Job ID = 6459892 SRX = SRX969924 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:49:04 prefetch.2.10.7: 1) Downloading 'SRR1931640'... 2020-06-21T13:49:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:54:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:54:14 prefetch.2.10.7: 1) 'SRR1931640' was downloaded successfully Read 35931394 spots for SRR1931640/SRR1931640.sra Written 35931394 spots for SRR1931640/SRR1931640.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:07 35931394 reads; of these: 35931394 (100.00%) were unpaired; of these: 1459810 (4.06%) aligned 0 times 24817311 (69.07%) aligned exactly 1 time 9654273 (26.87%) aligned >1 times 95.94% overall alignment rate Time searching: 00:10:08 Overall time: 00:10:08 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] 7828015 / 34471584 = 0.2271 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 23:14:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.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 23:14:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:14:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:14:18: 1000000 INFO @ Sun, 21 Jun 2020 23:14:25: 2000000 INFO @ Sun, 21 Jun 2020 23:14:32: 3000000 INFO @ Sun, 21 Jun 2020 23:14:39: 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 23:14:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.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 23:14:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:14:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:14:46: 5000000 INFO @ Sun, 21 Jun 2020 23:14:48: 1000000 INFO @ Sun, 21 Jun 2020 23:14:54: 6000000 INFO @ Sun, 21 Jun 2020 23:14:55: 2000000 INFO @ Sun, 21 Jun 2020 23:15:01: 7000000 INFO @ Sun, 21 Jun 2020 23:15:01: 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 23:15:09: 4000000 INFO @ Sun, 21 Jun 2020 23:15:09: 8000000 INFO @ Sun, 21 Jun 2020 23:15:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.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 23:15:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:15:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:15:16: 5000000 INFO @ Sun, 21 Jun 2020 23:15:17: 9000000 INFO @ Sun, 21 Jun 2020 23:15:18: 1000000 INFO @ Sun, 21 Jun 2020 23:15:24: 6000000 INFO @ Sun, 21 Jun 2020 23:15:24: 2000000 INFO @ Sun, 21 Jun 2020 23:15:25: 10000000 INFO @ Sun, 21 Jun 2020 23:15:31: 7000000 INFO @ Sun, 21 Jun 2020 23:15:31: 3000000 INFO @ Sun, 21 Jun 2020 23:15:32: 11000000 INFO @ Sun, 21 Jun 2020 23:15:38: 4000000 INFO @ Sun, 21 Jun 2020 23:15:39: 8000000 INFO @ Sun, 21 Jun 2020 23:15:40: 12000000 INFO @ Sun, 21 Jun 2020 23:15:45: 5000000 INFO @ Sun, 21 Jun 2020 23:15:46: 9000000 INFO @ Sun, 21 Jun 2020 23:15:47: 13000000 INFO @ Sun, 21 Jun 2020 23:15:52: 6000000 INFO @ Sun, 21 Jun 2020 23:15:53: 10000000 INFO @ Sun, 21 Jun 2020 23:15:55: 14000000 INFO @ Sun, 21 Jun 2020 23:15:59: 7000000 INFO @ Sun, 21 Jun 2020 23:16:01: 11000000 INFO @ Sun, 21 Jun 2020 23:16:02: 15000000 INFO @ Sun, 21 Jun 2020 23:16:06: 8000000 INFO @ Sun, 21 Jun 2020 23:16:08: 12000000 INFO @ Sun, 21 Jun 2020 23:16:09: 16000000 INFO @ Sun, 21 Jun 2020 23:16:13: 9000000 INFO @ Sun, 21 Jun 2020 23:16:15: 13000000 INFO @ Sun, 21 Jun 2020 23:16:17: 17000000 INFO @ Sun, 21 Jun 2020 23:16:20: 10000000 INFO @ Sun, 21 Jun 2020 23:16:23: 14000000 INFO @ Sun, 21 Jun 2020 23:16:24: 18000000 INFO @ Sun, 21 Jun 2020 23:16:26: 11000000 INFO @ Sun, 21 Jun 2020 23:16:30: 15000000 INFO @ Sun, 21 Jun 2020 23:16:32: 19000000 INFO @ Sun, 21 Jun 2020 23:16:33: 12000000 INFO @ Sun, 21 Jun 2020 23:16:37: 16000000 INFO @ Sun, 21 Jun 2020 23:16:39: 20000000 INFO @ Sun, 21 Jun 2020 23:16:40: 13000000 INFO @ Sun, 21 Jun 2020 23:16:45: 17000000 INFO @ Sun, 21 Jun 2020 23:16:46: 21000000 INFO @ Sun, 21 Jun 2020 23:16:47: 14000000 INFO @ Sun, 21 Jun 2020 23:16:52: 18000000 INFO @ Sun, 21 Jun 2020 23:16:54: 15000000 INFO @ Sun, 21 Jun 2020 23:16:54: 22000000 INFO @ Sun, 21 Jun 2020 23:16:59: 19000000 INFO @ Sun, 21 Jun 2020 23:17:01: 16000000 INFO @ Sun, 21 Jun 2020 23:17:01: 23000000 INFO @ Sun, 21 Jun 2020 23:17:06: 20000000 INFO @ Sun, 21 Jun 2020 23:17:08: 17000000 INFO @ Sun, 21 Jun 2020 23:17:08: 24000000 INFO @ Sun, 21 Jun 2020 23:17:14: 21000000 INFO @ Sun, 21 Jun 2020 23:17:15: 18000000 INFO @ Sun, 21 Jun 2020 23:17:15: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 23:17:21: 19000000 INFO @ Sun, 21 Jun 2020 23:17:21: 22000000 INFO @ Sun, 21 Jun 2020 23:17:23: 26000000 INFO @ Sun, 21 Jun 2020 23:17:27: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 23:17:27: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 23:17:27: #1 total tags in treatment: 26643569 INFO @ Sun, 21 Jun 2020 23:17:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:17:27: #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 23:17:28: #1 tags after filtering in treatment: 26643569 INFO @ Sun, 21 Jun 2020 23:17:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:17:28: #1 finished! INFO @ Sun, 21 Jun 2020 23:17:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:17:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:17:28: 20000000 INFO @ Sun, 21 Jun 2020 23:17:28: 23000000 INFO @ Sun, 21 Jun 2020 23:17:30: #2 number of paired peaks: 394 WARNING @ Sun, 21 Jun 2020 23:17:30: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Sun, 21 Jun 2020 23:17:30: start model_add_line... INFO @ Sun, 21 Jun 2020 23:17:30: start X-correlation... INFO @ Sun, 21 Jun 2020 23:17:30: end of X-cor INFO @ Sun, 21 Jun 2020 23:17:30: #2 finished! INFO @ Sun, 21 Jun 2020 23:17:30: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 23:17:30: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 21 Jun 2020 23:17:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.05_model.r WARNING @ Sun, 21 Jun 2020 23:17:30: #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 23:17:30: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 21 Jun 2020 23:17:30: #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 23:17:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:17:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:17:35: 24000000 INFO @ Sun, 21 Jun 2020 23:17:35: 21000000 INFO @ Sun, 21 Jun 2020 23:17:42: 25000000 INFO @ Sun, 21 Jun 2020 23:17:42: 22000000 INFO @ Sun, 21 Jun 2020 23:17:49: 26000000 INFO @ Sun, 21 Jun 2020 23:17:50: 23000000 INFO @ Sun, 21 Jun 2020 23:17:54: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 23:17:54: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 23:17:54: #1 total tags in treatment: 26643569 INFO @ Sun, 21 Jun 2020 23:17:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:17:54: #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 23:17:55: #1 tags after filtering in treatment: 26643569 INFO @ Sun, 21 Jun 2020 23:17:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:17:55: #1 finished! INFO @ Sun, 21 Jun 2020 23:17:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:17:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:17:57: #2 number of paired peaks: 394 WARNING @ Sun, 21 Jun 2020 23:17:57: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Sun, 21 Jun 2020 23:17:57: start model_add_line... INFO @ Sun, 21 Jun 2020 23:17:57: start X-correlation... INFO @ Sun, 21 Jun 2020 23:17:57: end of X-cor INFO @ Sun, 21 Jun 2020 23:17:57: #2 finished! INFO @ Sun, 21 Jun 2020 23:17:57: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 23:17:57: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 21 Jun 2020 23:17:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.10_model.r WARNING @ Sun, 21 Jun 2020 23:17:57: #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 23:17:57: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 21 Jun 2020 23:17:57: #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 23:17:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:17:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:17:57: 24000000 INFO @ Sun, 21 Jun 2020 23:18:04: 25000000 INFO @ Sun, 21 Jun 2020 23:18:10: 26000000 INFO @ Sun, 21 Jun 2020 23:18:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:18:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 23:18:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 23:18:14: #1 total tags in treatment: 26643569 INFO @ Sun, 21 Jun 2020 23:18:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:18:14: #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 23:18:15: #1 tags after filtering in treatment: 26643569 INFO @ Sun, 21 Jun 2020 23:18:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:18:15: #1 finished! INFO @ Sun, 21 Jun 2020 23:18:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:18:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:18:17: #2 number of paired peaks: 394 WARNING @ Sun, 21 Jun 2020 23:18:17: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Sun, 21 Jun 2020 23:18:17: start model_add_line... INFO @ Sun, 21 Jun 2020 23:18:17: start X-correlation... INFO @ Sun, 21 Jun 2020 23:18:17: end of X-cor INFO @ Sun, 21 Jun 2020 23:18:17: #2 finished! INFO @ Sun, 21 Jun 2020 23:18:17: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 23:18:17: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 21 Jun 2020 23:18:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.20_model.r WARNING @ Sun, 21 Jun 2020 23:18:17: #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 23:18:17: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 21 Jun 2020 23:18:17: #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 23:18:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:18:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 23:18:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.05_peaks.xls INFO @ Sun, 21 Jun 2020 23:18:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:18:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.05_summits.bed INFO @ Sun, 21 Jun 2020 23:18:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:18:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:18:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:18:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.10_peaks.xls INFO @ Sun, 21 Jun 2020 23:18:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:18:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.10_summits.bed INFO @ Sun, 21 Jun 2020 23:18:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:19:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:19:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:19:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969924/SRX969924.20_summits.bed INFO @ Sun, 21 Jun 2020 23:19:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling