2 predicted fragment length is 101 bps INFO @ Tue, 30 Jun 2020 01:54:32: #2 alternative fragment length(s) may be 4,63,101 bps INFO @ Tue, 30 Jun 2020 01:54:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.05_model.r INFO @ Tue, 30 Jun 2020 01:54:32: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:54:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:54:32: 18000000 INFO @ Tue, 30 Jun 2020 01:54:33: 13000000 INFO @ Tue, 30 Jun 2020 01:54:38: 19000000 INFO @ Tue, 30 Jun 2020 01:54:39: 14000000 INFO @ Tue, 30 Jun 2020 01:54:44: 20000000 INFO @ Tue, 30 Jun 2020 01:54:45: 15000000 INFO @ Tue, 30 Jun 2020 01:54:50: 21000000 INFO @ Tue, 30 Jun 2020 01:54:51: 16000000 INFO @ Tue, 30 Jun 2020 01:54:57: 22000000 INFO @ Tue, 30 Jun 2020 01:54:57: 17000000 INFO @ Tue, 30 Jun 2020 01:54:58: #1 tag size is determined as 41 bps INFO @ Tue, 30 Jun 2020 01:54:58: #1 tag size = 41 INFO @ Tue, 30 Jun 2020 01:54:58: #1 total tags in treatment: 22217950 INFO @ Tue, 30 Jun 2020 01:54:58: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:54:58: #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 01:54:59: #1 tags after filtering in treatment: 22217878 INFO @ Tue, 30 Jun 2020 01:54:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:54:59: #1 finished! INFO @ Tue, 30 Jun 2020 01:54:59: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:54:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:55:00: #2 number of paired peaks: 241 WARNING @ Tue, 30 Jun 2020 01:55:00: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Tue, 30 Jun 2020 01:55:00: start model_add_line... INFO @ Tue, 30 Jun 2020 01:55:01: start X-correlation... INFO @ Tue, 30 Jun 2020 01:55:01: end of X-cor INFO @ Tue, 30 Jun 2020 01:55:01: #2 finished! INFO @ Tue, 30 Jun 2020 01:55:01: #2 predicted fragment length is 101 bps INFO @ Tue, 30 Jun 2020 01:55:01: #2 alternative fragment length(s) may be 4,63,101 bps INFO @ Tue, 30 Jun 2020 01:55:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.10_model.r INFO @ Tue, 30 Jun 2020 01:55:01: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:55:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:55:04: 18000000 INFO @ Tue, 30 Jun 2020 01:55:10: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:55:16: 20000000 INFO @ Tue, 30 Jun 2020 01:55:19: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:55:22: 21000000 INFO @ Tue, 30 Jun 2020 01:55:28: 22000000 INFO @ Tue, 30 Jun 2020 01:55:29: #1 tag size is determined as 41 bps INFO @ Tue, 30 Jun 2020 01:55:29: #1 tag size = 41 INFO @ Tue, 30 Jun 2020 01:55:29: #1 total tags in treatment: 22217950 INFO @ Tue, 30 Jun 2020 01:55:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:55:29: #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 01:55:30: #1 tags after filtering in treatment: 22217878 INFO @ Tue, 30 Jun 2020 01:55:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:55:30: #1 finished! INFO @ Tue, 30 Jun 2020 01:55:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:55:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:55:32: #2 number of paired peaks: 241 WARNING @ Tue, 30 Jun 2020 01:55:32: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Tue, 30 Jun 2020 01:55:32: start model_add_line... INFO @ Tue, 30 Jun 2020 01:55:32: start X-correlation... INFO @ Tue, 30 Jun 2020 01:55:32: end of X-cor INFO @ Tue, 30 Jun 2020 01:55:32: #2 finished! INFO @ Tue, 30 Jun 2020 01:55:32: #2 predicted fragment length is 101 bps INFO @ Tue, 30 Jun 2020 01:55:32: #2 alternative fragment length(s) may be 4,63,101 bps INFO @ Tue, 30 Jun 2020 01:55:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.20_model.r INFO @ Tue, 30 Jun 2020 01:55:32: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:55:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:55:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:55:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:55:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.05_summits.bed INFO @ Tue, 30 Jun 2020 01:55:43: Done! pass1 - making usageList (659 chroms): 2 millis pass2 - checking and writing primary data (6987 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:55:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:56:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:56:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:56:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.10_summits.bed INFO @ Tue, 30 Jun 2020 01:56:13: Done! pass1 - making usageList (552 chroms): 1 millis pass2 - checking and writing primary data (2233 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:56:16: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:56:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:56:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:56:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX101480/SRX101480.20_summits.bed INFO @ Tue, 30 Jun 2020 01:56:40: Done! pass1 - making usageList (345 chroms): 1 millis pass2 - checking and writing primary data (793 records, 4 fields): 13 millis CompletedMACS2peakCalling