Job ID = 10165796 SRX = SRX2765812 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 40869305 spots for SRR5482399/SRR5482399.sra Written 40869305 spots for SRR5482399/SRR5482399.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166200 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:37 40869305 reads; of these: 40869305 (100.00%) were unpaired; of these: 2612405 (6.39%) aligned 0 times 24316767 (59.50%) aligned exactly 1 time 13940133 (34.11%) aligned >1 times 93.61% overall alignment rate Time searching: 00:14:38 Overall time: 00:14:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 7917318 / 38256900 = 0.2070 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 @ Thu, 08 Oct 2020 20:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.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 @ Thu, 08 Oct 2020 20:18:37: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:18:37: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:18:42: 1000000 INFO @ Thu, 08 Oct 2020 20:18:47: 2000000 INFO @ Thu, 08 Oct 2020 20:18:52: 3000000 INFO @ Thu, 08 Oct 2020 20:18:57: 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 @ Thu, 08 Oct 2020 20:19:03: 5000000 INFO @ Thu, 08 Oct 2020 20:19:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.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 @ Thu, 08 Oct 2020 20:19:04: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:19:04: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:19:08: 6000000 INFO @ Thu, 08 Oct 2020 20:19:10: 1000000 INFO @ Thu, 08 Oct 2020 20:19:14: 7000000 INFO @ Thu, 08 Oct 2020 20:19:15: 2000000 INFO @ Thu, 08 Oct 2020 20:19:19: 8000000 INFO @ Thu, 08 Oct 2020 20:19:21: 3000000 INFO @ Thu, 08 Oct 2020 20:19:25: 9000000 INFO @ Thu, 08 Oct 2020 20:19:26: 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 @ Thu, 08 Oct 2020 20:19:31: 10000000 INFO @ Thu, 08 Oct 2020 20:19:32: 5000000 INFO @ Thu, 08 Oct 2020 20:19:36: 11000000 INFO @ Thu, 08 Oct 2020 20:19:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.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 @ Thu, 08 Oct 2020 20:19:37: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:19:37: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:19:37: 6000000 INFO @ Thu, 08 Oct 2020 20:19:41: 12000000 INFO @ Thu, 08 Oct 2020 20:19:43: 1000000 INFO @ Thu, 08 Oct 2020 20:19:43: 7000000 INFO @ Thu, 08 Oct 2020 20:19:47: 13000000 INFO @ Thu, 08 Oct 2020 20:19:48: 2000000 INFO @ Thu, 08 Oct 2020 20:19:48: 8000000 INFO @ Thu, 08 Oct 2020 20:19:53: 14000000 INFO @ Thu, 08 Oct 2020 20:19:54: 3000000 INFO @ Thu, 08 Oct 2020 20:19:54: 9000000 INFO @ Thu, 08 Oct 2020 20:19:58: 15000000 INFO @ Thu, 08 Oct 2020 20:19:59: 4000000 INFO @ Thu, 08 Oct 2020 20:20:00: 10000000 INFO @ Thu, 08 Oct 2020 20:20:04: 16000000 INFO @ Thu, 08 Oct 2020 20:20:05: 5000000 INFO @ Thu, 08 Oct 2020 20:20:05: 11000000 INFO @ Thu, 08 Oct 2020 20:20:09: 17000000 INFO @ Thu, 08 Oct 2020 20:20:10: 6000000 INFO @ Thu, 08 Oct 2020 20:20:11: 12000000 INFO @ Thu, 08 Oct 2020 20:20:15: 18000000 INFO @ Thu, 08 Oct 2020 20:20:15: 7000000 INFO @ Thu, 08 Oct 2020 20:20:16: 13000000 INFO @ Thu, 08 Oct 2020 20:20:20: 19000000 INFO @ Thu, 08 Oct 2020 20:20:21: 8000000 INFO @ Thu, 08 Oct 2020 20:20:22: 14000000 INFO @ Thu, 08 Oct 2020 20:20:26: 20000000 INFO @ Thu, 08 Oct 2020 20:20:26: 9000000 INFO @ Thu, 08 Oct 2020 20:20:28: 15000000 INFO @ Thu, 08 Oct 2020 20:20:31: 21000000 INFO @ Thu, 08 Oct 2020 20:20:32: 10000000 INFO @ Thu, 08 Oct 2020 20:20:33: 16000000 INFO @ Thu, 08 Oct 2020 20:20:37: 22000000 INFO @ Thu, 08 Oct 2020 20:20:37: 11000000 INFO @ Thu, 08 Oct 2020 20:20:39: 17000000 INFO @ Thu, 08 Oct 2020 20:20:42: 23000000 INFO @ Thu, 08 Oct 2020 20:20:43: 12000000 INFO @ Thu, 08 Oct 2020 20:20:44: 18000000 INFO @ Thu, 08 Oct 2020 20:20:48: 24000000 INFO @ Thu, 08 Oct 2020 20:20:48: 13000000 INFO @ Thu, 08 Oct 2020 20:20:50: 19000000 INFO @ Thu, 08 Oct 2020 20:20:53: 25000000 INFO @ Thu, 08 Oct 2020 20:20:54: 14000000 INFO @ Thu, 08 Oct 2020 20:20:55: 20000000 INFO @ Thu, 08 Oct 2020 20:20:59: 26000000 INFO @ Thu, 08 Oct 2020 20:20:59: 15000000 INFO @ Thu, 08 Oct 2020 20:21:01: 21000000 INFO @ Thu, 08 Oct 2020 20:21:04: 27000000 INFO @ Thu, 08 Oct 2020 20:21:05: 16000000 INFO @ Thu, 08 Oct 2020 20:21:07: 22000000 INFO @ Thu, 08 Oct 2020 20:21:10: 28000000 INFO @ Thu, 08 Oct 2020 20:21:10: 17000000 INFO @ Thu, 08 Oct 2020 20:21:12: 23000000 INFO @ Thu, 08 Oct 2020 20:21:15: 29000000 INFO @ Thu, 08 Oct 2020 20:21:16: 18000000 INFO @ Thu, 08 Oct 2020 20:21:18: 24000000 INFO @ Thu, 08 Oct 2020 20:21:21: 30000000 INFO @ Thu, 08 Oct 2020 20:21:22: 19000000 INFO @ Thu, 08 Oct 2020 20:21:23: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:21:23: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:21:23: #1 total tags in treatment: 30339582 INFO @ Thu, 08 Oct 2020 20:21:23: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:21:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:21:23: #1 tags after filtering in treatment: 30339582 INFO @ Thu, 08 Oct 2020 20:21:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:21:23: #1 finished! INFO @ Thu, 08 Oct 2020 20:21:23: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:21:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:21:23: 25000000 INFO @ Thu, 08 Oct 2020 20:21:25: #2 number of paired peaks: 383 WARNING @ Thu, 08 Oct 2020 20:21:25: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Thu, 08 Oct 2020 20:21:25: start model_add_line... INFO @ Thu, 08 Oct 2020 20:21:25: start X-correlation... INFO @ Thu, 08 Oct 2020 20:21:25: end of X-cor INFO @ Thu, 08 Oct 2020 20:21:25: #2 finished! INFO @ Thu, 08 Oct 2020 20:21:25: #2 predicted fragment length is 2 bps INFO @ Thu, 08 Oct 2020 20:21:25: #2 alternative fragment length(s) may be 2,27,50,567 bps INFO @ Thu, 08 Oct 2020 20:21:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.05_model.r WARNING @ Thu, 08 Oct 2020 20:21:25: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:21:25: #2 You may need to consider one of the other alternative d(s): 2,27,50,567 WARNING @ Thu, 08 Oct 2020 20:21:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:21:25: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:21:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:21:27: 20000000 INFO @ Thu, 08 Oct 2020 20:21:29: 26000000 INFO @ Thu, 08 Oct 2020 20:21:33: 21000000 INFO @ Thu, 08 Oct 2020 20:21:35: 27000000 INFO @ Thu, 08 Oct 2020 20:21:38: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:21:40: 28000000 INFO @ Thu, 08 Oct 2020 20:21:44: 23000000 INFO @ Thu, 08 Oct 2020 20:21:46: 29000000 INFO @ Thu, 08 Oct 2020 20:21:49: 24000000 INFO @ Thu, 08 Oct 2020 20:21:51: 30000000 INFO @ Thu, 08 Oct 2020 20:21:53: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:21:53: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:21:53: #1 total tags in treatment: 30339582 INFO @ Thu, 08 Oct 2020 20:21:53: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:21:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:21:54: #1 tags after filtering in treatment: 30339582 INFO @ Thu, 08 Oct 2020 20:21:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:21:54: #1 finished! INFO @ Thu, 08 Oct 2020 20:21:54: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:21:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:21:54: 25000000 INFO @ Thu, 08 Oct 2020 20:21:56: #2 number of paired peaks: 383 WARNING @ Thu, 08 Oct 2020 20:21:56: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Thu, 08 Oct 2020 20:21:56: start model_add_line... INFO @ Thu, 08 Oct 2020 20:21:56: start X-correlation... INFO @ Thu, 08 Oct 2020 20:21:56: end of X-cor INFO @ Thu, 08 Oct 2020 20:21:56: #2 finished! INFO @ Thu, 08 Oct 2020 20:21:56: #2 predicted fragment length is 2 bps INFO @ Thu, 08 Oct 2020 20:21:56: #2 alternative fragment length(s) may be 2,27,50,567 bps INFO @ Thu, 08 Oct 2020 20:21:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.10_model.r WARNING @ Thu, 08 Oct 2020 20:21:56: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:21:56: #2 You may need to consider one of the other alternative d(s): 2,27,50,567 WARNING @ Thu, 08 Oct 2020 20:21:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:21:56: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:21:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:22:00: 26000000 INFO @ Thu, 08 Oct 2020 20:22:05: 27000000 INFO @ Thu, 08 Oct 2020 20:22:10: 28000000 INFO @ Thu, 08 Oct 2020 20:22:14: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:22:16: 29000000 INFO @ Thu, 08 Oct 2020 20:22:21: 30000000 INFO @ Thu, 08 Oct 2020 20:22:23: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:22:23: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:22:23: #1 total tags in treatment: 30339582 INFO @ Thu, 08 Oct 2020 20:22:23: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:22:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:22:24: #1 tags after filtering in treatment: 30339582 INFO @ Thu, 08 Oct 2020 20:22:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:22:24: #1 finished! INFO @ Thu, 08 Oct 2020 20:22:24: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:22:25: #2 number of paired peaks: 383 WARNING @ Thu, 08 Oct 2020 20:22:25: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Thu, 08 Oct 2020 20:22:25: start model_add_line... INFO @ Thu, 08 Oct 2020 20:22:26: start X-correlation... INFO @ Thu, 08 Oct 2020 20:22:26: end of X-cor INFO @ Thu, 08 Oct 2020 20:22:26: #2 finished! INFO @ Thu, 08 Oct 2020 20:22:26: #2 predicted fragment length is 2 bps INFO @ Thu, 08 Oct 2020 20:22:26: #2 alternative fragment length(s) may be 2,27,50,567 bps INFO @ Thu, 08 Oct 2020 20:22:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.20_model.r WARNING @ Thu, 08 Oct 2020 20:22:26: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:22:26: #2 You may need to consider one of the other alternative d(s): 2,27,50,567 WARNING @ Thu, 08 Oct 2020 20:22:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:22:26: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:22:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:22:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:22:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:22:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.05_summits.bed INFO @ Thu, 08 Oct 2020 20:22:37: Done! INFO @ Thu, 08 Oct 2020 20:22:45: #3 Call peaks for each chromosome... BigWig に変換しました。 pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:23:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:23:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:23:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.10_summits.bed INFO @ Thu, 08 Oct 2020 20:23:08: Done! INFO @ Thu, 08 Oct 2020 20:23:13: #3 Call peaks for each chromosome... pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:23:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:23:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:23:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2765812/SRX2765812.20_summits.bed INFO @ Thu, 08 Oct 2020 20:23:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling