Job ID = 6529514 SRX = SRX287881 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: 00:06:53 22133183 reads; of these: 22133183 (100.00%) were unpaired; of these: 1385327 (6.26%) aligned 0 times 13961447 (63.08%) aligned exactly 1 time 6786409 (30.66%) aligned >1 times 93.74% overall alignment rate Time searching: 00:06:53 Overall time: 00:06:53 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] 4723400 / 20747856 = 0.2277 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 02:29:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.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 02:29:18: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:29:18: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:29:26: 1000000 INFO @ Tue, 30 Jun 2020 02:29:32: 2000000 INFO @ Tue, 30 Jun 2020 02:29:39: 3000000 INFO @ Tue, 30 Jun 2020 02:29:46: 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 02:29:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.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 02:29:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:29:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:29:54: 5000000 INFO @ Tue, 30 Jun 2020 02:29:56: 1000000 INFO @ Tue, 30 Jun 2020 02:30:01: 6000000 INFO @ Tue, 30 Jun 2020 02:30:04: 2000000 INFO @ Tue, 30 Jun 2020 02:30:09: 7000000 INFO @ Tue, 30 Jun 2020 02:30:12: 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 @ Tue, 30 Jun 2020 02:30:17: 8000000 INFO @ Tue, 30 Jun 2020 02:30:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.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 02:30:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:30:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:30:20: 4000000 INFO @ Tue, 30 Jun 2020 02:30:26: 9000000 INFO @ Tue, 30 Jun 2020 02:30:27: 1000000 INFO @ Tue, 30 Jun 2020 02:30:28: 5000000 INFO @ Tue, 30 Jun 2020 02:30:34: 10000000 INFO @ Tue, 30 Jun 2020 02:30:35: 2000000 INFO @ Tue, 30 Jun 2020 02:30:36: 6000000 INFO @ Tue, 30 Jun 2020 02:30:42: 11000000 INFO @ Tue, 30 Jun 2020 02:30:43: 3000000 INFO @ Tue, 30 Jun 2020 02:30:44: 7000000 INFO @ Tue, 30 Jun 2020 02:30:50: 12000000 INFO @ Tue, 30 Jun 2020 02:30:51: 4000000 INFO @ Tue, 30 Jun 2020 02:30:52: 8000000 INFO @ Tue, 30 Jun 2020 02:30:58: 13000000 INFO @ Tue, 30 Jun 2020 02:30:59: 5000000 INFO @ Tue, 30 Jun 2020 02:31:00: 9000000 INFO @ Tue, 30 Jun 2020 02:31:06: 14000000 INFO @ Tue, 30 Jun 2020 02:31:07: 6000000 INFO @ Tue, 30 Jun 2020 02:31:08: 10000000 INFO @ Tue, 30 Jun 2020 02:31:14: 15000000 INFO @ Tue, 30 Jun 2020 02:31:15: 7000000 INFO @ Tue, 30 Jun 2020 02:31:15: 11000000 INFO @ Tue, 30 Jun 2020 02:31:22: 16000000 INFO @ Tue, 30 Jun 2020 02:31:22: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:31:22: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:31:22: #1 total tags in treatment: 16024456 INFO @ Tue, 30 Jun 2020 02:31:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:31:22: #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 02:31:22: 8000000 INFO @ Tue, 30 Jun 2020 02:31:23: #1 tags after filtering in treatment: 16024456 INFO @ Tue, 30 Jun 2020 02:31:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:31:23: #1 finished! INFO @ Tue, 30 Jun 2020 02:31:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:31:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:31:23: 12000000 INFO @ Tue, 30 Jun 2020 02:31:24: #2 number of paired peaks: 715 WARNING @ Tue, 30 Jun 2020 02:31:24: Fewer paired peaks (715) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 715 pairs to build model! INFO @ Tue, 30 Jun 2020 02:31:24: start model_add_line... INFO @ Tue, 30 Jun 2020 02:31:24: start X-correlation... INFO @ Tue, 30 Jun 2020 02:31:24: end of X-cor INFO @ Tue, 30 Jun 2020 02:31:24: #2 finished! INFO @ Tue, 30 Jun 2020 02:31:24: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:31:24: #2 alternative fragment length(s) may be 2,37,577 bps INFO @ Tue, 30 Jun 2020 02:31:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.05_model.r WARNING @ Tue, 30 Jun 2020 02:31:24: #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, 30 Jun 2020 02:31:24: #2 You may need to consider one of the other alternative d(s): 2,37,577 WARNING @ Tue, 30 Jun 2020 02:31:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:31:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:31:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:31:30: 9000000 INFO @ Tue, 30 Jun 2020 02:31:31: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:31:38: 10000000 INFO @ Tue, 30 Jun 2020 02:31:39: 14000000 INFO @ Tue, 30 Jun 2020 02:31:46: 11000000 INFO @ Tue, 30 Jun 2020 02:31:47: 15000000 INFO @ Tue, 30 Jun 2020 02:31:54: 12000000 INFO @ Tue, 30 Jun 2020 02:31:55: 16000000 INFO @ Tue, 30 Jun 2020 02:31:55: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:31:55: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:31:55: #1 total tags in treatment: 16024456 INFO @ Tue, 30 Jun 2020 02:31:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:31:55: #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 02:31:56: #1 tags after filtering in treatment: 16024456 INFO @ Tue, 30 Jun 2020 02:31:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:31:56: #1 finished! INFO @ Tue, 30 Jun 2020 02:31:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:31:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:31:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:31:57: #2 number of paired peaks: 715 WARNING @ Tue, 30 Jun 2020 02:31:57: Fewer paired peaks (715) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 715 pairs to build model! INFO @ Tue, 30 Jun 2020 02:31:57: start model_add_line... INFO @ Tue, 30 Jun 2020 02:31:57: start X-correlation... INFO @ Tue, 30 Jun 2020 02:31:57: end of X-cor INFO @ Tue, 30 Jun 2020 02:31:57: #2 finished! INFO @ Tue, 30 Jun 2020 02:31:57: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:31:57: #2 alternative fragment length(s) may be 2,37,577 bps INFO @ Tue, 30 Jun 2020 02:31:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.10_model.r WARNING @ Tue, 30 Jun 2020 02:31:57: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:31:57: #2 You may need to consider one of the other alternative d(s): 2,37,577 WARNING @ Tue, 30 Jun 2020 02:31:57: #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 02:31:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:31:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:32:02: 13000000 INFO @ Tue, 30 Jun 2020 02:32:09: 14000000 INFO @ Tue, 30 Jun 2020 02:32:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:32:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:32:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.05_summits.bed INFO @ Tue, 30 Jun 2020 02:32:13: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:32:16: 15000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:32:23: 16000000 INFO @ Tue, 30 Jun 2020 02:32:23: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:32:23: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:32:23: #1 total tags in treatment: 16024456 INFO @ Tue, 30 Jun 2020 02:32:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:32:23: #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 02:32:24: #1 tags after filtering in treatment: 16024456 INFO @ Tue, 30 Jun 2020 02:32:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:32:24: #1 finished! INFO @ Tue, 30 Jun 2020 02:32:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:32:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:32:25: #2 number of paired peaks: 715 WARNING @ Tue, 30 Jun 2020 02:32:25: Fewer paired peaks (715) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 715 pairs to build model! INFO @ Tue, 30 Jun 2020 02:32:25: start model_add_line... INFO @ Tue, 30 Jun 2020 02:32:25: start X-correlation... INFO @ Tue, 30 Jun 2020 02:32:25: end of X-cor INFO @ Tue, 30 Jun 2020 02:32:25: #2 finished! INFO @ Tue, 30 Jun 2020 02:32:25: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:32:25: #2 alternative fragment length(s) may be 2,37,577 bps INFO @ Tue, 30 Jun 2020 02:32:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.20_model.r WARNING @ Tue, 30 Jun 2020 02:32:25: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:32:25: #2 You may need to consider one of the other alternative d(s): 2,37,577 WARNING @ Tue, 30 Jun 2020 02:32:25: #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 02:32:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:32:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:32:31: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:32:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:32:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:32:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.10_summits.bed INFO @ Tue, 30 Jun 2020 02:32:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:32:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:33:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:33:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:33:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287881/SRX287881.20_summits.bed INFO @ Tue, 30 Jun 2020 02:33:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling