Job ID = 6459894 SRX = SRX969926 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:37:43 prefetch.2.10.7: 1) Downloading 'SRR1931642'... 2020-06-21T13:37:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:43:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:43:47 prefetch.2.10.7: 1) 'SRR1931642' was downloaded successfully Read 39090135 spots for SRR1931642/SRR1931642.sra Written 39090135 spots for SRR1931642/SRR1931642.sra 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: 00:11:51 39090135 reads; of these: 39090135 (100.00%) were unpaired; of these: 1811866 (4.64%) aligned 0 times 25001918 (63.96%) aligned exactly 1 time 12276351 (31.41%) aligned >1 times 95.36% overall alignment rate Time searching: 00:11:51 Overall time: 00:11:51 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] 9749522 / 37278269 = 0.2615 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 @ Sun, 21 Jun 2020 23:05:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.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 @ Sun, 21 Jun 2020 23:05:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:05:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:05:57: 1000000 INFO @ Sun, 21 Jun 2020 23:06:03: 2000000 INFO @ Sun, 21 Jun 2020 23:06:08: 3000000 INFO @ Sun, 21 Jun 2020 23:06:14: 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 @ Sun, 21 Jun 2020 23:06:20: 5000000 INFO @ Sun, 21 Jun 2020 23:06:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.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 @ Sun, 21 Jun 2020 23:06:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:06:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:06:27: 6000000 INFO @ Sun, 21 Jun 2020 23:06:29: 1000000 INFO @ Sun, 21 Jun 2020 23:06:35: 7000000 INFO @ Sun, 21 Jun 2020 23:06:38: 2000000 INFO @ Sun, 21 Jun 2020 23:06:42: 8000000 INFO @ Sun, 21 Jun 2020 23:06:46: 3000000 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 @ Sun, 21 Jun 2020 23:06:49: 9000000 INFO @ Sun, 21 Jun 2020 23:06:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.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 @ Sun, 21 Jun 2020 23:06:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:06:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:06:54: 4000000 INFO @ Sun, 21 Jun 2020 23:06:57: 10000000 INFO @ Sun, 21 Jun 2020 23:06:58: 1000000 INFO @ Sun, 21 Jun 2020 23:07:03: 5000000 INFO @ Sun, 21 Jun 2020 23:07:04: 11000000 INFO @ Sun, 21 Jun 2020 23:07:06: 2000000 INFO @ Sun, 21 Jun 2020 23:07:11: 6000000 INFO @ Sun, 21 Jun 2020 23:07:12: 12000000 INFO @ Sun, 21 Jun 2020 23:07:14: 3000000 INFO @ Sun, 21 Jun 2020 23:07:19: 7000000 INFO @ Sun, 21 Jun 2020 23:07:19: 13000000 INFO @ Sun, 21 Jun 2020 23:07:21: 4000000 INFO @ Sun, 21 Jun 2020 23:07:27: 14000000 INFO @ Sun, 21 Jun 2020 23:07:28: 8000000 INFO @ Sun, 21 Jun 2020 23:07:29: 5000000 INFO @ Sun, 21 Jun 2020 23:07:34: 15000000 INFO @ Sun, 21 Jun 2020 23:07:36: 9000000 INFO @ Sun, 21 Jun 2020 23:07:36: 6000000 INFO @ Sun, 21 Jun 2020 23:07:42: 16000000 INFO @ Sun, 21 Jun 2020 23:07:44: 7000000 INFO @ Sun, 21 Jun 2020 23:07:44: 10000000 INFO @ Sun, 21 Jun 2020 23:07:50: 17000000 INFO @ Sun, 21 Jun 2020 23:07:51: 8000000 INFO @ Sun, 21 Jun 2020 23:07:52: 11000000 INFO @ Sun, 21 Jun 2020 23:07:57: 18000000 INFO @ Sun, 21 Jun 2020 23:07:59: 9000000 INFO @ Sun, 21 Jun 2020 23:08:00: 12000000 INFO @ Sun, 21 Jun 2020 23:08:05: 19000000 INFO @ Sun, 21 Jun 2020 23:08:07: 10000000 INFO @ Sun, 21 Jun 2020 23:08:08: 13000000 INFO @ Sun, 21 Jun 2020 23:08:12: 20000000 INFO @ Sun, 21 Jun 2020 23:08:14: 11000000 INFO @ Sun, 21 Jun 2020 23:08:16: 14000000 INFO @ Sun, 21 Jun 2020 23:08:20: 21000000 INFO @ Sun, 21 Jun 2020 23:08:22: 12000000 INFO @ Sun, 21 Jun 2020 23:08:25: 15000000 INFO @ Sun, 21 Jun 2020 23:08:28: 22000000 INFO @ Sun, 21 Jun 2020 23:08:29: 13000000 INFO @ Sun, 21 Jun 2020 23:08:33: 16000000 INFO @ Sun, 21 Jun 2020 23:08:35: 23000000 INFO @ Sun, 21 Jun 2020 23:08:37: 14000000 INFO @ Sun, 21 Jun 2020 23:08:41: 17000000 INFO @ Sun, 21 Jun 2020 23:08:43: 24000000 INFO @ Sun, 21 Jun 2020 23:08:44: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 23:08:49: 18000000 INFO @ Sun, 21 Jun 2020 23:08:50: 25000000 INFO @ Sun, 21 Jun 2020 23:08:52: 16000000 INFO @ Sun, 21 Jun 2020 23:08:58: 19000000 INFO @ Sun, 21 Jun 2020 23:08:58: 26000000 INFO @ Sun, 21 Jun 2020 23:09:00: 17000000 INFO @ Sun, 21 Jun 2020 23:09:06: 20000000 INFO @ Sun, 21 Jun 2020 23:09:06: 27000000 INFO @ Sun, 21 Jun 2020 23:09:07: 18000000 INFO @ Sun, 21 Jun 2020 23:09:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 23:09:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 23:09:10: #1 total tags in treatment: 27528747 INFO @ Sun, 21 Jun 2020 23:09:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:09:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 23:09:11: #1 tags after filtering in treatment: 27528747 INFO @ Sun, 21 Jun 2020 23:09:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:09:11: #1 finished! INFO @ Sun, 21 Jun 2020 23:09:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:09:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:09:13: #2 number of paired peaks: 575 WARNING @ Sun, 21 Jun 2020 23:09:13: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Sun, 21 Jun 2020 23:09:13: start model_add_line... INFO @ Sun, 21 Jun 2020 23:09:13: start X-correlation... INFO @ Sun, 21 Jun 2020 23:09:13: end of X-cor INFO @ Sun, 21 Jun 2020 23:09:13: #2 finished! INFO @ Sun, 21 Jun 2020 23:09:13: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 23:09:13: #2 alternative fragment length(s) may be 2,598 bps INFO @ Sun, 21 Jun 2020 23:09:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.05_model.r WARNING @ Sun, 21 Jun 2020 23:09:13: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:09:13: #2 You may need to consider one of the other alternative d(s): 2,598 WARNING @ Sun, 21 Jun 2020 23:09:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 23:09:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:09:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:09:14: 21000000 INFO @ Sun, 21 Jun 2020 23:09:15: 19000000 INFO @ Sun, 21 Jun 2020 23:09:22: 20000000 INFO @ Sun, 21 Jun 2020 23:09:22: 22000000 INFO @ Sun, 21 Jun 2020 23:09:29: 21000000 INFO @ Sun, 21 Jun 2020 23:09:30: 23000000 INFO @ Sun, 21 Jun 2020 23:09:37: 22000000 INFO @ Sun, 21 Jun 2020 23:09:38: 24000000 INFO @ Sun, 21 Jun 2020 23:09:45: 23000000 INFO @ Sun, 21 Jun 2020 23:09:46: 25000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 23:09:52: 24000000 INFO @ Sun, 21 Jun 2020 23:09:54: 26000000 INFO @ Sun, 21 Jun 2020 23:09:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:10:00: 25000000 INFO @ Sun, 21 Jun 2020 23:10:02: 27000000 INFO @ Sun, 21 Jun 2020 23:10:07: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 23:10:07: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 23:10:07: #1 total tags in treatment: 27528747 INFO @ Sun, 21 Jun 2020 23:10:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:10:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 23:10:07: 26000000 INFO @ Sun, 21 Jun 2020 23:10:08: #1 tags after filtering in treatment: 27528747 INFO @ Sun, 21 Jun 2020 23:10:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:10:08: #1 finished! INFO @ Sun, 21 Jun 2020 23:10:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:10:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:10:09: #2 number of paired peaks: 575 WARNING @ Sun, 21 Jun 2020 23:10:09: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Sun, 21 Jun 2020 23:10:09: start model_add_line... INFO @ Sun, 21 Jun 2020 23:10:09: start X-correlation... INFO @ Sun, 21 Jun 2020 23:10:10: end of X-cor INFO @ Sun, 21 Jun 2020 23:10:10: #2 finished! INFO @ Sun, 21 Jun 2020 23:10:10: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 23:10:10: #2 alternative fragment length(s) may be 2,598 bps INFO @ Sun, 21 Jun 2020 23:10:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.10_model.r WARNING @ Sun, 21 Jun 2020 23:10:10: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:10:10: #2 You may need to consider one of the other alternative d(s): 2,598 WARNING @ Sun, 21 Jun 2020 23:10:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 23:10:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:10:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:10:14: 27000000 INFO @ Sun, 21 Jun 2020 23:10:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.05_peaks.xls INFO @ Sun, 21 Jun 2020 23:10:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:10:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.05_summits.bed INFO @ Sun, 21 Jun 2020 23:10:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:10:18: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 23:10:18: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 23:10:18: #1 total tags in treatment: 27528747 INFO @ Sun, 21 Jun 2020 23:10:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:10:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 23:10:18: #1 tags after filtering in treatment: 27528747 INFO @ Sun, 21 Jun 2020 23:10:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:10:18: #1 finished! INFO @ Sun, 21 Jun 2020 23:10:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:10:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:10:20: #2 number of paired peaks: 575 WARNING @ Sun, 21 Jun 2020 23:10:20: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Sun, 21 Jun 2020 23:10:20: start model_add_line... INFO @ Sun, 21 Jun 2020 23:10:20: start X-correlation... INFO @ Sun, 21 Jun 2020 23:10:20: end of X-cor INFO @ Sun, 21 Jun 2020 23:10:20: #2 finished! INFO @ Sun, 21 Jun 2020 23:10:20: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 23:10:20: #2 alternative fragment length(s) may be 2,598 bps INFO @ Sun, 21 Jun 2020 23:10:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.20_model.r WARNING @ Sun, 21 Jun 2020 23:10:20: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:10:20: #2 You may need to consider one of the other alternative d(s): 2,598 WARNING @ Sun, 21 Jun 2020 23:10:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 23:10:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:10:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:10:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:11:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:11:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.10_peaks.xls INFO @ Sun, 21 Jun 2020 23:11:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:11:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.10_summits.bed INFO @ Sun, 21 Jun 2020 23:11:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:11:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:11:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:11:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969926/SRX969926.20_summits.bed INFO @ Sun, 21 Jun 2020 23:11:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling