Job ID = 6455170 SRX = SRX2804228 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:51:55 prefetch.2.10.7: 1) Downloading 'SRR5534656'... 2020-06-21T09:51:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:55:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:55:01 prefetch.2.10.7: 1) 'SRR5534656' was downloaded successfully 2020-06-21T09:55:01 prefetch.2.10.7: 'SRR5534656' has 0 unresolved dependencies Read 32306620 spots for SRR5534656/SRR5534656.sra Written 32306620 spots for SRR5534656/SRR5534656.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: 00:10:00 32306620 reads; of these: 32306620 (100.00%) were unpaired; of these: 1023493 (3.17%) aligned 0 times 21592605 (66.84%) aligned exactly 1 time 9690522 (30.00%) aligned >1 times 96.83% overall alignment rate Time searching: 00:10:00 Overall time: 00:10:00 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] 7107495 / 31283127 = 0.2272 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 19:12:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.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 19:12:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:36: 1000000 INFO @ Sun, 21 Jun 2020 19:12:41: 2000000 INFO @ Sun, 21 Jun 2020 19:12:47: 3000000 INFO @ Sun, 21 Jun 2020 19:12:53: 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 19:12:58: 5000000 INFO @ Sun, 21 Jun 2020 19:13:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.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 19:13:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:04: 6000000 INFO @ Sun, 21 Jun 2020 19:13:06: 1000000 INFO @ Sun, 21 Jun 2020 19:13:10: 7000000 INFO @ Sun, 21 Jun 2020 19:13:11: 2000000 INFO @ Sun, 21 Jun 2020 19:13:16: 8000000 INFO @ Sun, 21 Jun 2020 19:13:17: 3000000 INFO @ Sun, 21 Jun 2020 19:13:22: 9000000 INFO @ Sun, 21 Jun 2020 19:13:23: 4000000 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 19:13:28: 10000000 INFO @ Sun, 21 Jun 2020 19:13:29: 5000000 INFO @ Sun, 21 Jun 2020 19:13:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.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 19:13:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:34: 11000000 INFO @ Sun, 21 Jun 2020 19:13:35: 1000000 INFO @ Sun, 21 Jun 2020 19:13:35: 6000000 INFO @ Sun, 21 Jun 2020 19:13:39: 2000000 INFO @ Sun, 21 Jun 2020 19:13:40: 12000000 INFO @ Sun, 21 Jun 2020 19:13:41: 7000000 INFO @ Sun, 21 Jun 2020 19:13:44: 3000000 INFO @ Sun, 21 Jun 2020 19:13:46: 13000000 INFO @ Sun, 21 Jun 2020 19:13:46: 8000000 INFO @ Sun, 21 Jun 2020 19:13:49: 4000000 INFO @ Sun, 21 Jun 2020 19:13:52: 14000000 INFO @ Sun, 21 Jun 2020 19:13:52: 9000000 INFO @ Sun, 21 Jun 2020 19:13:54: 5000000 INFO @ Sun, 21 Jun 2020 19:13:58: 15000000 INFO @ Sun, 21 Jun 2020 19:13:58: 10000000 INFO @ Sun, 21 Jun 2020 19:13:59: 6000000 INFO @ Sun, 21 Jun 2020 19:14:04: 11000000 INFO @ Sun, 21 Jun 2020 19:14:04: 16000000 INFO @ Sun, 21 Jun 2020 19:14:04: 7000000 INFO @ Sun, 21 Jun 2020 19:14:09: 8000000 INFO @ Sun, 21 Jun 2020 19:14:09: 12000000 INFO @ Sun, 21 Jun 2020 19:14:10: 17000000 INFO @ Sun, 21 Jun 2020 19:14:14: 9000000 INFO @ Sun, 21 Jun 2020 19:14:15: 13000000 INFO @ Sun, 21 Jun 2020 19:14:15: 18000000 INFO @ Sun, 21 Jun 2020 19:14:19: 10000000 INFO @ Sun, 21 Jun 2020 19:14:21: 14000000 INFO @ Sun, 21 Jun 2020 19:14:21: 19000000 INFO @ Sun, 21 Jun 2020 19:14:24: 11000000 INFO @ Sun, 21 Jun 2020 19:14:27: 15000000 INFO @ Sun, 21 Jun 2020 19:14:27: 20000000 INFO @ Sun, 21 Jun 2020 19:14:29: 12000000 INFO @ Sun, 21 Jun 2020 19:14:33: 16000000 INFO @ Sun, 21 Jun 2020 19:14:33: 21000000 INFO @ Sun, 21 Jun 2020 19:14:34: 13000000 INFO @ Sun, 21 Jun 2020 19:14:39: 17000000 INFO @ Sun, 21 Jun 2020 19:14:39: 22000000 INFO @ Sun, 21 Jun 2020 19:14:39: 14000000 INFO @ Sun, 21 Jun 2020 19:14:44: 15000000 INFO @ Sun, 21 Jun 2020 19:14:44: 18000000 INFO @ Sun, 21 Jun 2020 19:14:45: 23000000 INFO @ Sun, 21 Jun 2020 19:14:49: 16000000 INFO @ Sun, 21 Jun 2020 19:14:50: 19000000 INFO @ Sun, 21 Jun 2020 19:14:51: 24000000 INFO @ Sun, 21 Jun 2020 19:14:52: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:14:52: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:14:52: #1 total tags in treatment: 24175632 INFO @ Sun, 21 Jun 2020 19:14:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:52: #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 19:14:53: #1 tags after filtering in treatment: 24175632 INFO @ Sun, 21 Jun 2020 19:14:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:53: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:54: 17000000 INFO @ Sun, 21 Jun 2020 19:14:54: #2 number of paired peaks: 443 WARNING @ Sun, 21 Jun 2020 19:14:54: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Sun, 21 Jun 2020 19:14:54: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:54: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:54: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:54: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:54: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:14:54: #2 alternative fragment length(s) may be 2,585 bps INFO @ Sun, 21 Jun 2020 19:14:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.05_model.r WARNING @ Sun, 21 Jun 2020 19:14:54: #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 19:14:54: #2 You may need to consider one of the other alternative d(s): 2,585 WARNING @ Sun, 21 Jun 2020 19:14:54: #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 19:14:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:56: 20000000 INFO @ Sun, 21 Jun 2020 19:14:59: 18000000 INFO @ Sun, 21 Jun 2020 19:15:02: 21000000 INFO @ Sun, 21 Jun 2020 19:15:04: 19000000 INFO @ Sun, 21 Jun 2020 19:15:08: 22000000 INFO @ Sun, 21 Jun 2020 19:15:09: 20000000 INFO @ Sun, 21 Jun 2020 19:15:13: 23000000 INFO @ Sun, 21 Jun 2020 19:15:14: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:15:19: 22000000 INFO @ Sun, 21 Jun 2020 19:15:19: 24000000 INFO @ Sun, 21 Jun 2020 19:15:20: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:15:20: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:15:20: #1 total tags in treatment: 24175632 INFO @ Sun, 21 Jun 2020 19:15:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:20: #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 19:15:21: #1 tags after filtering in treatment: 24175632 INFO @ Sun, 21 Jun 2020 19:15:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:23: #2 number of paired peaks: 443 WARNING @ Sun, 21 Jun 2020 19:15:23: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:23: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:23: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:23: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:15:23: #2 alternative fragment length(s) may be 2,585 bps INFO @ Sun, 21 Jun 2020 19:15:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.10_model.r WARNING @ Sun, 21 Jun 2020 19:15:23: #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 19:15:23: #2 You may need to consider one of the other alternative d(s): 2,585 WARNING @ Sun, 21 Jun 2020 19:15:23: #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 19:15:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:23: 23000000 INFO @ Sun, 21 Jun 2020 19:15:28: 24000000 INFO @ Sun, 21 Jun 2020 19:15:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:15:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:15:29: #1 total tags in treatment: 24175632 INFO @ Sun, 21 Jun 2020 19:15:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:29: #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 19:15:30: #1 tags after filtering in treatment: 24175632 INFO @ Sun, 21 Jun 2020 19:15:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:32: #2 number of paired peaks: 443 WARNING @ Sun, 21 Jun 2020 19:15:32: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:32: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:32: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:32: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:32: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:32: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:15:32: #2 alternative fragment length(s) may be 2,585 bps INFO @ Sun, 21 Jun 2020 19:15:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.20_model.r WARNING @ Sun, 21 Jun 2020 19:15:32: #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 19:15:32: #2 You may need to consider one of the other alternative d(s): 2,585 WARNING @ Sun, 21 Jun 2020 19:15:32: #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 19:15:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.05_summits.bed INFO @ Sun, 21 Jun 2020 19:15:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:16:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:16:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:16:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.10_summits.bed INFO @ Sun, 21 Jun 2020 19:16:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:16:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2804228/SRX2804228.20_summits.bed INFO @ Sun, 21 Jun 2020 19:16:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling