Job ID = 14167400 SRX = SRX9717951 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: 00:17:24 54090415 reads; of these: 54090415 (100.00%) were unpaired; of these: 14088915 (26.05%) aligned 0 times 29354885 (54.27%) aligned exactly 1 time 10646615 (19.68%) aligned >1 times 73.95% overall alignment rate Time searching: 00:17:24 Overall time: 00:17:24 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 20 files... [bam_rmdupse_core] 19834591 / 40001500 = 0.4958 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 12:35:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.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 @ Fri, 10 Dec 2021 12:35:00: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:35:00: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:35:06: 1000000 INFO @ Fri, 10 Dec 2021 12:35:11: 2000000 INFO @ Fri, 10 Dec 2021 12:35:16: 3000000 INFO @ Fri, 10 Dec 2021 12:35:22: 4000000 INFO @ Fri, 10 Dec 2021 12:35:27: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 12:35:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.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 @ Fri, 10 Dec 2021 12:35:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:35:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:35:32: 6000000 INFO @ Fri, 10 Dec 2021 12:35:36: 1000000 INFO @ Fri, 10 Dec 2021 12:35:37: 7000000 INFO @ Fri, 10 Dec 2021 12:35:41: 2000000 INFO @ Fri, 10 Dec 2021 12:35:43: 8000000 INFO @ Fri, 10 Dec 2021 12:35:46: 3000000 INFO @ Fri, 10 Dec 2021 12:35:48: 9000000 INFO @ Fri, 10 Dec 2021 12:35:51: 4000000 INFO @ Fri, 10 Dec 2021 12:35:53: 10000000 INFO @ Fri, 10 Dec 2021 12:35:56: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 12:35:58: 11000000 INFO @ Fri, 10 Dec 2021 12:36:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.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 @ Fri, 10 Dec 2021 12:36:00: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:36:00: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:36:02: 6000000 INFO @ Fri, 10 Dec 2021 12:36:04: 12000000 INFO @ Fri, 10 Dec 2021 12:36:07: 1000000 INFO @ Fri, 10 Dec 2021 12:36:07: 7000000 INFO @ Fri, 10 Dec 2021 12:36:10: 13000000 INFO @ Fri, 10 Dec 2021 12:36:12: 8000000 INFO @ Fri, 10 Dec 2021 12:36:13: 2000000 INFO @ Fri, 10 Dec 2021 12:36:16: 14000000 INFO @ Fri, 10 Dec 2021 12:36:17: 9000000 INFO @ Fri, 10 Dec 2021 12:36:19: 3000000 INFO @ Fri, 10 Dec 2021 12:36:22: 15000000 INFO @ Fri, 10 Dec 2021 12:36:22: 10000000 INFO @ Fri, 10 Dec 2021 12:36:25: 4000000 INFO @ Fri, 10 Dec 2021 12:36:27: 11000000 INFO @ Fri, 10 Dec 2021 12:36:28: 16000000 INFO @ Fri, 10 Dec 2021 12:36:31: 5000000 INFO @ Fri, 10 Dec 2021 12:36:33: 12000000 INFO @ Fri, 10 Dec 2021 12:36:35: 17000000 INFO @ Fri, 10 Dec 2021 12:36:37: 6000000 INFO @ Fri, 10 Dec 2021 12:36:38: 13000000 INFO @ Fri, 10 Dec 2021 12:36:41: 18000000 INFO @ Fri, 10 Dec 2021 12:36:43: 7000000 INFO @ Fri, 10 Dec 2021 12:36:43: 14000000 INFO @ Fri, 10 Dec 2021 12:36:47: 19000000 INFO @ Fri, 10 Dec 2021 12:36:48: 15000000 INFO @ Fri, 10 Dec 2021 12:36:49: 8000000 INFO @ Fri, 10 Dec 2021 12:36:53: 20000000 INFO @ Fri, 10 Dec 2021 12:36:53: 16000000 INFO @ Fri, 10 Dec 2021 12:36:54: 9000000 INFO @ Fri, 10 Dec 2021 12:36:54: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:36:54: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:36:54: #1 total tags in treatment: 20166909 INFO @ Fri, 10 Dec 2021 12:36:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:36:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:36:55: #1 tags after filtering in treatment: 20166908 INFO @ Fri, 10 Dec 2021 12:36:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:36:55: #1 finished! INFO @ Fri, 10 Dec 2021 12:36:55: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:36:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:36:57: #2 number of paired peaks: 110 WARNING @ Fri, 10 Dec 2021 12:36:57: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Fri, 10 Dec 2021 12:36:57: start model_add_line... INFO @ Fri, 10 Dec 2021 12:36:57: start X-correlation... INFO @ Fri, 10 Dec 2021 12:36:57: end of X-cor INFO @ Fri, 10 Dec 2021 12:36:57: #2 finished! INFO @ Fri, 10 Dec 2021 12:36:57: #2 predicted fragment length is 3 bps INFO @ Fri, 10 Dec 2021 12:36:57: #2 alternative fragment length(s) may be 3,42,514,547,573,588,593 bps INFO @ Fri, 10 Dec 2021 12:36:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.05_model.r WARNING @ Fri, 10 Dec 2021 12:36:57: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:36:57: #2 You may need to consider one of the other alternative d(s): 3,42,514,547,573,588,593 WARNING @ Fri, 10 Dec 2021 12:36:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:36:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:36:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:36:59: 17000000 INFO @ Fri, 10 Dec 2021 12:37:00: 10000000 INFO @ Fri, 10 Dec 2021 12:37:04: 18000000 INFO @ Fri, 10 Dec 2021 12:37:05: 11000000 INFO @ Fri, 10 Dec 2021 12:37:09: 19000000 INFO @ Fri, 10 Dec 2021 12:37:10: 12000000 INFO @ Fri, 10 Dec 2021 12:37:15: 20000000 INFO @ Fri, 10 Dec 2021 12:37:16: 13000000 INFO @ Fri, 10 Dec 2021 12:37:16: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:37:16: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:37:16: #1 total tags in treatment: 20166909 INFO @ Fri, 10 Dec 2021 12:37:16: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:37:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:37:17: #1 tags after filtering in treatment: 20166908 INFO @ Fri, 10 Dec 2021 12:37:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:37:17: #1 finished! INFO @ Fri, 10 Dec 2021 12:37:17: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:37:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:37:18: #2 number of paired peaks: 110 WARNING @ Fri, 10 Dec 2021 12:37:18: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Fri, 10 Dec 2021 12:37:18: start model_add_line... INFO @ Fri, 10 Dec 2021 12:37:18: start X-correlation... INFO @ Fri, 10 Dec 2021 12:37:18: end of X-cor INFO @ Fri, 10 Dec 2021 12:37:18: #2 finished! INFO @ Fri, 10 Dec 2021 12:37:18: #2 predicted fragment length is 3 bps INFO @ Fri, 10 Dec 2021 12:37:18: #2 alternative fragment length(s) may be 3,42,514,547,573,588,593 bps INFO @ Fri, 10 Dec 2021 12:37:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.10_model.r WARNING @ Fri, 10 Dec 2021 12:37:18: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:37:18: #2 You may need to consider one of the other alternative d(s): 3,42,514,547,573,588,593 WARNING @ Fri, 10 Dec 2021 12:37:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:37:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:37:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:37:21: 14000000 INFO @ Fri, 10 Dec 2021 12:37:26: 15000000 INFO @ Fri, 10 Dec 2021 12:37:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:37:31: 16000000 INFO @ Fri, 10 Dec 2021 12:37:37: 17000000 INFO @ Fri, 10 Dec 2021 12:37:42: 18000000 INFO @ Fri, 10 Dec 2021 12:37:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:37:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:37:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.05_summits.bed INFO @ Fri, 10 Dec 2021 12:37:47: Done! INFO @ Fri, 10 Dec 2021 12:37:48: 19000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:37:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:37:53: 20000000 INFO @ Fri, 10 Dec 2021 12:37:54: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:37:54: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:37:54: #1 total tags in treatment: 20166909 INFO @ Fri, 10 Dec 2021 12:37:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:37:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:37:55: #1 tags after filtering in treatment: 20166908 INFO @ Fri, 10 Dec 2021 12:37:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:37:55: #1 finished! INFO @ Fri, 10 Dec 2021 12:37:55: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:37:55: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:37:57: #2 number of paired peaks: 110 WARNING @ Fri, 10 Dec 2021 12:37:57: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Fri, 10 Dec 2021 12:37:57: start model_add_line... INFO @ Fri, 10 Dec 2021 12:37:57: start X-correlation... INFO @ Fri, 10 Dec 2021 12:37:57: end of X-cor INFO @ Fri, 10 Dec 2021 12:37:57: #2 finished! INFO @ Fri, 10 Dec 2021 12:37:57: #2 predicted fragment length is 3 bps INFO @ Fri, 10 Dec 2021 12:37:57: #2 alternative fragment length(s) may be 3,42,514,547,573,588,593 bps INFO @ Fri, 10 Dec 2021 12:37:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.20_model.r WARNING @ Fri, 10 Dec 2021 12:37:57: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:37:57: #2 You may need to consider one of the other alternative d(s): 3,42,514,547,573,588,593 WARNING @ Fri, 10 Dec 2021 12:37:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:37:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:37:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:38:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:38:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:38:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.10_summits.bed INFO @ Fri, 10 Dec 2021 12:38:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:38:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:38:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:38:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:38:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9717951/SRX9717951.20_summits.bed INFO @ Fri, 10 Dec 2021 12:38:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。