Job ID = 6529299 SRX = SRX1361353 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: 00:09:56 29500321 reads; of these: 29500321 (100.00%) were unpaired; of these: 1937763 (6.57%) aligned 0 times 15013819 (50.89%) aligned exactly 1 time 12548739 (42.54%) aligned >1 times 93.43% overall alignment rate Time searching: 00:09:56 Overall time: 00:09:56 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 12 files... [bam_rmdupse_core] 7895850 / 27562558 = 0.2865 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 @ Tue, 30 Jun 2020 02:04:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.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, 30 Jun 2020 02:04:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:04:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:04:32: 1000000 INFO @ Tue, 30 Jun 2020 02:04:38: 2000000 INFO @ Tue, 30 Jun 2020 02:04:44: 3000000 INFO @ Tue, 30 Jun 2020 02:04:50: 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 @ Tue, 30 Jun 2020 02:04:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.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, 30 Jun 2020 02:04:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:04:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:04:56: 5000000 INFO @ Tue, 30 Jun 2020 02:05:02: 1000000 INFO @ Tue, 30 Jun 2020 02:05:03: 6000000 INFO @ Tue, 30 Jun 2020 02:05:08: 2000000 INFO @ Tue, 30 Jun 2020 02:05:09: 7000000 INFO @ Tue, 30 Jun 2020 02:05:15: 3000000 INFO @ Tue, 30 Jun 2020 02:05:16: 8000000 INFO @ Tue, 30 Jun 2020 02:05:21: 4000000 INFO @ Tue, 30 Jun 2020 02:05:23: 9000000 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 @ Tue, 30 Jun 2020 02:05:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.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, 30 Jun 2020 02:05:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:05:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:05:28: 5000000 INFO @ Tue, 30 Jun 2020 02:05:30: 10000000 INFO @ Tue, 30 Jun 2020 02:05:33: 1000000 INFO @ Tue, 30 Jun 2020 02:05:36: 6000000 INFO @ Tue, 30 Jun 2020 02:05:38: 11000000 INFO @ Tue, 30 Jun 2020 02:05:40: 2000000 INFO @ Tue, 30 Jun 2020 02:05:43: 7000000 INFO @ Tue, 30 Jun 2020 02:05:46: 12000000 INFO @ Tue, 30 Jun 2020 02:05:48: 3000000 INFO @ Tue, 30 Jun 2020 02:05:50: 8000000 INFO @ Tue, 30 Jun 2020 02:05:53: 13000000 INFO @ Tue, 30 Jun 2020 02:05:55: 4000000 INFO @ Tue, 30 Jun 2020 02:05:58: 9000000 INFO @ Tue, 30 Jun 2020 02:06:01: 14000000 INFO @ Tue, 30 Jun 2020 02:06:03: 5000000 INFO @ Tue, 30 Jun 2020 02:06:06: 10000000 INFO @ Tue, 30 Jun 2020 02:06:10: 15000000 INFO @ Tue, 30 Jun 2020 02:06:11: 6000000 INFO @ Tue, 30 Jun 2020 02:06:13: 11000000 INFO @ Tue, 30 Jun 2020 02:06:17: 16000000 INFO @ Tue, 30 Jun 2020 02:06:18: 7000000 INFO @ Tue, 30 Jun 2020 02:06:21: 12000000 INFO @ Tue, 30 Jun 2020 02:06:25: 17000000 INFO @ Tue, 30 Jun 2020 02:06:26: 8000000 INFO @ Tue, 30 Jun 2020 02:06:29: 13000000 INFO @ Tue, 30 Jun 2020 02:06:33: 18000000 INFO @ Tue, 30 Jun 2020 02:06:34: 9000000 INFO @ Tue, 30 Jun 2020 02:06:37: 14000000 INFO @ Tue, 30 Jun 2020 02:06:42: 19000000 INFO @ Tue, 30 Jun 2020 02:06:43: 10000000 INFO @ Tue, 30 Jun 2020 02:06:45: 15000000 INFO @ Tue, 30 Jun 2020 02:06:47: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:06:47: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:06:47: #1 total tags in treatment: 19666708 INFO @ Tue, 30 Jun 2020 02:06:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:06:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:06:48: #1 tags after filtering in treatment: 19666676 INFO @ Tue, 30 Jun 2020 02:06:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:06:48: #1 finished! INFO @ Tue, 30 Jun 2020 02:06:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:06:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:06:50: #2 number of paired peaks: 1777 INFO @ Tue, 30 Jun 2020 02:06:50: start model_add_line... INFO @ Tue, 30 Jun 2020 02:06:50: start X-correlation... INFO @ Tue, 30 Jun 2020 02:06:50: end of X-cor INFO @ Tue, 30 Jun 2020 02:06:50: #2 finished! INFO @ Tue, 30 Jun 2020 02:06:50: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:06:50: #2 alternative fragment length(s) may be 2,15,23 bps INFO @ Tue, 30 Jun 2020 02:06:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.05_model.r WARNING @ Tue, 30 Jun 2020 02:06:50: #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, 30 Jun 2020 02:06:50: #2 You may need to consider one of the other alternative d(s): 2,15,23 WARNING @ Tue, 30 Jun 2020 02:06:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:06:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:06:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:06:51: 11000000 INFO @ Tue, 30 Jun 2020 02:06:53: 16000000 INFO @ Tue, 30 Jun 2020 02:06:58: 12000000 INFO @ Tue, 30 Jun 2020 02:07:00: 17000000 INFO @ Tue, 30 Jun 2020 02:07:06: 13000000 INFO @ Tue, 30 Jun 2020 02:07:07: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:07:14: 14000000 INFO @ Tue, 30 Jun 2020 02:07:15: 19000000 INFO @ Tue, 30 Jun 2020 02:07:20: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:07:20: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:07:20: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:07:20: #1 total tags in treatment: 19666708 INFO @ Tue, 30 Jun 2020 02:07:20: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:07:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:07:21: #1 tags after filtering in treatment: 19666676 INFO @ Tue, 30 Jun 2020 02:07:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:07:21: #1 finished! INFO @ Tue, 30 Jun 2020 02:07:21: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:07:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:07:22: #2 number of paired peaks: 1777 INFO @ Tue, 30 Jun 2020 02:07:22: start model_add_line... INFO @ Tue, 30 Jun 2020 02:07:23: start X-correlation... INFO @ Tue, 30 Jun 2020 02:07:23: end of X-cor INFO @ Tue, 30 Jun 2020 02:07:23: #2 finished! INFO @ Tue, 30 Jun 2020 02:07:23: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:07:23: #2 alternative fragment length(s) may be 2,15,23 bps INFO @ Tue, 30 Jun 2020 02:07:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.10_model.r WARNING @ Tue, 30 Jun 2020 02:07:23: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:07:23: #2 You may need to consider one of the other alternative d(s): 2,15,23 WARNING @ Tue, 30 Jun 2020 02:07:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:07:23: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:07:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:07:23: 15000000 INFO @ Tue, 30 Jun 2020 02:07:30: 16000000 INFO @ Tue, 30 Jun 2020 02:07:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:07:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:07:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.05_summits.bed INFO @ Tue, 30 Jun 2020 02:07:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:07:37: 17000000 INFO @ Tue, 30 Jun 2020 02:07:45: 18000000 INFO @ Tue, 30 Jun 2020 02:07:52: 19000000 INFO @ Tue, 30 Jun 2020 02:07:53: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:07:57: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:07:57: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:07:57: #1 total tags in treatment: 19666708 INFO @ Tue, 30 Jun 2020 02:07:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:07:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:07:58: #1 tags after filtering in treatment: 19666676 INFO @ Tue, 30 Jun 2020 02:07:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:07:58: #1 finished! INFO @ Tue, 30 Jun 2020 02:07:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:07:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:07:59: #2 number of paired peaks: 1777 INFO @ Tue, 30 Jun 2020 02:07:59: start model_add_line... INFO @ Tue, 30 Jun 2020 02:07:59: start X-correlation... INFO @ Tue, 30 Jun 2020 02:07:59: end of X-cor INFO @ Tue, 30 Jun 2020 02:07:59: #2 finished! INFO @ Tue, 30 Jun 2020 02:07:59: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:07:59: #2 alternative fragment length(s) may be 2,15,23 bps INFO @ Tue, 30 Jun 2020 02:07:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.20_model.r WARNING @ Tue, 30 Jun 2020 02:08:00: #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, 30 Jun 2020 02:08:00: #2 You may need to consider one of the other alternative d(s): 2,15,23 WARNING @ Tue, 30 Jun 2020 02:08:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:08:00: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:08:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:08:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:08:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:08:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.10_summits.bed INFO @ Tue, 30 Jun 2020 02:08:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:08:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:08:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:08:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:08:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1361353/SRX1361353.20_summits.bed INFO @ Tue, 30 Jun 2020 02:08:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling