Job ID = 6458777 SRX = SRX5436050 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:49:55 prefetch.2.10.7: 1) Downloading 'SRR8637382'... 2020-06-21T12:49:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:53:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:53:21 prefetch.2.10.7: 1) 'SRR8637382' was downloaded successfully Read 34862720 spots for SRR8637382/SRR8637382.sra Written 34862720 spots for SRR8637382/SRR8637382.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: 00:10:03 34862720 reads; of these: 34862720 (100.00%) were unpaired; of these: 1139606 (3.27%) aligned 0 times 23221506 (66.61%) aligned exactly 1 time 10501608 (30.12%) aligned >1 times 96.73% overall alignment rate Time searching: 00:10:03 Overall time: 00:10:03 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] 6347181 / 33723114 = 0.1882 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 22:12:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.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 22:12:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:12:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:12:49: 1000000 INFO @ Sun, 21 Jun 2020 22:12:56: 2000000 INFO @ Sun, 21 Jun 2020 22:13:02: 3000000 INFO @ Sun, 21 Jun 2020 22:13:09: 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 22:13:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.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 22:13:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:13:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:13:16: 5000000 INFO @ Sun, 21 Jun 2020 22:13:20: 1000000 INFO @ Sun, 21 Jun 2020 22:13:23: 6000000 INFO @ Sun, 21 Jun 2020 22:13:28: 2000000 INFO @ Sun, 21 Jun 2020 22:13:31: 7000000 INFO @ Sun, 21 Jun 2020 22:13:35: 3000000 INFO @ Sun, 21 Jun 2020 22:13:38: 8000000 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 22:13:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.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 22:13:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:13:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:13:42: 4000000 INFO @ Sun, 21 Jun 2020 22:13:45: 9000000 INFO @ Sun, 21 Jun 2020 22:13:50: 5000000 INFO @ Sun, 21 Jun 2020 22:13:50: 1000000 INFO @ Sun, 21 Jun 2020 22:13:53: 10000000 INFO @ Sun, 21 Jun 2020 22:13:58: 6000000 INFO @ Sun, 21 Jun 2020 22:13:58: 2000000 INFO @ Sun, 21 Jun 2020 22:14:00: 11000000 INFO @ Sun, 21 Jun 2020 22:14:05: 7000000 INFO @ Sun, 21 Jun 2020 22:14:05: 3000000 INFO @ Sun, 21 Jun 2020 22:14:08: 12000000 INFO @ Sun, 21 Jun 2020 22:14:13: 8000000 INFO @ Sun, 21 Jun 2020 22:14:13: 4000000 INFO @ Sun, 21 Jun 2020 22:14:16: 13000000 INFO @ Sun, 21 Jun 2020 22:14:20: 9000000 INFO @ Sun, 21 Jun 2020 22:14:20: 5000000 INFO @ Sun, 21 Jun 2020 22:14:24: 14000000 INFO @ Sun, 21 Jun 2020 22:14:28: 6000000 INFO @ Sun, 21 Jun 2020 22:14:28: 10000000 INFO @ Sun, 21 Jun 2020 22:14:32: 15000000 INFO @ Sun, 21 Jun 2020 22:14:36: 7000000 INFO @ Sun, 21 Jun 2020 22:14:36: 11000000 INFO @ Sun, 21 Jun 2020 22:14:39: 16000000 INFO @ Sun, 21 Jun 2020 22:14:43: 8000000 INFO @ Sun, 21 Jun 2020 22:14:44: 12000000 INFO @ Sun, 21 Jun 2020 22:14:47: 17000000 INFO @ Sun, 21 Jun 2020 22:14:50: 9000000 INFO @ Sun, 21 Jun 2020 22:14:51: 13000000 INFO @ Sun, 21 Jun 2020 22:14:55: 18000000 INFO @ Sun, 21 Jun 2020 22:14:58: 10000000 INFO @ Sun, 21 Jun 2020 22:14:59: 14000000 INFO @ Sun, 21 Jun 2020 22:15:03: 19000000 INFO @ Sun, 21 Jun 2020 22:15:05: 11000000 INFO @ Sun, 21 Jun 2020 22:15:07: 15000000 INFO @ Sun, 21 Jun 2020 22:15:11: 20000000 INFO @ Sun, 21 Jun 2020 22:15:13: 12000000 INFO @ Sun, 21 Jun 2020 22:15:15: 16000000 INFO @ Sun, 21 Jun 2020 22:15:19: 21000000 INFO @ Sun, 21 Jun 2020 22:15:20: 13000000 INFO @ Sun, 21 Jun 2020 22:15:23: 17000000 INFO @ Sun, 21 Jun 2020 22:15:28: 22000000 INFO @ Sun, 21 Jun 2020 22:15:28: 14000000 INFO @ Sun, 21 Jun 2020 22:15:31: 18000000 INFO @ Sun, 21 Jun 2020 22:15:36: 15000000 INFO @ Sun, 21 Jun 2020 22:15:36: 23000000 INFO @ Sun, 21 Jun 2020 22:15:39: 19000000 INFO @ Sun, 21 Jun 2020 22:15:43: 16000000 INFO @ Sun, 21 Jun 2020 22:15:44: 24000000 INFO @ Sun, 21 Jun 2020 22:15:47: 20000000 INFO @ Sun, 21 Jun 2020 22:15:51: 17000000 INFO @ Sun, 21 Jun 2020 22:15:52: 25000000 INFO @ Sun, 21 Jun 2020 22:15:55: 21000000 INFO @ Sun, 21 Jun 2020 22:15:58: 18000000 INFO @ Sun, 21 Jun 2020 22:16:00: 26000000 INFO @ Sun, 21 Jun 2020 22:16:03: 22000000 INFO @ Sun, 21 Jun 2020 22:16:06: 19000000 INFO @ Sun, 21 Jun 2020 22:16:08: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:16:11: 23000000 INFO @ Sun, 21 Jun 2020 22:16:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:16:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:16:11: #1 total tags in treatment: 27375933 INFO @ Sun, 21 Jun 2020 22:16:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:16:11: #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 22:16:12: #1 tags after filtering in treatment: 27375875 INFO @ Sun, 21 Jun 2020 22:16:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:16:12: #1 finished! INFO @ Sun, 21 Jun 2020 22:16:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:16:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:16:13: 20000000 INFO @ Sun, 21 Jun 2020 22:16:14: #2 number of paired peaks: 1201 INFO @ Sun, 21 Jun 2020 22:16:14: start model_add_line... INFO @ Sun, 21 Jun 2020 22:16:14: start X-correlation... INFO @ Sun, 21 Jun 2020 22:16:14: end of X-cor INFO @ Sun, 21 Jun 2020 22:16:14: #2 finished! INFO @ Sun, 21 Jun 2020 22:16:14: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:16:14: #2 alternative fragment length(s) may be 1,36 bps INFO @ Sun, 21 Jun 2020 22:16:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.05_model.r WARNING @ Sun, 21 Jun 2020 22:16:14: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:16:14: #2 You may need to consider one of the other alternative d(s): 1,36 WARNING @ Sun, 21 Jun 2020 22:16:14: #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 22:16:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:16:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:16:19: 24000000 INFO @ Sun, 21 Jun 2020 22:16:20: 21000000 INFO @ Sun, 21 Jun 2020 22:16:26: 25000000 INFO @ Sun, 21 Jun 2020 22:16:28: 22000000 INFO @ Sun, 21 Jun 2020 22:16:34: 26000000 INFO @ Sun, 21 Jun 2020 22:16:35: 23000000 INFO @ Sun, 21 Jun 2020 22:16:42: 27000000 INFO @ Sun, 21 Jun 2020 22:16:43: 24000000 INFO @ Sun, 21 Jun 2020 22:16:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:16:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:16:45: #1 total tags in treatment: 27375933 INFO @ Sun, 21 Jun 2020 22:16:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:16:45: #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 22:16:45: #1 tags after filtering in treatment: 27375875 INFO @ Sun, 21 Jun 2020 22:16:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:16:45: #1 finished! INFO @ Sun, 21 Jun 2020 22:16:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:16:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:16:47: #2 number of paired peaks: 1201 INFO @ Sun, 21 Jun 2020 22:16:47: start model_add_line... INFO @ Sun, 21 Jun 2020 22:16:47: start X-correlation... INFO @ Sun, 21 Jun 2020 22:16:47: end of X-cor INFO @ Sun, 21 Jun 2020 22:16:47: #2 finished! INFO @ Sun, 21 Jun 2020 22:16:47: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:16:47: #2 alternative fragment length(s) may be 1,36 bps INFO @ Sun, 21 Jun 2020 22:16:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.10_model.r WARNING @ Sun, 21 Jun 2020 22:16:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:16:47: #2 You may need to consider one of the other alternative d(s): 1,36 WARNING @ Sun, 21 Jun 2020 22:16:47: #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 22:16:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:16:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:16:49: 25000000 INFO @ Sun, 21 Jun 2020 22:16:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:16:56: 26000000 INFO @ Sun, 21 Jun 2020 22:17:02: 27000000 INFO @ Sun, 21 Jun 2020 22:17:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:17:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:17:05: #1 total tags in treatment: 27375933 INFO @ Sun, 21 Jun 2020 22:17:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:17:05: #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 22:17:05: #1 tags after filtering in treatment: 27375875 INFO @ Sun, 21 Jun 2020 22:17:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:17:05: #1 finished! INFO @ Sun, 21 Jun 2020 22:17:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:17:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:17:07: #2 number of paired peaks: 1201 INFO @ Sun, 21 Jun 2020 22:17:07: start model_add_line... INFO @ Sun, 21 Jun 2020 22:17:08: start X-correlation... INFO @ Sun, 21 Jun 2020 22:17:08: end of X-cor INFO @ Sun, 21 Jun 2020 22:17:08: #2 finished! INFO @ Sun, 21 Jun 2020 22:17:08: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:17:08: #2 alternative fragment length(s) may be 1,36 bps INFO @ Sun, 21 Jun 2020 22:17:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.20_model.r WARNING @ Sun, 21 Jun 2020 22:17:08: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:17:08: #2 You may need to consider one of the other alternative d(s): 1,36 WARNING @ Sun, 21 Jun 2020 22:17:08: #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 22:17:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:17:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:17:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:17:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:17:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.05_summits.bed INFO @ Sun, 21 Jun 2020 22:17:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:17:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:17:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:17:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:17:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.10_summits.bed INFO @ Sun, 21 Jun 2020 22:17:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:17:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:18:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:18:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:18:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436050/SRX5436050.20_summits.bed INFO @ Sun, 21 Jun 2020 22:18:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling