Job ID = 16439511 SRX = SRX13227894 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:13:58 36266588 reads; of these: 36266588 (100.00%) were unpaired; of these: 1227644 (3.39%) aligned 0 times 25205809 (69.50%) aligned exactly 1 time 9833135 (27.11%) aligned >1 times 96.61% overall alignment rate Time searching: 00:13:58 Overall time: 00:13:58 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] 5912942 / 35038944 = 0.1688 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:49:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.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 @ Tue, 02 Aug 2022 15:49:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:49:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:49:26: 1000000 INFO @ Tue, 02 Aug 2022 15:49:33: 2000000 INFO @ Tue, 02 Aug 2022 15:49:40: 3000000 INFO @ Tue, 02 Aug 2022 15:49:46: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:49:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.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 @ Tue, 02 Aug 2022 15:49:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:49:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:49:53: 5000000 INFO @ Tue, 02 Aug 2022 15:49:56: 1000000 INFO @ Tue, 02 Aug 2022 15:49:59: 6000000 INFO @ Tue, 02 Aug 2022 15:50:02: 2000000 INFO @ Tue, 02 Aug 2022 15:50:06: 7000000 INFO @ Tue, 02 Aug 2022 15:50:09: 3000000 INFO @ Tue, 02 Aug 2022 15:50:12: 8000000 INFO @ Tue, 02 Aug 2022 15:50:16: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:50:18: 9000000 INFO @ Tue, 02 Aug 2022 15:50:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.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 @ Tue, 02 Aug 2022 15:50:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:50:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:50:22: 5000000 INFO @ Tue, 02 Aug 2022 15:50:25: 10000000 INFO @ Tue, 02 Aug 2022 15:50:26: 1000000 INFO @ Tue, 02 Aug 2022 15:50:29: 6000000 INFO @ Tue, 02 Aug 2022 15:50:31: 11000000 INFO @ Tue, 02 Aug 2022 15:50:32: 2000000 INFO @ Tue, 02 Aug 2022 15:50:36: 7000000 INFO @ Tue, 02 Aug 2022 15:50:37: 12000000 INFO @ Tue, 02 Aug 2022 15:50:38: 3000000 INFO @ Tue, 02 Aug 2022 15:50:43: 8000000 INFO @ Tue, 02 Aug 2022 15:50:44: 13000000 INFO @ Tue, 02 Aug 2022 15:50:44: 4000000 INFO @ Tue, 02 Aug 2022 15:50:49: 9000000 INFO @ Tue, 02 Aug 2022 15:50:50: 14000000 INFO @ Tue, 02 Aug 2022 15:50:50: 5000000 INFO @ Tue, 02 Aug 2022 15:50:56: 10000000 INFO @ Tue, 02 Aug 2022 15:50:56: 15000000 INFO @ Tue, 02 Aug 2022 15:50:56: 6000000 INFO @ Tue, 02 Aug 2022 15:51:02: 16000000 INFO @ Tue, 02 Aug 2022 15:51:02: 11000000 INFO @ Tue, 02 Aug 2022 15:51:02: 7000000 INFO @ Tue, 02 Aug 2022 15:51:08: 17000000 INFO @ Tue, 02 Aug 2022 15:51:08: 8000000 INFO @ Tue, 02 Aug 2022 15:51:09: 12000000 INFO @ Tue, 02 Aug 2022 15:51:14: 18000000 INFO @ Tue, 02 Aug 2022 15:51:14: 9000000 INFO @ Tue, 02 Aug 2022 15:51:15: 13000000 INFO @ Tue, 02 Aug 2022 15:51:20: 19000000 INFO @ Tue, 02 Aug 2022 15:51:20: 10000000 INFO @ Tue, 02 Aug 2022 15:51:22: 14000000 INFO @ Tue, 02 Aug 2022 15:51:26: 20000000 INFO @ Tue, 02 Aug 2022 15:51:26: 11000000 INFO @ Tue, 02 Aug 2022 15:51:28: 15000000 INFO @ Tue, 02 Aug 2022 15:51:32: 21000000 INFO @ Tue, 02 Aug 2022 15:51:32: 12000000 INFO @ Tue, 02 Aug 2022 15:51:35: 16000000 INFO @ Tue, 02 Aug 2022 15:51:38: 22000000 INFO @ Tue, 02 Aug 2022 15:51:38: 13000000 INFO @ Tue, 02 Aug 2022 15:51:41: 17000000 INFO @ Tue, 02 Aug 2022 15:51:44: 23000000 INFO @ Tue, 02 Aug 2022 15:51:44: 14000000 INFO @ Tue, 02 Aug 2022 15:51:48: 18000000 INFO @ Tue, 02 Aug 2022 15:51:50: 15000000 INFO @ Tue, 02 Aug 2022 15:51:50: 24000000 INFO @ Tue, 02 Aug 2022 15:51:55: 19000000 INFO @ Tue, 02 Aug 2022 15:51:56: 16000000 INFO @ Tue, 02 Aug 2022 15:51:56: 25000000 INFO @ Tue, 02 Aug 2022 15:52:01: 20000000 INFO @ Tue, 02 Aug 2022 15:52:02: 17000000 INFO @ Tue, 02 Aug 2022 15:52:02: 26000000 INFO @ Tue, 02 Aug 2022 15:52:08: 18000000 INFO @ Tue, 02 Aug 2022 15:52:08: 21000000 INFO @ Tue, 02 Aug 2022 15:52:08: 27000000 INFO @ Tue, 02 Aug 2022 15:52:13: 19000000 INFO @ Tue, 02 Aug 2022 15:52:14: 28000000 INFO @ Tue, 02 Aug 2022 15:52:15: 22000000 INFO @ Tue, 02 Aug 2022 15:52:19: 20000000 INFO @ Tue, 02 Aug 2022 15:52:20: 29000000 INFO @ Tue, 02 Aug 2022 15:52:21: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:52:21: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:52:21: #1 total tags in treatment: 29126002 INFO @ Tue, 02 Aug 2022 15:52:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:52:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:52:22: 23000000 INFO @ Tue, 02 Aug 2022 15:52:22: #1 tags after filtering in treatment: 29126002 INFO @ Tue, 02 Aug 2022 15:52:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:52:22: #1 finished! INFO @ Tue, 02 Aug 2022 15:52:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:52:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:52:24: #2 number of paired peaks: 237 WARNING @ Tue, 02 Aug 2022 15:52:24: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Tue, 02 Aug 2022 15:52:24: start model_add_line... INFO @ Tue, 02 Aug 2022 15:52:24: start X-correlation... INFO @ Tue, 02 Aug 2022 15:52:24: end of X-cor INFO @ Tue, 02 Aug 2022 15:52:24: #2 finished! INFO @ Tue, 02 Aug 2022 15:52:24: #2 predicted fragment length is 2 bps INFO @ Tue, 02 Aug 2022 15:52:24: #2 alternative fragment length(s) may be 2,35,588 bps INFO @ Tue, 02 Aug 2022 15:52:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.05_model.r WARNING @ Tue, 02 Aug 2022 15:52:24: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:52:24: #2 You may need to consider one of the other alternative d(s): 2,35,588 WARNING @ Tue, 02 Aug 2022 15:52:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:52:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:52:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:52:25: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:52:29: 24000000 INFO @ Tue, 02 Aug 2022 15:52:31: 22000000 INFO @ Tue, 02 Aug 2022 15:52:36: 25000000 INFO @ Tue, 02 Aug 2022 15:52:37: 23000000 INFO @ Tue, 02 Aug 2022 15:52:43: 26000000 INFO @ Tue, 02 Aug 2022 15:52:43: 24000000 INFO @ Tue, 02 Aug 2022 15:52:49: 25000000 INFO @ Tue, 02 Aug 2022 15:52:50: 27000000 INFO @ Tue, 02 Aug 2022 15:52:55: 26000000 INFO @ Tue, 02 Aug 2022 15:52:57: 28000000 INFO @ Tue, 02 Aug 2022 15:53:01: 27000000 INFO @ Tue, 02 Aug 2022 15:53:04: 29000000 INFO @ Tue, 02 Aug 2022 15:53:05: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:53:05: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:53:05: #1 total tags in treatment: 29126002 INFO @ Tue, 02 Aug 2022 15:53:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:53:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:53:05: #1 tags after filtering in treatment: 29126002 INFO @ Tue, 02 Aug 2022 15:53:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:53:05: #1 finished! INFO @ Tue, 02 Aug 2022 15:53:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:53:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:53:07: 28000000 INFO @ Tue, 02 Aug 2022 15:53:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:53:07: #2 number of paired peaks: 237 WARNING @ Tue, 02 Aug 2022 15:53:07: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Tue, 02 Aug 2022 15:53:07: start model_add_line... INFO @ Tue, 02 Aug 2022 15:53:07: start X-correlation... INFO @ Tue, 02 Aug 2022 15:53:07: end of X-cor INFO @ Tue, 02 Aug 2022 15:53:07: #2 finished! INFO @ Tue, 02 Aug 2022 15:53:07: #2 predicted fragment length is 2 bps INFO @ Tue, 02 Aug 2022 15:53:07: #2 alternative fragment length(s) may be 2,35,588 bps INFO @ Tue, 02 Aug 2022 15:53:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.10_model.r WARNING @ Tue, 02 Aug 2022 15:53:07: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:53:07: #2 You may need to consider one of the other alternative d(s): 2,35,588 WARNING @ Tue, 02 Aug 2022 15:53:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:53:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:53:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:53:12: 29000000 INFO @ Tue, 02 Aug 2022 15:53:13: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:53:13: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:53:13: #1 total tags in treatment: 29126002 INFO @ Tue, 02 Aug 2022 15:53:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:53:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:53:14: #1 tags after filtering in treatment: 29126002 INFO @ Tue, 02 Aug 2022 15:53:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:53:14: #1 finished! INFO @ Tue, 02 Aug 2022 15:53:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:53:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:53:16: #2 number of paired peaks: 237 WARNING @ Tue, 02 Aug 2022 15:53:16: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Tue, 02 Aug 2022 15:53:16: start model_add_line... INFO @ Tue, 02 Aug 2022 15:53:16: start X-correlation... INFO @ Tue, 02 Aug 2022 15:53:16: end of X-cor INFO @ Tue, 02 Aug 2022 15:53:16: #2 finished! INFO @ Tue, 02 Aug 2022 15:53:16: #2 predicted fragment length is 2 bps INFO @ Tue, 02 Aug 2022 15:53:16: #2 alternative fragment length(s) may be 2,35,588 bps INFO @ Tue, 02 Aug 2022 15:53:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.20_model.r WARNING @ Tue, 02 Aug 2022 15:53:16: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:53:16: #2 You may need to consider one of the other alternative d(s): 2,35,588 WARNING @ Tue, 02 Aug 2022 15:53:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:53:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:53:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:53:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:53:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:53:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.05_summits.bed INFO @ Tue, 02 Aug 2022 15:53:28: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:53:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:54:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:54:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:54:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:54:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.10_summits.bed INFO @ Tue, 02 Aug 2022 15:54:11: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:54:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:54:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:54:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227894/SRX13227894.20_summits.bed INFO @ Tue, 02 Aug 2022 15:54:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling